Starting phenix.real_space_refine on Sat Dec 28 03:12:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qqn_18599/12_2024/8qqn_18599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qqn_18599/12_2024/8qqn_18599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.342 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qqn_18599/12_2024/8qqn_18599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qqn_18599/12_2024/8qqn_18599.map" model { file = "/net/cci-nas-00/data/ceres_data/8qqn_18599/12_2024/8qqn_18599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qqn_18599/12_2024/8qqn_18599.cif" } resolution = 2.342 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 144 5.16 5 C 31092 2.51 5 N 8544 2.21 5 O 10500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 337 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 50328 Number of models: 1 Model: "" Number of chains: 36 Chain: "PX" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PA" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PB" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PC" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PD" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PE" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PF" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PG" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PH" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PI" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PJ" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PK" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PL" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3106 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'HIP:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "PM" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PN" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PO" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PP" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PQ" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PR" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PS" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PT" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PU" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PV" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PW" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1087 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "PX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "PW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.79, per 1000 atoms: 0.41 Number of scatterers: 50328 At special positions: 0 Unit cell: (155.743, 155.743, 172.137, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 36 15.00 Mg 12 11.99 O 10500 8.00 N 8544 7.00 C 31092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 9.29 Conformation dependent library (CDL) restraints added in 4.8 seconds 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11832 Finding SS restraints... Secondary structure from input PDB file: 302 helices and 73 sheets defined 55.5% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'PX' and resid 10 through 17 Processing helix chain 'PX' and resid 18 through 31 Processing helix chain 'PX' and resid 41 through 60 Processing helix chain 'PX' and resid 73 through 90 Processing helix chain 'PX' and resid 114 through 118 Processing helix chain 'PX' and resid 119 through 129 removed outlier: 3.791A pdb=" N GLUPX 127 " --> pdb=" O ARGPX 123 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYRPX 128 " --> pdb=" O METPX 124 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALPX 129 " --> pdb=" O ALAPX 125 " (cutoff:3.500A) Processing helix chain 'PX' and resid 130 through 133 Processing helix chain 'PA' and resid 56 through 69 Processing helix chain 'PA' and resid 70 through 86 removed outlier: 3.979A pdb=" N ALAPA 74 " --> pdb=" O GLYPA 70 " (cutoff:3.500A) Processing helix chain 'PA' and resid 95 through 100 Processing helix chain 'PA' and resid 109 through 118 Processing helix chain 'PA' and resid 120 through 135 Processing helix chain 'PA' and resid 157 through 159 No H-bonds generated for 'chain 'PA' and resid 157 through 159' Processing helix chain 'PA' and resid 211 through 216 Processing helix chain 'PA' and resid 216 through 238 Processing helix chain 'PA' and resid 255 through 267 removed outlier: 3.907A pdb=" N ARGPA 261 " --> pdb=" O ASNPA 257 " (cutoff:3.500A) Processing helix chain 'PA' and resid 294 through 311 Processing helix chain 'PA' and resid 313 through 318 Processing helix chain 'PA' and resid 326 through 356 Processing helix chain 'PA' and resid 356 through 365 removed outlier: 3.596A pdb=" N SERPA 365 " --> pdb=" O VALPA 361 " (cutoff:3.500A) Processing helix chain 'PA' and resid 383 through 395 Processing helix chain 'PA' and resid 396 through 398 No H-bonds generated for 'chain 'PA' and resid 396 through 398' Processing helix chain 'PA' and resid 399 through 408 Processing helix chain 'PA' and resid 414 through 420 Processing helix chain 'PA' and resid 423 through 434 Processing helix chain 'PB' and resid 56 through 69 Processing helix chain 'PB' and resid 70 through 86 removed outlier: 3.896A pdb=" N ALAPB 74 " --> pdb=" O GLYPB 70 " (cutoff:3.500A) Processing helix chain 'PB' and resid 95 through 100 removed outlier: 3.552A pdb=" N LYSPB 100 " --> pdb=" O ASPPB 97 " (cutoff:3.500A) Processing helix chain 'PB' and resid 109 through 118 Processing helix chain 'PB' and resid 120 through 135 Processing helix chain 'PB' and resid 157 through 159 No H-bonds generated for 'chain 'PB' and resid 157 through 159' Processing helix chain 'PB' and resid 211 through 216 Processing helix chain 'PB' and resid 216 through 238 Processing helix chain 'PB' and resid 255 through 267 removed outlier: 3.802A pdb=" N ARGPB 261 " --> pdb=" O ASNPB 257 " (cutoff:3.500A) Processing helix chain 'PB' and resid 294 through 310 Processing helix chain 'PB' and resid 313 through 318 Processing helix chain 'PB' and resid 326 through 356 Processing helix chain 'PB' and resid 356 through 365 removed outlier: 3.509A pdb=" N SERPB 365 " --> pdb=" O VALPB 361 " (cutoff:3.500A) Processing helix chain 'PB' and resid 383 through 395 Processing helix chain 'PB' and resid 396 through 398 No H-bonds generated for 'chain 'PB' and resid 396 through 398' Processing helix chain 'PB' and resid 399 through 408 Processing helix chain 'PB' and resid 414 through 420 Processing helix chain 'PB' and resid 423 through 434 Processing helix chain 'PC' and resid 56 through 69 Processing helix chain 'PC' and resid 70 through 86 removed outlier: 3.975A pdb=" N ALAPC 74 " --> pdb=" O GLYPC 70 " (cutoff:3.500A) Processing helix chain 'PC' and resid 95 through 100 Processing helix chain 'PC' and resid 109 through 118 Processing helix chain 'PC' and resid 120 through 135 Processing helix chain 'PC' and resid 157 through 159 No H-bonds generated for 'chain 'PC' and resid 157 through 159' Processing helix chain 'PC' and resid 211 through 216 Processing helix chain 'PC' and resid 216 through 238 Processing helix chain 'PC' and resid 255 through 267 removed outlier: 3.839A pdb=" N ARGPC 261 " --> pdb=" O ASNPC 257 " (cutoff:3.500A) Processing helix chain 'PC' and resid 294 through 311 Processing helix chain 'PC' and resid 313 through 318 Processing helix chain 'PC' and resid 326 through 356 Processing helix chain 'PC' and resid 356 through 365 Processing helix chain 'PC' and resid 383 through 395 Processing helix chain 'PC' and resid 396 through 398 No H-bonds generated for 'chain 'PC' and resid 396 through 398' Processing helix chain 'PC' and resid 399 through 407 Processing helix chain 'PC' and resid 414 through 420 Processing helix chain 'PC' and resid 423 through 434 Processing helix chain 'PD' and resid 56 through 69 Processing helix chain 'PD' and resid 70 through 86 removed outlier: 3.884A pdb=" N ALAPD 74 " --> pdb=" O GLYPD 70 " (cutoff:3.500A) Processing helix chain 'PD' and resid 96 through 100 Processing helix chain 'PD' and resid 109 through 118 Processing helix chain 'PD' and resid 120 through 135 Processing helix chain 'PD' and resid 157 through 159 No H-bonds generated for 'chain 'PD' and resid 157 through 159' Processing helix chain 'PD' and resid 211 through 216 Processing helix chain 'PD' and resid 216 through 238 Processing helix chain 'PD' and resid 255 through 267 removed outlier: 3.754A pdb=" N ARGPD 261 " --> pdb=" O ASNPD 257 " (cutoff:3.500A) Processing helix chain 'PD' and resid 294 through 311 Processing helix chain 'PD' and resid 313 through 318 Processing helix chain 'PD' and resid 326 through 356 Processing helix chain 'PD' and resid 356 through 365 removed outlier: 3.525A pdb=" N SERPD 365 " --> pdb=" O VALPD 361 " (cutoff:3.500A) Processing helix chain 'PD' and resid 383 through 395 Processing helix chain 'PD' and resid 396 through 398 No H-bonds generated for 'chain 'PD' and resid 396 through 398' Processing helix chain 'PD' and resid 399 through 408 Processing helix chain 'PD' and resid 414 through 420 Processing helix chain 'PD' and resid 423 through 434 Processing helix chain 'PE' and resid 56 through 69 Processing helix chain 'PE' and resid 70 through 86 removed outlier: 3.884A pdb=" N ALAPE 74 " --> pdb=" O GLYPE 70 " (cutoff:3.500A) Processing helix chain 'PE' and resid 95 through 100 removed outlier: 3.514A pdb=" N LYSPE 100 " --> pdb=" O ASPPE 97 " (cutoff:3.500A) Processing helix chain 'PE' and resid 109 through 118 Processing helix chain 'PE' and resid 120 through 135 Processing helix chain 'PE' and resid 157 through 159 No H-bonds generated for 'chain 'PE' and resid 157 through 159' Processing helix chain 'PE' and resid 211 through 216 Processing helix chain 'PE' and resid 216 through 238 Processing helix chain 'PE' and resid 255 through 266 removed outlier: 3.675A pdb=" N ARGPE 261 " --> pdb=" O ASNPE 257 " (cutoff:3.500A) Processing helix chain 'PE' and resid 294 through 310 Processing helix chain 'PE' and resid 313 through 318 Processing helix chain 'PE' and resid 326 through 356 Processing helix chain 'PE' and resid 356 through 365 removed outlier: 3.530A pdb=" N SERPE 365 " --> pdb=" O VALPE 361 " (cutoff:3.500A) Processing helix chain 'PE' and resid 383 through 395 Processing helix chain 'PE' and resid 396 through 398 No H-bonds generated for 'chain 'PE' and resid 396 through 398' Processing helix chain 'PE' and resid 399 through 408 Processing helix chain 'PE' and resid 414 through 420 Processing helix chain 'PE' and resid 423 through 434 Processing helix chain 'PF' and resid 56 through 69 Processing helix chain 'PF' and resid 70 through 86 removed outlier: 3.973A pdb=" N ALAPF 74 " --> pdb=" O GLYPF 70 " (cutoff:3.500A) Processing helix chain 'PF' and resid 95 through 100 removed outlier: 3.571A pdb=" N LYSPF 100 " --> pdb=" O ASPPF 97 " (cutoff:3.500A) Processing helix chain 'PF' and resid 109 through 118 Processing helix chain 'PF' and resid 120 through 135 Processing helix chain 'PF' and resid 157 through 159 No H-bonds generated for 'chain 'PF' and resid 157 through 159' Processing helix chain 'PF' and resid 211 through 216 Processing helix chain 'PF' and resid 216 through 238 Processing helix chain 'PF' and resid 255 through 266 removed outlier: 3.680A pdb=" N ARGPF 261 " --> pdb=" O ASNPF 257 " (cutoff:3.500A) Processing helix chain 'PF' and resid 294 through 311 Processing helix chain 'PF' and resid 313 through 318 Processing helix chain 'PF' and resid 326 through 356 Processing helix chain 'PF' and resid 356 through 365 removed outlier: 3.575A pdb=" N SERPF 365 " --> pdb=" O VALPF 361 " (cutoff:3.500A) Processing helix chain 'PF' and resid 383 through 395 Processing helix chain 'PF' and resid 396 through 398 No H-bonds generated for 'chain 'PF' and resid 396 through 398' Processing helix chain 'PF' and resid 399 through 407 Processing helix chain 'PF' and resid 414 through 420 Processing helix chain 'PF' and resid 423 through 434 Processing helix chain 'PG' and resid 56 through 69 Processing helix chain 'PG' and resid 70 through 86 removed outlier: 4.073A pdb=" N ALAPG 74 " --> pdb=" O GLYPG 70 " (cutoff:3.500A) Processing helix chain 'PG' and resid 95 through 100 Processing helix chain 'PG' and resid 109 through 118 Processing helix chain 'PG' and resid 120 through 135 Processing helix chain 'PG' and resid 157 through 159 No H-bonds generated for 'chain 'PG' and resid 157 through 159' Processing helix chain 'PG' and resid 211 through 216 Processing helix chain 'PG' and resid 216 through 238 Processing helix chain 'PG' and resid 255 through 267 removed outlier: 3.756A pdb=" N ARGPG 261 " --> pdb=" O ASNPG 257 " (cutoff:3.500A) Processing helix chain 'PG' and resid 294 through 311 Processing helix chain 'PG' and resid 313 through 318 Processing helix chain 'PG' and resid 326 through 356 Processing helix chain 'PG' and resid 356 through 365 removed outlier: 3.511A pdb=" N SERPG 365 " --> pdb=" O VALPG 361 " (cutoff:3.500A) Processing helix chain 'PG' and resid 383 through 395 Processing helix chain 'PG' and resid 396 through 398 No H-bonds generated for 'chain 'PG' and resid 396 through 398' Processing helix chain 'PG' and resid 399 through 408 Processing helix chain 'PG' and resid 414 through 420 Processing helix chain 'PG' and resid 423 through 434 Processing helix chain 'PH' and resid 56 through 69 Processing helix chain 'PH' and resid 70 through 86 removed outlier: 4.007A pdb=" N ALAPH 74 " --> pdb=" O GLYPH 70 " (cutoff:3.500A) Processing helix chain 'PH' and resid 96 through 100 Processing helix chain 'PH' and resid 109 through 118 Processing helix chain 'PH' and resid 120 through 135 Processing helix chain 'PH' and resid 157 through 159 No H-bonds generated for 'chain 'PH' and resid 157 through 159' Processing helix chain 'PH' and resid 211 through 216 Processing helix chain 'PH' and resid 216 through 238 Processing helix chain 'PH' and resid 255 through 266 removed outlier: 3.840A pdb=" N ARGPH 261 " --> pdb=" O ASNPH 257 " (cutoff:3.500A) Processing helix chain 'PH' and resid 294 through 311 Processing helix chain 'PH' and resid 313 through 318 Processing helix chain 'PH' and resid 326 through 356 Processing helix chain 'PH' and resid 356 through 365 removed outlier: 3.501A pdb=" N SERPH 365 " --> pdb=" O VALPH 361 " (cutoff:3.500A) Processing helix chain 'PH' and resid 383 through 395 Processing helix chain 'PH' and resid 396 through 398 No H-bonds generated for 'chain 'PH' and resid 396 through 398' Processing helix chain 'PH' and resid 399 through 407 Processing helix chain 'PH' and resid 414 through 420 Processing helix chain 'PH' and resid 423 through 434 Processing helix chain 'PI' and resid 56 through 69 Processing helix chain 'PI' and resid 70 through 86 removed outlier: 4.012A pdb=" N ALAPI 74 " --> pdb=" O GLYPI 70 " (cutoff:3.500A) Processing helix chain 'PI' and resid 95 through 100 Processing helix chain 'PI' and resid 109 through 118 Processing helix chain 'PI' and resid 120 through 135 Processing helix chain 'PI' and resid 157 through 159 No H-bonds generated for 'chain 'PI' and resid 157 through 159' Processing helix chain 'PI' and resid 211 through 216 Processing helix chain 'PI' and resid 216 through 238 Processing helix chain 'PI' and resid 255 through 266 removed outlier: 3.714A pdb=" N ARGPI 261 " --> pdb=" O ASNPI 257 " (cutoff:3.500A) Processing helix chain 'PI' and resid 294 through 311 Processing helix chain 'PI' and resid 313 through 318 Processing helix chain 'PI' and resid 326 through 356 Processing helix chain 'PI' and resid 356 through 365 removed outlier: 3.612A pdb=" N SERPI 365 " --> pdb=" O VALPI 361 " (cutoff:3.500A) Processing helix chain 'PI' and resid 383 through 395 Processing helix chain 'PI' and resid 396 through 398 No H-bonds generated for 'chain 'PI' and resid 396 through 398' Processing helix chain 'PI' and resid 399 through 407 Processing helix chain 'PI' and resid 414 through 420 Processing helix chain 'PI' and resid 423 through 434 Processing helix chain 'PJ' and resid 56 through 69 Processing helix chain 'PJ' and resid 70 through 86 removed outlier: 4.000A pdb=" N ALAPJ 74 " --> pdb=" O GLYPJ 70 " (cutoff:3.500A) Processing helix chain 'PJ' and resid 96 through 100 Processing helix chain 'PJ' and resid 109 through 118 Processing helix chain 'PJ' and resid 120 through 135 Processing helix chain 'PJ' and resid 157 through 159 No H-bonds generated for 'chain 'PJ' and resid 157 through 159' Processing helix chain 'PJ' and resid 211 through 216 Processing helix chain 'PJ' and resid 216 through 238 Processing helix chain 'PJ' and resid 255 through 266 removed outlier: 3.784A pdb=" N ARGPJ 261 " --> pdb=" O ASNPJ 257 " (cutoff:3.500A) Processing helix chain 'PJ' and resid 294 through 311 Processing helix chain 'PJ' and resid 313 through 318 Processing helix chain 'PJ' and resid 326 through 356 Processing helix chain 'PJ' and resid 356 through 365 removed outlier: 3.603A pdb=" N SERPJ 365 " --> pdb=" O VALPJ 361 " (cutoff:3.500A) Processing helix chain 'PJ' and resid 383 through 395 Processing helix chain 'PJ' and resid 396 through 398 No H-bonds generated for 'chain 'PJ' and resid 396 through 398' Processing helix chain 'PJ' and resid 399 through 407 Processing helix chain 'PJ' and resid 414 through 420 Processing helix chain 'PJ' and resid 423 through 434 Processing helix chain 'PK' and resid 56 through 69 Processing helix chain 'PK' and resid 70 through 86 removed outlier: 3.938A pdb=" N ALAPK 74 " --> pdb=" O GLYPK 70 " (cutoff:3.500A) Processing helix chain 'PK' and resid 95 through 100 Processing helix chain 'PK' and resid 109 through 118 Processing helix chain 'PK' and resid 120 through 135 Processing helix chain 'PK' and resid 157 through 159 No H-bonds generated for 'chain 'PK' and resid 157 through 159' Processing helix chain 'PK' and resid 211 through 216 Processing helix chain 'PK' and resid 216 through 238 Processing helix chain 'PK' and resid 255 through 267 removed outlier: 3.741A pdb=" N ARGPK 261 " --> pdb=" O ASNPK 257 " (cutoff:3.500A) Processing helix chain 'PK' and resid 294 through 310 Processing helix chain 'PK' and resid 313 through 318 Processing helix chain 'PK' and resid 326 through 356 Processing helix chain 'PK' and resid 356 through 365 Processing helix chain 'PK' and resid 383 through 395 Processing helix chain 'PK' and resid 396 through 398 No H-bonds generated for 'chain 'PK' and resid 396 through 398' Processing helix chain 'PK' and resid 399 through 408 Processing helix chain 'PK' and resid 414 through 420 Processing helix chain 'PK' and resid 423 through 434 Processing helix chain 'PL' and resid 56 through 69 Processing helix chain 'PL' and resid 70 through 86 removed outlier: 3.966A pdb=" N ALAPL 74 " --> pdb=" O GLYPL 70 " (cutoff:3.500A) Processing helix chain 'PL' and resid 95 through 100 Processing helix chain 'PL' and resid 109 through 118 Processing helix chain 'PL' and resid 120 through 135 Processing helix chain 'PL' and resid 157 through 159 No H-bonds generated for 'chain 'PL' and resid 157 through 159' Processing helix chain 'PL' and resid 211 through 216 Processing helix chain 'PL' and resid 216 through 238 Processing helix chain 'PL' and resid 255 through 267 removed outlier: 3.803A pdb=" N ARGPL 261 " --> pdb=" O ASNPL 257 " (cutoff:3.500A) Processing helix chain 'PL' and resid 294 through 311 Processing helix chain 'PL' and resid 313 through 318 Processing helix chain 'PL' and resid 326 through 356 Processing helix chain 'PL' and resid 356 through 365 Processing helix chain 'PL' and resid 383 through 395 Processing helix chain 'PL' and resid 396 through 398 No H-bonds generated for 'chain 'PL' and resid 396 through 398' Processing helix chain 'PL' and resid 399 through 407 Processing helix chain 'PL' and resid 414 through 420 Processing helix chain 'PL' and resid 423 through 434 Processing helix chain 'PM' and resid 10 through 17 Processing helix chain 'PM' and resid 18 through 31 Processing helix chain 'PM' and resid 41 through 60 Processing helix chain 'PM' and resid 73 through 90 Processing helix chain 'PM' and resid 114 through 118 Processing helix chain 'PM' and resid 119 through 128 removed outlier: 3.734A pdb=" N GLUPM 127 " --> pdb=" O ARGPM 123 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYRPM 128 " --> pdb=" O METPM 124 " (cutoff:3.500A) Processing helix chain 'PM' and resid 129 through 133 Processing helix chain 'PN' and resid 10 through 17 Processing helix chain 'PN' and resid 18 through 31 Processing helix chain 'PN' and resid 41 through 60 Processing helix chain 'PN' and resid 73 through 90 Processing helix chain 'PN' and resid 115 through 118 Processing helix chain 'PN' and resid 119 through 128 removed outlier: 3.775A pdb=" N GLUPN 127 " --> pdb=" O ARGPN 123 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYRPN 128 " --> pdb=" O METPN 124 " (cutoff:3.500A) Processing helix chain 'PN' and resid 129 through 133 Processing helix chain 'PO' and resid 10 through 17 Processing helix chain 'PO' and resid 18 through 31 Processing helix chain 'PO' and resid 41 through 60 Processing helix chain 'PO' and resid 73 through 90 Processing helix chain 'PO' and resid 114 through 118 Processing helix chain 'PO' and resid 119 through 128 removed outlier: 3.775A pdb=" N GLUPO 127 " --> pdb=" O ARGPO 123 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYRPO 128 " --> pdb=" O METPO 124 " (cutoff:3.500A) Processing helix chain 'PO' and resid 129 through 133 Processing helix chain 'PP' and resid 5 through 9 removed outlier: 3.585A pdb=" N VALPP 9 " --> pdb=" O ILEPP 6 " (cutoff:3.500A) Processing helix chain 'PP' and resid 10 through 17 Processing helix chain 'PP' and resid 18 through 31 Processing helix chain 'PP' and resid 41 through 60 Processing helix chain 'PP' and resid 73 through 90 Processing helix chain 'PP' and resid 114 through 118 Processing helix chain 'PP' and resid 119 through 127 removed outlier: 3.743A pdb=" N GLUPP 127 " --> pdb=" O ARGPP 123 " (cutoff:3.500A) Processing helix chain 'PP' and resid 128 through 133 removed outlier: 6.250A pdb=" N GLUPP 131 " --> pdb=" O TYRPP 128 " (cutoff:3.500A) Processing helix chain 'PQ' and resid 10 through 17 Processing helix chain 'PQ' and resid 18 through 31 Processing helix chain 'PQ' and resid 41 through 60 Processing helix chain 'PQ' and resid 73 through 90 Processing helix chain 'PQ' and resid 114 through 118 Processing helix chain 'PQ' and resid 119 through 129 removed outlier: 3.757A pdb=" N GLUPQ 127 " --> pdb=" O ARGPQ 123 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYRPQ 128 " --> pdb=" O METPQ 124 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VALPQ 129 " --> pdb=" O ALAPQ 125 " (cutoff:3.500A) Processing helix chain 'PQ' and resid 130 through 133 Processing helix chain 'PR' and resid 5 through 9 removed outlier: 3.537A pdb=" N VALPR 9 " --> pdb=" O ILEPR 6 " (cutoff:3.500A) Processing helix chain 'PR' and resid 10 through 17 Processing helix chain 'PR' and resid 18 through 31 Processing helix chain 'PR' and resid 41 through 60 Processing helix chain 'PR' and resid 73 through 90 Processing helix chain 'PR' and resid 114 through 118 Processing helix chain 'PR' and resid 119 through 129 removed outlier: 3.758A pdb=" N GLUPR 127 " --> pdb=" O ARGPR 123 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYRPR 128 " --> pdb=" O METPR 124 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VALPR 129 " --> pdb=" O ALAPR 125 " (cutoff:3.500A) Processing helix chain 'PR' and resid 130 through 133 Processing helix chain 'PS' and resid 10 through 17 Processing helix chain 'PS' and resid 18 through 31 Processing helix chain 'PS' and resid 41 through 60 Processing helix chain 'PS' and resid 73 through 90 Processing helix chain 'PS' and resid 114 through 118 Processing helix chain 'PS' and resid 119 through 129 removed outlier: 3.779A pdb=" N GLUPS 127 " --> pdb=" O ARGPS 123 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYRPS 128 " --> pdb=" O METPS 124 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VALPS 129 " --> pdb=" O ALAPS 125 " (cutoff:3.500A) Processing helix chain 'PS' and resid 130 through 133 Processing helix chain 'PT' and resid 10 through 17 Processing helix chain 'PT' and resid 18 through 31 Processing helix chain 'PT' and resid 41 through 60 Processing helix chain 'PT' and resid 73 through 90 Processing helix chain 'PT' and resid 114 through 118 Processing helix chain 'PT' and resid 119 through 129 removed outlier: 3.833A pdb=" N GLUPT 127 " --> pdb=" O ARGPT 123 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYRPT 128 " --> pdb=" O METPT 124 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VALPT 129 " --> pdb=" O ALAPT 125 " (cutoff:3.500A) Processing helix chain 'PT' and resid 130 through 133 Processing helix chain 'PU' and resid 10 through 17 Processing helix chain 'PU' and resid 18 through 31 Processing helix chain 'PU' and resid 41 through 60 Processing helix chain 'PU' and resid 73 through 90 Processing helix chain 'PU' and resid 114 through 118 Processing helix chain 'PU' and resid 119 through 129 removed outlier: 3.734A pdb=" N GLUPU 127 " --> pdb=" O ARGPU 123 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYRPU 128 " --> pdb=" O METPU 124 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VALPU 129 " --> pdb=" O ALAPU 125 " (cutoff:3.500A) Processing helix chain 'PU' and resid 130 through 133 Processing helix chain 'PV' and resid 10 through 17 Processing helix chain 'PV' and resid 18 through 31 Processing helix chain 'PV' and resid 41 through 60 Processing helix chain 'PV' and resid 73 through 90 Processing helix chain 'PV' and resid 114 through 118 Processing helix chain 'PV' and resid 119 through 129 removed outlier: 3.829A pdb=" N GLUPV 127 " --> pdb=" O ARGPV 123 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYRPV 128 " --> pdb=" O METPV 124 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALPV 129 " --> pdb=" O ALAPV 125 " (cutoff:3.500A) Processing helix chain 'PV' and resid 130 through 133 Processing helix chain 'PW' and resid 10 through 17 Processing helix chain 'PW' and resid 18 through 31 Processing helix chain 'PW' and resid 41 through 60 Processing helix chain 'PW' and resid 73 through 90 Processing helix chain 'PW' and resid 114 through 118 Processing helix chain 'PW' and resid 119 through 129 removed outlier: 3.796A pdb=" N GLUPW 127 " --> pdb=" O ARGPW 123 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYRPW 128 " --> pdb=" O METPW 124 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VALPW 129 " --> pdb=" O ALAPW 125 " (cutoff:3.500A) Processing helix chain 'PW' and resid 130 through 133 Processing sheet with id=AA1, first strand: chain 'PX' and resid 63 through 64 Processing sheet with id=AA2, first strand: chain 'PX' and resid 94 through 98 removed outlier: 5.982A pdb=" N GLNPX 95 " --> pdb=" O TYRPX 106 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SERPX 103 " --> pdb=" O GLUPM 97 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLUPM 97 " --> pdb=" O SERPX 103 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SERPX 105 " --> pdb=" O GLNPM 95 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLNPM 95 " --> pdb=" O TYRPM 106 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SERPM 103 " --> pdb=" O GLUPN 97 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLUPN 97 " --> pdb=" O SERPM 103 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N SERPM 105 " --> pdb=" O GLNPN 95 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLNPN 95 " --> pdb=" O TYRPN 106 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SERPN 103 " --> pdb=" O GLUPO 97 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLUPO 97 " --> pdb=" O SERPN 103 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SERPN 105 " --> pdb=" O GLNPO 95 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLNPO 95 " --> pdb=" O TYRPO 106 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SERPO 103 " --> pdb=" O GLUPP 97 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLUPP 97 " --> pdb=" O SERPO 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SERPO 105 " --> pdb=" O GLNPP 95 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLNPP 95 " --> pdb=" O TYRPP 106 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SERPP 103 " --> pdb=" O GLUPQ 97 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLUPQ 97 " --> pdb=" O SERPP 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SERPP 105 " --> pdb=" O GLNPQ 95 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLNPQ 95 " --> pdb=" O TYRPQ 106 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SERPQ 103 " --> pdb=" O GLUPR 97 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLUPR 97 " --> pdb=" O SERPQ 103 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SERPQ 105 " --> pdb=" O GLNPR 95 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLNPR 95 " --> pdb=" O TYRPR 106 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SERPR 103 " --> pdb=" O GLUPS 97 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLUPS 97 " --> pdb=" O SERPR 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SERPR 105 " --> pdb=" O GLNPS 95 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLNPS 95 " --> pdb=" O TYRPS 106 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SERPS 103 " --> pdb=" O GLUPT 97 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLUPT 97 " --> pdb=" O SERPS 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SERPS 105 " --> pdb=" O GLNPT 95 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLNPT 95 " --> pdb=" O TYRPT 106 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SERPT 103 " --> pdb=" O GLUPU 97 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLUPU 97 " --> pdb=" O SERPT 103 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SERPT 105 " --> pdb=" O GLNPU 95 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLNPU 95 " --> pdb=" O TYRPU 106 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SERPU 103 " --> pdb=" O GLUPV 97 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLUPV 97 " --> pdb=" O SERPU 103 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SERPU 105 " --> pdb=" O GLNPV 95 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLNPV 95 " --> pdb=" O TYRPV 106 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SERPV 103 " --> pdb=" O GLUPW 97 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLUPW 97 " --> pdb=" O SERPV 103 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SERPV 105 " --> pdb=" O GLNPW 95 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLNPW 95 " --> pdb=" O TYRPW 106 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SERPW 103 " --> pdb=" O GLUPX 97 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLUPX 97 " --> pdb=" O SERPW 103 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SERPW 105 " --> pdb=" O GLNPX 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'PX' and resid 137 through 139 removed outlier: 6.403A pdb=" N ARGPD 242 " --> pdb=" O TYRPE 277 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THRPE 279 " --> pdb=" O ARGPD 242 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VALPD 244 " --> pdb=" O THRPE 279 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'PA' and resid 89 through 93 Processing sheet with id=AA5, first strand: chain 'PA' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'PA' and resid 150 through 155 removed outlier: 6.786A pdb=" N GLNPA 143 " --> pdb=" O LYSPA 151 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALAPA 153 " --> pdb=" O GLUPA 141 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLUPA 141 " --> pdb=" O ALAPA 153 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VALPA 139 " --> pdb=" O PROPA 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'PA' and resid 161 through 165 Processing sheet with id=AA8, first strand: chain 'PA' and resid 283 through 288 removed outlier: 6.421A pdb=" N ARGPA 242 " --> pdb=" O TYRPB 277 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THRPB 279 " --> pdb=" O ARGPA 242 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VALPA 244 " --> pdb=" O THRPB 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'PL' and resid 283 through 288 Processing sheet with id=AB1, first strand: chain 'PB' and resid 89 through 93 Processing sheet with id=AB2, first strand: chain 'PB' and resid 101 through 102 Processing sheet with id=AB3, first strand: chain 'PB' and resid 150 through 155 removed outlier: 6.806A pdb=" N GLNPB 143 " --> pdb=" O LYSPB 151 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALAPB 153 " --> pdb=" O GLUPB 141 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLUPB 141 " --> pdb=" O ALAPB 153 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VALPB 139 " --> pdb=" O PROPB 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'PB' and resid 161 through 165 Processing sheet with id=AB5, first strand: chain 'PB' and resid 283 through 288 removed outlier: 6.376A pdb=" N ARGPB 242 " --> pdb=" O TYRPC 277 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THRPC 279 " --> pdb=" O ARGPB 242 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VALPB 244 " --> pdb=" O THRPC 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'PC' and resid 89 through 93 Processing sheet with id=AB7, first strand: chain 'PC' and resid 101 through 102 Processing sheet with id=AB8, first strand: chain 'PC' and resid 150 through 155 removed outlier: 6.758A pdb=" N GLNPC 143 " --> pdb=" O LYSPC 151 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALAPC 153 " --> pdb=" O GLUPC 141 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLUPC 141 " --> pdb=" O ALAPC 153 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VALPC 139 " --> pdb=" O PROPC 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'PC' and resid 161 through 165 Processing sheet with id=AC1, first strand: chain 'PC' and resid 283 through 288 Processing sheet with id=AC2, first strand: chain 'PD' and resid 89 through 93 Processing sheet with id=AC3, first strand: chain 'PD' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'PD' and resid 150 through 155 Processing sheet with id=AC5, first strand: chain 'PD' and resid 161 through 165 Processing sheet with id=AC6, first strand: chain 'PE' and resid 89 through 93 Processing sheet with id=AC7, first strand: chain 'PE' and resid 101 through 102 Processing sheet with id=AC8, first strand: chain 'PE' and resid 150 through 155 removed outlier: 6.819A pdb=" N GLNPE 143 " --> pdb=" O LYSPE 151 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALAPE 153 " --> pdb=" O GLUPE 141 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLUPE 141 " --> pdb=" O ALAPE 153 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VALPE 139 " --> pdb=" O PROPE 155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'PE' and resid 161 through 165 Processing sheet with id=AD1, first strand: chain 'PE' and resid 283 through 288 removed outlier: 6.364A pdb=" N ARGPE 242 " --> pdb=" O TYRPF 277 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THRPF 279 " --> pdb=" O ARGPE 242 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VALPE 244 " --> pdb=" O THRPF 279 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'PF' and resid 89 through 93 Processing sheet with id=AD3, first strand: chain 'PF' and resid 101 through 102 Processing sheet with id=AD4, first strand: chain 'PF' and resid 150 through 155 removed outlier: 6.763A pdb=" N GLNPF 143 " --> pdb=" O LYSPF 151 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALAPF 153 " --> pdb=" O GLUPF 141 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLUPF 141 " --> pdb=" O ALAPF 153 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VALPF 139 " --> pdb=" O PROPF 155 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'PF' and resid 161 through 165 Processing sheet with id=AD6, first strand: chain 'PF' and resid 283 through 288 removed outlier: 6.398A pdb=" N ARGPF 242 " --> pdb=" O TYRPG 277 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THRPG 279 " --> pdb=" O ARGPF 242 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VALPF 244 " --> pdb=" O THRPG 279 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'PG' and resid 89 through 93 Processing sheet with id=AD8, first strand: chain 'PG' and resid 101 through 102 Processing sheet with id=AD9, first strand: chain 'PG' and resid 150 through 155 removed outlier: 6.774A pdb=" N GLNPG 143 " --> pdb=" O LYSPG 151 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALAPG 153 " --> pdb=" O GLUPG 141 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLUPG 141 " --> pdb=" O ALAPG 153 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VALPG 139 " --> pdb=" O PROPG 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'PG' and resid 161 through 165 Processing sheet with id=AE2, first strand: chain 'PG' and resid 283 through 288 removed outlier: 6.402A pdb=" N ARGPG 242 " --> pdb=" O TYRPH 277 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THRPH 279 " --> pdb=" O ARGPG 242 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VALPG 244 " --> pdb=" O THRPH 279 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'PH' and resid 89 through 93 Processing sheet with id=AE4, first strand: chain 'PH' and resid 101 through 102 Processing sheet with id=AE5, first strand: chain 'PH' and resid 150 through 155 removed outlier: 6.748A pdb=" N GLNPH 143 " --> pdb=" O LYSPH 151 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALAPH 153 " --> pdb=" O GLUPH 141 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLUPH 141 " --> pdb=" O ALAPH 153 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VALPH 139 " --> pdb=" O PROPH 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'PH' and resid 161 through 165 Processing sheet with id=AE7, first strand: chain 'PH' and resid 283 through 288 removed outlier: 6.423A pdb=" N ARGPH 242 " --> pdb=" O TYRPI 277 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THRPI 279 " --> pdb=" O ARGPH 242 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VALPH 244 " --> pdb=" O THRPI 279 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'PI' and resid 89 through 93 Processing sheet with id=AE9, first strand: chain 'PI' and resid 101 through 102 Processing sheet with id=AF1, first strand: chain 'PI' and resid 150 through 155 removed outlier: 6.791A pdb=" N GLNPI 143 " --> pdb=" O LYSPI 151 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALAPI 153 " --> pdb=" O GLUPI 141 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLUPI 141 " --> pdb=" O ALAPI 153 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VALPI 139 " --> pdb=" O PROPI 155 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'PI' and resid 161 through 165 Processing sheet with id=AF3, first strand: chain 'PI' and resid 283 through 288 removed outlier: 6.412A pdb=" N ARGPI 242 " --> pdb=" O TYRPJ 277 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THRPJ 279 " --> pdb=" O ARGPI 242 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VALPI 244 " --> pdb=" O THRPJ 279 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'PJ' and resid 89 through 94 removed outlier: 4.726A pdb=" N ASPPJ 372 " --> pdb=" O GLUPJ 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'PJ' and resid 101 through 102 Processing sheet with id=AF6, first strand: chain 'PJ' and resid 150 through 155 Processing sheet with id=AF7, first strand: chain 'PJ' and resid 161 through 165 Processing sheet with id=AF8, first strand: chain 'PJ' and resid 283 through 288 removed outlier: 6.415A pdb=" N ARGPJ 242 " --> pdb=" O TYRPK 277 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THRPK 279 " --> pdb=" O ARGPJ 242 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VALPJ 244 " --> pdb=" O THRPK 279 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'PK' and resid 89 through 93 Processing sheet with id=AG1, first strand: chain 'PK' and resid 101 through 102 Processing sheet with id=AG2, first strand: chain 'PK' and resid 150 through 155 removed outlier: 6.744A pdb=" N GLNPK 143 " --> pdb=" O LYSPK 151 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALAPK 153 " --> pdb=" O GLUPK 141 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLUPK 141 " --> pdb=" O ALAPK 153 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VALPK 139 " --> pdb=" O PROPK 155 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'PK' and resid 161 through 165 Processing sheet with id=AG4, first strand: chain 'PK' and resid 283 through 288 Processing sheet with id=AG5, first strand: chain 'PL' and resid 89 through 93 Processing sheet with id=AG6, first strand: chain 'PL' and resid 101 through 102 Processing sheet with id=AG7, first strand: chain 'PL' and resid 150 through 155 removed outlier: 6.806A pdb=" N GLNPL 143 " --> pdb=" O LYSPL 151 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALAPL 153 " --> pdb=" O GLUPL 141 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLUPL 141 " --> pdb=" O ALAPL 153 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VALPL 139 " --> pdb=" O PROPL 155 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'PL' and resid 161 through 165 Processing sheet with id=AG9, first strand: chain 'PM' and resid 63 through 64 Processing sheet with id=AH1, first strand: chain 'PN' and resid 63 through 64 Processing sheet with id=AH2, first strand: chain 'PO' and resid 63 through 64 Processing sheet with id=AH3, first strand: chain 'PP' and resid 63 through 64 Processing sheet with id=AH4, first strand: chain 'PQ' and resid 63 through 64 Processing sheet with id=AH5, first strand: chain 'PR' and resid 63 through 64 Processing sheet with id=AH6, first strand: chain 'PS' and resid 63 through 64 Processing sheet with id=AH7, first strand: chain 'PT' and resid 63 through 64 Processing sheet with id=AH8, first strand: chain 'PU' and resid 63 through 64 Processing sheet with id=AH9, first strand: chain 'PV' and resid 63 through 64 Processing sheet with id=AI1, first strand: chain 'PW' and resid 63 through 64 2827 hydrogen bonds defined for protein. 7971 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: 17.46 Time building geometry restraints manager: 11.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11548 1.33 - 1.46: 12174 1.46 - 1.58: 27206 1.58 - 1.70: 0 1.70 - 1.82: 312 Bond restraints: 51240 Sorted by residual: bond pdb=" ND1 HIPPD 243 " pdb=" P HIPPD 243 " ideal model delta sigma weight residual 1.928 1.712 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" ND1 HIPPC 243 " pdb=" P HIPPC 243 " ideal model delta sigma weight residual 1.928 1.712 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" ND1 HIPPL 243 " pdb=" P HIPPL 243 " ideal model delta sigma weight residual 1.928 1.712 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" ND1 HIPPA 243 " pdb=" P HIPPA 243 " ideal model delta sigma weight residual 1.928 1.712 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" ND1 HIPPA 291 " pdb=" P HIPPA 291 " ideal model delta sigma weight residual 1.928 1.713 0.215 2.00e-02 2.50e+03 1.16e+02 ... (remaining 51235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 66741 3.33 - 6.66: 2674 6.66 - 10.00: 149 10.00 - 13.33: 0 13.33 - 16.66: 12 Bond angle restraints: 69576 Sorted by residual: angle pdb=" CG ARGPL 205 " pdb=" CD ARGPL 205 " pdb=" NE ARGPL 205 " ideal model delta sigma weight residual 112.00 128.66 -16.66 2.20e+00 2.07e-01 5.73e+01 angle pdb=" CG ARGPK 205 " pdb=" CD ARGPK 205 " pdb=" NE ARGPK 205 " ideal model delta sigma weight residual 112.00 128.06 -16.06 2.20e+00 2.07e-01 5.33e+01 angle pdb=" CG ARGPI 205 " pdb=" CD ARGPI 205 " pdb=" NE ARGPI 205 " ideal model delta sigma weight residual 112.00 128.02 -16.02 2.20e+00 2.07e-01 5.30e+01 angle pdb=" CG ARGPG 205 " pdb=" CD ARGPG 205 " pdb=" NE ARGPG 205 " ideal model delta sigma weight residual 112.00 127.86 -15.86 2.20e+00 2.07e-01 5.20e+01 angle pdb=" CG ARGPC 205 " pdb=" CD ARGPC 205 " pdb=" NE ARGPC 205 " ideal model delta sigma weight residual 112.00 127.75 -15.75 2.20e+00 2.07e-01 5.13e+01 ... (remaining 69571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 28071 17.97 - 35.94: 2081 35.94 - 53.91: 351 53.91 - 71.89: 177 71.89 - 89.86: 76 Dihedral angle restraints: 30756 sinusoidal: 12336 harmonic: 18420 Sorted by residual: dihedral pdb=" CA TYRPJ 137 " pdb=" C TYRPJ 137 " pdb=" N ALAPJ 138 " pdb=" CA ALAPJ 138 " ideal model delta harmonic sigma weight residual 180.00 152.04 27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYRPC 137 " pdb=" C TYRPC 137 " pdb=" N ALAPC 138 " pdb=" CA ALAPC 138 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA TYRPF 137 " pdb=" C TYRPF 137 " pdb=" N ALAPF 138 " pdb=" CA ALAPF 138 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 30753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4722 0.090 - 0.180: 2123 0.180 - 0.271: 516 0.271 - 0.361: 123 0.361 - 0.451: 52 Chirality restraints: 7536 Sorted by residual: chirality pdb=" CA PHEPG 334 " pdb=" N PHEPG 334 " pdb=" C PHEPG 334 " pdb=" CB PHEPG 334 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA PHEPJ 334 " pdb=" N PHEPJ 334 " pdb=" C PHEPJ 334 " pdb=" CB PHEPJ 334 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA ASPPL 68 " pdb=" N ASPPL 68 " pdb=" C ASPPL 68 " pdb=" CB ASPPL 68 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 7533 not shown) Planarity restraints: 9348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIPPC 291 " -0.073 2.00e-02 2.50e+03 8.83e-02 1.36e+02 pdb=" CG HIPPC 291 " 0.010 2.00e-02 2.50e+03 pdb=" ND1 HIPPC 291 " -0.081 2.00e-02 2.50e+03 pdb=" CD2 HIPPC 291 " 0.121 2.00e-02 2.50e+03 pdb=" CE1 HIPPC 291 " -0.119 2.00e-02 2.50e+03 pdb=" NE2 HIPPC 291 " 0.028 2.00e-02 2.50e+03 pdb=" P HIPPC 291 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIPPI 243 " -0.046 2.00e-02 2.50e+03 8.45e-02 1.25e+02 pdb=" CG HIPPI 243 " -0.008 2.00e-02 2.50e+03 pdb=" ND1 HIPPI 243 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 HIPPI 243 " 0.109 2.00e-02 2.50e+03 pdb=" CE1 HIPPI 243 " -0.091 2.00e-02 2.50e+03 pdb=" NE2 HIPPI 243 " 0.032 2.00e-02 2.50e+03 pdb=" P HIPPI 243 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIPPL 243 " -0.040 2.00e-02 2.50e+03 8.40e-02 1.23e+02 pdb=" CG HIPPL 243 " -0.012 2.00e-02 2.50e+03 pdb=" ND1 HIPPL 243 " -0.120 2.00e-02 2.50e+03 pdb=" CD2 HIPPL 243 " 0.103 2.00e-02 2.50e+03 pdb=" CE1 HIPPL 243 " -0.086 2.00e-02 2.50e+03 pdb=" NE2 HIPPL 243 " 0.037 2.00e-02 2.50e+03 pdb=" P HIPPL 243 " 0.118 2.00e-02 2.50e+03 ... (remaining 9345 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 93 2.56 - 3.15: 38239 3.15 - 3.73: 78570 3.73 - 4.32: 114035 4.32 - 4.90: 188839 Nonbonded interactions: 419776 Sorted by model distance: nonbonded pdb=" OE2 GLUPP 131 " pdb="MG MGPP 201 " model vdw 1.980 2.170 nonbonded pdb=" OE2 GLUPT 131 " pdb="MG MGPT 201 " model vdw 1.985 2.170 nonbonded pdb=" OE2 GLUPV 131 " pdb="MG MGPV 201 " model vdw 1.990 2.170 nonbonded pdb=" OE2 GLUPW 131 " pdb="MG MGPW 201 " model vdw 1.993 2.170 nonbonded pdb=" OE2 GLUPU 131 " pdb="MG MGPU 201 " model vdw 1.997 2.170 ... (remaining 419771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'PA' selection = chain 'PB' selection = chain 'PC' selection = chain 'PD' selection = chain 'PE' selection = chain 'PF' selection = chain 'PG' selection = chain 'PH' selection = chain 'PI' selection = chain 'PJ' selection = chain 'PK' selection = chain 'PL' } ncs_group { reference = chain 'PM' selection = chain 'PN' selection = chain 'PO' selection = chain 'PP' selection = chain 'PQ' selection = chain 'PR' selection = chain 'PS' selection = chain 'PT' selection = chain 'PU' selection = chain 'PV' selection = chain 'PW' selection = chain 'PX' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.050 Extract box with map and model: 1.420 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 83.680 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 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 : 0.010 0.216 51240 Z= 0.648 Angle : 1.492 16.659 69576 Z= 0.958 Chirality : 0.109 0.451 7536 Planarity : 0.009 0.088 9348 Dihedral : 14.715 89.856 18924 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.83 % Allowed : 4.36 % Favored : 94.81 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.10), residues: 6252 helix: 0.26 (0.08), residues: 3156 sheet: 1.00 (0.20), residues: 516 loop : -0.52 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.014 TRPPG 195 HIS 0.013 0.003 HISPL 299 PHE 0.042 0.009 PHEPB 278 TYR 0.081 0.011 TYRPA 137 ARG 0.035 0.002 ARGPD 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2400 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 2356 time to evaluate : 4.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PX 11 LYS cc_start: 0.9295 (ttmt) cc_final: 0.9090 (ttpt) REVERT: PX 108 THR cc_start: 0.9072 (p) cc_final: 0.8826 (p) REVERT: PX 132 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: PA 59 ASP cc_start: 0.8948 (m-30) cc_final: 0.8629 (m-30) REVERT: PA 64 LYS cc_start: 0.9202 (tptm) cc_final: 0.8595 (tptm) REVERT: PA 68 ASP cc_start: 0.8451 (p0) cc_final: 0.8141 (p0) REVERT: PA 144 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7630 (mt-10) REVERT: PA 177 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8013 (ttt180) REVERT: PA 226 ASN cc_start: 0.9060 (m-40) cc_final: 0.8859 (m-40) REVERT: PA 315 GLU cc_start: 0.8976 (mp0) cc_final: 0.8687 (mp0) REVERT: PA 326 SER cc_start: 0.8826 (t) cc_final: 0.8558 (p) REVERT: PA 364 TYR cc_start: 0.9221 (m-80) cc_final: 0.8914 (m-80) REVERT: PA 392 GLN cc_start: 0.9078 (mt0) cc_final: 0.8829 (mt0) REVERT: PA 415 ASP cc_start: 0.8997 (m-30) cc_final: 0.8259 (m-30) REVERT: PB 59 ASP cc_start: 0.8943 (m-30) cc_final: 0.8583 (m-30) REVERT: PB 112 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8163 (mt-10) REVERT: PB 144 GLU cc_start: 0.8606 (mt-10) cc_final: 0.7875 (mt-10) REVERT: PB 192 ASP cc_start: 0.8461 (t0) cc_final: 0.8257 (t0) REVERT: PB 326 SER cc_start: 0.8916 (t) cc_final: 0.8712 (p) REVERT: PB 338 LYS cc_start: 0.9355 (mtmt) cc_final: 0.9133 (mttm) REVERT: PB 383 ASP cc_start: 0.8707 (t0) cc_final: 0.8339 (t0) REVERT: PB 392 GLN cc_start: 0.9141 (mt0) cc_final: 0.8884 (mt0) REVERT: PB 415 ASP cc_start: 0.9070 (m-30) cc_final: 0.8618 (m-30) REVERT: PC 79 TYR cc_start: 0.9270 (m-10) cc_final: 0.9053 (m-10) REVERT: PC 144 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8360 (mt-10) REVERT: PC 149 GLU cc_start: 0.8213 (mp0) cc_final: 0.7769 (mp0) REVERT: PC 177 ARG cc_start: 0.8563 (ttt180) cc_final: 0.8200 (ttp80) REVERT: PC 180 THR cc_start: 0.8961 (p) cc_final: 0.8710 (t) REVERT: PC 301 MET cc_start: 0.8831 (ttp) cc_final: 0.8544 (ttt) REVERT: PC 303 MET cc_start: 0.9003 (tpp) cc_final: 0.8755 (tpt) REVERT: PC 315 GLU cc_start: 0.9032 (mp0) cc_final: 0.8450 (mp0) REVERT: PC 389 ASP cc_start: 0.8750 (m-30) cc_final: 0.8511 (m-30) REVERT: PC 414 ASP cc_start: 0.8758 (t0) cc_final: 0.8417 (t0) REVERT: PD 64 LYS cc_start: 0.9216 (tptm) cc_final: 0.8610 (tptp) REVERT: PD 68 ASP cc_start: 0.8390 (p0) cc_final: 0.8082 (p0) REVERT: PD 144 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7664 (mt-10) REVERT: PD 166 ASP cc_start: 0.8624 (p0) cc_final: 0.8229 (p0) REVERT: PD 168 GLN cc_start: 0.8829 (pm20) cc_final: 0.8371 (pm20) REVERT: PD 192 ASP cc_start: 0.8463 (t0) cc_final: 0.8245 (t0) REVERT: PD 226 ASN cc_start: 0.9088 (m-40) cc_final: 0.8873 (m-40) REVERT: PD 315 GLU cc_start: 0.8999 (mp0) cc_final: 0.8687 (mp0) REVERT: PD 326 SER cc_start: 0.9019 (t) cc_final: 0.8771 (p) REVERT: PD 364 TYR cc_start: 0.9218 (m-80) cc_final: 0.8847 (m-80) REVERT: PD 393 GLN cc_start: 0.9365 (mt0) cc_final: 0.9164 (mt0) REVERT: PD 414 ASP cc_start: 0.8735 (t0) cc_final: 0.8379 (t0) REVERT: PE 59 ASP cc_start: 0.8926 (m-30) cc_final: 0.8577 (m-30) REVERT: PE 144 GLU cc_start: 0.8625 (mt-10) cc_final: 0.7809 (mt-10) REVERT: PE 192 ASP cc_start: 0.8494 (t0) cc_final: 0.8259 (t0) REVERT: PE 326 SER cc_start: 0.8948 (t) cc_final: 0.8701 (p) REVERT: PE 383 ASP cc_start: 0.8791 (t0) cc_final: 0.8330 (t0) REVERT: PE 392 GLN cc_start: 0.9126 (mt0) cc_final: 0.8899 (mt0) REVERT: PF 149 GLU cc_start: 0.8166 (mp0) cc_final: 0.7750 (mp0) REVERT: PF 303 MET cc_start: 0.9071 (tpp) cc_final: 0.8725 (mmm) REVERT: PF 315 GLU cc_start: 0.8993 (mp0) cc_final: 0.8374 (mp0) REVERT: PF 326 SER cc_start: 0.8950 (t) cc_final: 0.8724 (p) REVERT: PF 383 ASP cc_start: 0.8810 (t0) cc_final: 0.8515 (t0) REVERT: PF 389 ASP cc_start: 0.8752 (m-30) cc_final: 0.8392 (m-30) REVERT: PF 392 GLN cc_start: 0.9165 (mt0) cc_final: 0.8866 (mt0) REVERT: PF 414 ASP cc_start: 0.8763 (t0) cc_final: 0.8466 (t0) REVERT: PF 430 ASP cc_start: 0.8769 (m-30) cc_final: 0.8480 (m-30) REVERT: PF 431 GLU cc_start: 0.8914 (tt0) cc_final: 0.8684 (tt0) REVERT: PG 59 ASP cc_start: 0.8912 (m-30) cc_final: 0.8592 (m-30) REVERT: PG 68 ASP cc_start: 0.8393 (p0) cc_final: 0.8067 (p0) REVERT: PG 144 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7796 (mt-10) REVERT: PG 149 GLU cc_start: 0.8339 (mp0) cc_final: 0.8037 (mp0) REVERT: PG 166 ASP cc_start: 0.8725 (p0) cc_final: 0.8471 (p0) REVERT: PG 168 GLN cc_start: 0.8928 (pm20) cc_final: 0.8595 (pm20) REVERT: PG 192 ASP cc_start: 0.8436 (t0) cc_final: 0.8222 (t0) REVERT: PG 303 MET cc_start: 0.9053 (tpp) cc_final: 0.8831 (mmm) REVERT: PG 315 GLU cc_start: 0.9014 (mp0) cc_final: 0.8672 (mp0) REVERT: PG 392 GLN cc_start: 0.9047 (mt0) cc_final: 0.8821 (mt0) REVERT: PG 397 TYR cc_start: 0.9521 (m-80) cc_final: 0.9244 (m-80) REVERT: PG 414 ASP cc_start: 0.8699 (t0) cc_final: 0.8341 (t0) REVERT: PH 59 ASP cc_start: 0.8925 (m-30) cc_final: 0.8578 (m-30) REVERT: PH 96 ASP cc_start: 0.8636 (t70) cc_final: 0.8347 (t0) REVERT: PH 144 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7857 (mt-10) REVERT: PH 177 ARG cc_start: 0.8602 (ttt180) cc_final: 0.8038 (ttp80) REVERT: PH 179 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8637 (mtmm) REVERT: PH 192 ASP cc_start: 0.8472 (t0) cc_final: 0.8264 (t0) REVERT: PH 206 ASP cc_start: 0.8816 (t0) cc_final: 0.8518 (t0) REVERT: PH 338 LYS cc_start: 0.9367 (mtmt) cc_final: 0.9152 (mttm) REVERT: PH 383 ASP cc_start: 0.8734 (t0) cc_final: 0.8299 (t0) REVERT: PH 392 GLN cc_start: 0.9167 (mt0) cc_final: 0.8928 (mt0) REVERT: PH 414 ASP cc_start: 0.8802 (t0) cc_final: 0.8424 (t0) REVERT: PI 59 ASP cc_start: 0.8886 (m-30) cc_final: 0.8524 (m-30) REVERT: PI 94 GLU cc_start: 0.8704 (tp30) cc_final: 0.8503 (tp30) REVERT: PI 112 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8299 (mt-10) REVERT: PI 144 GLU cc_start: 0.8582 (mt-10) cc_final: 0.7696 (mt-10) REVERT: PI 149 GLU cc_start: 0.8169 (mp0) cc_final: 0.7753 (mp0) REVERT: PI 192 ASP cc_start: 0.8484 (t0) cc_final: 0.8214 (t0) REVERT: PI 301 MET cc_start: 0.8919 (ttp) cc_final: 0.8690 (ttt) REVERT: PI 303 MET cc_start: 0.9039 (tpp) cc_final: 0.8454 (tpp) REVERT: PI 315 GLU cc_start: 0.9012 (mp0) cc_final: 0.8335 (mp0) REVERT: PI 326 SER cc_start: 0.8882 (t) cc_final: 0.8585 (p) REVERT: PI 364 TYR cc_start: 0.9183 (m-80) cc_final: 0.8932 (m-80) REVERT: PI 389 ASP cc_start: 0.8816 (m-30) cc_final: 0.8544 (m-30) REVERT: PI 408 ASP cc_start: 0.8854 (t0) cc_final: 0.8624 (t0) REVERT: PI 414 ASP cc_start: 0.8732 (t0) cc_final: 0.8425 (t0) REVERT: PJ 59 ASP cc_start: 0.8848 (m-30) cc_final: 0.8532 (m-30) REVERT: PJ 62 ASP cc_start: 0.8771 (m-30) cc_final: 0.8535 (m-30) REVERT: PJ 68 ASP cc_start: 0.8506 (p0) cc_final: 0.8148 (p0) REVERT: PJ 144 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7738 (mt-10) REVERT: PJ 149 GLU cc_start: 0.8196 (mp0) cc_final: 0.7941 (mp0) REVERT: PJ 303 MET cc_start: 0.9088 (tpp) cc_final: 0.8860 (mmm) REVERT: PJ 304 ARG cc_start: 0.8812 (ttm-80) cc_final: 0.8583 (ttm110) REVERT: PJ 315 GLU cc_start: 0.9009 (mp0) cc_final: 0.8706 (mp0) REVERT: PJ 326 SER cc_start: 0.9016 (t) cc_final: 0.8718 (p) REVERT: PJ 392 GLN cc_start: 0.9083 (mt0) cc_final: 0.8825 (mt0) REVERT: PJ 419 ASP cc_start: 0.8825 (t70) cc_final: 0.8497 (t0) REVERT: PK 59 ASP cc_start: 0.8899 (m-30) cc_final: 0.8533 (m-30) REVERT: PK 64 LYS cc_start: 0.9180 (tptm) cc_final: 0.8824 (tptm) REVERT: PK 112 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8219 (mt-10) REVERT: PK 144 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7786 (mt-10) REVERT: PK 179 LYS cc_start: 0.8807 (mtpp) cc_final: 0.8398 (mtpp) REVERT: PK 192 ASP cc_start: 0.8471 (t0) cc_final: 0.8199 (t0) REVERT: PK 219 GLU cc_start: 0.8610 (mp0) cc_final: 0.8208 (mp0) REVERT: PK 326 SER cc_start: 0.8877 (t) cc_final: 0.8676 (p) REVERT: PK 338 LYS cc_start: 0.9375 (mtmt) cc_final: 0.9160 (mttm) REVERT: PK 383 ASP cc_start: 0.8660 (t0) cc_final: 0.8169 (t0) REVERT: PK 392 GLN cc_start: 0.9153 (mt0) cc_final: 0.8842 (mt0) REVERT: PK 415 ASP cc_start: 0.9144 (m-30) cc_final: 0.8807 (m-30) REVERT: PL 59 ASP cc_start: 0.8859 (m-30) cc_final: 0.8499 (m-30) REVERT: PL 115 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8764 (mt-10) REVERT: PL 144 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8430 (mt-10) REVERT: PL 149 GLU cc_start: 0.8170 (mp0) cc_final: 0.7732 (mp0) REVERT: PL 177 ARG cc_start: 0.8564 (ttt180) cc_final: 0.8219 (ttt180) REVERT: PL 180 THR cc_start: 0.8884 (p) cc_final: 0.8638 (t) REVERT: PL 192 ASP cc_start: 0.8509 (t0) cc_final: 0.8293 (t0) REVERT: PL 224 LYS cc_start: 0.9435 (mttt) cc_final: 0.9226 (mmtt) REVERT: PL 301 MET cc_start: 0.8875 (ttp) cc_final: 0.8558 (ttt) REVERT: PL 303 MET cc_start: 0.8964 (tpp) cc_final: 0.8401 (tpp) REVERT: PL 315 GLU cc_start: 0.9026 (mp0) cc_final: 0.8373 (mp0) REVERT: PL 326 SER cc_start: 0.8973 (t) cc_final: 0.8754 (p) REVERT: PL 389 ASP cc_start: 0.8814 (m-30) cc_final: 0.8459 (m-30) REVERT: PL 392 GLN cc_start: 0.9184 (mt0) cc_final: 0.8881 (mt0) REVERT: PL 408 ASP cc_start: 0.8925 (t0) cc_final: 0.8702 (t0) REVERT: PL 414 ASP cc_start: 0.8765 (t0) cc_final: 0.8445 (t0) REVERT: PM 11 LYS cc_start: 0.9286 (ttmt) cc_final: 0.8879 (ttmt) REVERT: PN 10 SER cc_start: 0.9217 (t) cc_final: 0.8843 (p) REVERT: PN 13 ASP cc_start: 0.9110 (m-30) cc_final: 0.8777 (m-30) REVERT: PN 64 MET cc_start: 0.9224 (mtm) cc_final: 0.8905 (mtm) REVERT: PN 131 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7933 (mt-10) REVERT: PO 13 ASP cc_start: 0.9052 (m-30) cc_final: 0.8770 (m-30) REVERT: PO 55 GLU cc_start: 0.8819 (tt0) cc_final: 0.8377 (tt0) REVERT: PO 64 MET cc_start: 0.9324 (mtm) cc_final: 0.9110 (mtp) REVERT: PO 132 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8627 (m-30) REVERT: PP 11 LYS cc_start: 0.9314 (ttmt) cc_final: 0.8879 (ttmt) REVERT: PP 40 THR cc_start: 0.9302 (m) cc_final: 0.9082 (m) REVERT: PQ 108 THR cc_start: 0.8963 (m) cc_final: 0.8508 (p) REVERT: PQ 128 TYR cc_start: 0.9214 (m-80) cc_final: 0.8983 (m-80) REVERT: PR 13 ASP cc_start: 0.9094 (m-30) cc_final: 0.8819 (m-30) REVERT: PR 55 GLU cc_start: 0.8825 (tt0) cc_final: 0.8440 (tt0) REVERT: PR 95 GLN cc_start: 0.8595 (tt0) cc_final: 0.8363 (tp40) REVERT: PR 127 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7786 (mm-30) REVERT: PR 131 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7622 (mt-10) REVERT: PS 11 LYS cc_start: 0.9298 (ttmt) cc_final: 0.8945 (ttmt) REVERT: PS 13 ASP cc_start: 0.9101 (m-30) cc_final: 0.8830 (m-30) REVERT: PU 55 GLU cc_start: 0.8756 (tt0) cc_final: 0.8416 (tt0) REVERT: PU 132 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8544 (m-30) REVERT: PV 11 LYS cc_start: 0.9325 (ttmt) cc_final: 0.8961 (ttmt) REVERT: PV 64 MET cc_start: 0.9228 (mtm) cc_final: 0.9024 (mtp) outliers start: 44 outliers final: 3 residues processed: 2395 average time/residue: 1.3844 time to fit residues: 4077.1467 Evaluate side-chains 1630 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1624 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PX residue 132 ASP Chi-restraints excluded: chain PA residue 292 ASN Chi-restraints excluded: chain PN residue 129 VAL Chi-restraints excluded: chain PO residue 132 ASP Chi-restraints excluded: chain PS residue 119 THR Chi-restraints excluded: chain PU residue 132 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 537 optimal weight: 6.9990 chunk 482 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 325 optimal weight: 0.9980 chunk 257 optimal weight: 10.0000 chunk 498 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 303 optimal weight: 9.9990 chunk 371 optimal weight: 0.5980 chunk 577 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PX 28 GLN PX 39 ASN PX 117 GLN PA 225 GLN PA 241 GLN PA 292 ASN PA 299 HIS PA 392 GLN PB 181 HIS PB 299 HIS PB 318 ASN PB 392 GLN PC 181 HIS PC 185 GLN PC 299 HIS PC 318 ASN PC 393 GLN PD 292 ASN PD 299 HIS PE 143 GLN PE 185 GLN PE 200 ASN PE 299 HIS PE 318 ASN PE 392 GLN PF 72 GLN PF 185 GLN PF 299 HIS PF 318 ASN PF 392 GLN PG 168 GLN PG 181 HIS PG 225 GLN PG 318 ASN PG 392 GLN PH 172 GLN PH 181 HIS PH 185 GLN PH 200 ASN PH 241 GLN PH 299 HIS PH 392 GLN PI 72 GLN PI 181 HIS PI 185 GLN PI 232 GLN PI 299 HIS PI 318 ASN PJ 101 GLN PJ 143 GLN PJ 181 HIS PJ 225 GLN PJ 299 HIS PJ 392 GLN PK 181 HIS PK 185 GLN PK 200 ASN PK 299 HIS PK 318 ASN PK 392 GLN PL 72 GLN PL 185 GLN PL 232 GLN PL 299 HIS PL 318 ASN PL 392 GLN PM 39 ASN PN 28 GLN PN 117 GLN PO 28 GLN PO 39 ASN PO 117 GLN PQ 28 GLN PQ 117 GLN PQ 133 ASN PR 28 GLN PR 39 ASN PR 117 GLN PS 39 ASN PT 28 GLN PT 117 GLN PU 28 GLN PU 39 ASN PU 117 GLN PV 39 ASN PW 28 GLN Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 51240 Z= 0.188 Angle : 0.574 7.549 69576 Z= 0.303 Chirality : 0.040 0.159 7536 Planarity : 0.004 0.041 9348 Dihedral : 8.335 89.667 7006 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.48 % Allowed : 14.26 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.10), residues: 6252 helix: 1.87 (0.09), residues: 3168 sheet: 1.94 (0.23), residues: 396 loop : -0.46 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPPG 134 HIS 0.005 0.001 HISPH 175 PHE 0.015 0.002 PHEPK 334 TYR 0.013 0.001 TYRPW 76 ARG 0.008 0.001 ARGPK 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2013 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1828 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PA 59 ASP cc_start: 0.8925 (m-30) cc_final: 0.8666 (m-30) REVERT: PA 68 ASP cc_start: 0.8255 (p0) cc_final: 0.7775 (p0) REVERT: PA 144 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8243 (mt-10) REVERT: PA 149 GLU cc_start: 0.8434 (mp0) cc_final: 0.8007 (mp0) REVERT: PA 164 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: PA 170 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8700 (mmmm) REVERT: PA 179 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8579 (mtmp) REVERT: PA 210 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9219 (mp) REVERT: PA 219 GLU cc_start: 0.8617 (mp0) cc_final: 0.8289 (mp0) REVERT: PA 261 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8441 (mmm-85) REVERT: PA 315 GLU cc_start: 0.8928 (mp0) cc_final: 0.8606 (mp0) REVERT: PA 379 ASP cc_start: 0.8845 (t0) cc_final: 0.8488 (t0) REVERT: PA 397 TYR cc_start: 0.9453 (m-80) cc_final: 0.9188 (m-80) REVERT: PB 42 MET cc_start: 0.8002 (tpt) cc_final: 0.7617 (tpp) REVERT: PB 59 ASP cc_start: 0.8988 (m-30) cc_final: 0.8749 (m-30) REVERT: PB 144 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8154 (mt-10) REVERT: PB 376 GLU cc_start: 0.8494 (tt0) cc_final: 0.8253 (tm-30) REVERT: PB 426 ASP cc_start: 0.9134 (m-30) cc_final: 0.8868 (m-30) REVERT: PB 428 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8544 (mt-10) REVERT: PC 59 ASP cc_start: 0.8948 (m-30) cc_final: 0.8723 (m-30) REVERT: PC 144 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8038 (mt-10) REVERT: PC 170 LYS cc_start: 0.8924 (ttmm) cc_final: 0.8690 (mmmm) REVERT: PC 261 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8418 (mmm-85) REVERT: PC 303 MET cc_start: 0.9006 (tpp) cc_final: 0.8798 (mmm) REVERT: PC 364 TYR cc_start: 0.9182 (m-80) cc_final: 0.8877 (m-80) REVERT: PC 389 ASP cc_start: 0.8816 (m-30) cc_final: 0.8573 (m-30) REVERT: PD 68 ASP cc_start: 0.8219 (p0) cc_final: 0.7700 (p0) REVERT: PD 98 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8864 (mp0) REVERT: PD 112 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8538 (mt-10) REVERT: PD 144 GLU cc_start: 0.8664 (mt-10) cc_final: 0.7928 (mt-10) REVERT: PD 192 ASP cc_start: 0.8435 (t0) cc_final: 0.8226 (t0) REVERT: PD 315 GLU cc_start: 0.8956 (mp0) cc_final: 0.8629 (mp0) REVERT: PD 379 ASP cc_start: 0.8844 (t0) cc_final: 0.8537 (t0) REVERT: PD 397 TYR cc_start: 0.9454 (m-80) cc_final: 0.9195 (m-80) REVERT: PD 408 ASP cc_start: 0.8910 (t0) cc_final: 0.8568 (t0) REVERT: PE 59 ASP cc_start: 0.8982 (m-30) cc_final: 0.8728 (m-30) REVERT: PE 67 ARG cc_start: 0.9217 (tpp80) cc_final: 0.8963 (tpp80) REVERT: PE 144 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8336 (mt-10) REVERT: PE 386 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8498 (mp0) REVERT: PE 428 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8525 (mt-10) REVERT: PF 59 ASP cc_start: 0.8948 (m-30) cc_final: 0.8739 (m-30) REVERT: PF 144 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: PF 149 GLU cc_start: 0.8515 (mp0) cc_final: 0.8063 (mp0) REVERT: PF 303 MET cc_start: 0.9108 (tpp) cc_final: 0.8824 (mmm) REVERT: PF 315 GLU cc_start: 0.8951 (mp0) cc_final: 0.8562 (mp0) REVERT: PF 389 ASP cc_start: 0.8786 (m-30) cc_final: 0.8527 (m-30) REVERT: PG 59 ASP cc_start: 0.8925 (m-30) cc_final: 0.8664 (m-30) REVERT: PG 67 ARG cc_start: 0.9192 (tpp80) cc_final: 0.8476 (tpt90) REVERT: PG 68 ASP cc_start: 0.8168 (p0) cc_final: 0.7672 (p0) REVERT: PG 144 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8191 (mt-10) REVERT: PG 149 GLU cc_start: 0.8647 (mp0) cc_final: 0.8187 (mp0) REVERT: PG 185 GLN cc_start: 0.8348 (tt0) cc_final: 0.8074 (tt0) REVERT: PG 192 ASP cc_start: 0.8426 (t0) cc_final: 0.8217 (t0) REVERT: PG 219 GLU cc_start: 0.8689 (mp0) cc_final: 0.8334 (mp0) REVERT: PG 261 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8434 (mmm-85) REVERT: PG 272 ASP cc_start: 0.8523 (p0) cc_final: 0.8309 (p0) REVERT: PG 315 GLU cc_start: 0.8958 (mp0) cc_final: 0.8725 (mp0) REVERT: PG 364 TYR cc_start: 0.9213 (m-80) cc_final: 0.8902 (m-80) REVERT: PG 379 ASP cc_start: 0.8766 (t0) cc_final: 0.8363 (t0) REVERT: PG 426 ASP cc_start: 0.9039 (m-30) cc_final: 0.8805 (m-30) REVERT: PH 42 MET cc_start: 0.7948 (tpt) cc_final: 0.6707 (tmm) REVERT: PH 59 ASP cc_start: 0.9017 (m-30) cc_final: 0.8787 (m-30) REVERT: PH 112 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8436 (mt-10) REVERT: PH 144 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8134 (mt-10) REVERT: PH 386 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8505 (mp0) REVERT: PH 415 ASP cc_start: 0.9140 (m-30) cc_final: 0.8919 (m-30) REVERT: PH 428 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8595 (mt-10) REVERT: PI 59 ASP cc_start: 0.8905 (m-30) cc_final: 0.8670 (m-30) REVERT: PI 144 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8056 (mt-10) REVERT: PI 149 GLU cc_start: 0.8542 (mp0) cc_final: 0.8122 (mp0) REVERT: PI 170 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8754 (mmmm) REVERT: PI 179 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8465 (mtmt) REVERT: PI 303 MET cc_start: 0.9033 (tpp) cc_final: 0.8670 (mmm) REVERT: PI 315 GLU cc_start: 0.9004 (mp0) cc_final: 0.8804 (mp0) REVERT: PI 389 ASP cc_start: 0.8875 (m-30) cc_final: 0.8573 (m-30) REVERT: PJ 59 ASP cc_start: 0.8919 (m-30) cc_final: 0.8668 (m-30) REVERT: PJ 68 ASP cc_start: 0.8272 (p0) cc_final: 0.7838 (p0) REVERT: PJ 144 GLU cc_start: 0.8666 (mt-10) cc_final: 0.7948 (mt-10) REVERT: PJ 149 GLU cc_start: 0.8592 (mp0) cc_final: 0.8173 (mp0) REVERT: PJ 219 GLU cc_start: 0.8699 (mp0) cc_final: 0.8328 (mp0) REVERT: PJ 261 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8568 (mmm-85) REVERT: PJ 272 ASP cc_start: 0.8673 (p0) cc_final: 0.8439 (p0) REVERT: PJ 315 GLU cc_start: 0.8925 (mp0) cc_final: 0.8633 (mp0) REVERT: PJ 379 ASP cc_start: 0.8776 (t0) cc_final: 0.8399 (t0) REVERT: PJ 397 TYR cc_start: 0.9401 (m-80) cc_final: 0.9184 (m-80) REVERT: PJ 426 ASP cc_start: 0.8900 (m-30) cc_final: 0.8530 (m-30) REVERT: PK 59 ASP cc_start: 0.8960 (m-30) cc_final: 0.8730 (m-30) REVERT: PK 144 GLU cc_start: 0.8622 (mt-10) cc_final: 0.7832 (mt-10) REVERT: PK 170 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8413 (mmmm) REVERT: PK 226 ASN cc_start: 0.8898 (m-40) cc_final: 0.8629 (m-40) REVERT: PK 315 GLU cc_start: 0.8934 (mp0) cc_final: 0.8627 (mp0) REVERT: PK 428 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8572 (mt-10) REVERT: PL 59 ASP cc_start: 0.8907 (m-30) cc_final: 0.8676 (m-30) REVERT: PL 144 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8315 (mp0) REVERT: PL 149 GLU cc_start: 0.8509 (mp0) cc_final: 0.8060 (mp0) REVERT: PL 170 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8546 (mmmm) REVERT: PL 177 ARG cc_start: 0.8761 (ttt180) cc_final: 0.8019 (ttt90) REVERT: PL 261 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8422 (mmm-85) REVERT: PL 303 MET cc_start: 0.8943 (tpp) cc_final: 0.8725 (mmm) REVERT: PL 315 GLU cc_start: 0.8990 (mp0) cc_final: 0.8702 (mp0) REVERT: PL 389 ASP cc_start: 0.8826 (m-30) cc_final: 0.8525 (m-30) REVERT: PM 13 ASP cc_start: 0.9074 (m-30) cc_final: 0.8810 (m-30) REVERT: PN 66 ARG cc_start: 0.9201 (mtt90) cc_final: 0.8897 (mtt180) REVERT: PO 13 ASP cc_start: 0.9024 (m-30) cc_final: 0.8764 (m-30) REVERT: PO 100 GLU cc_start: 0.5774 (mt-10) cc_final: 0.4935 (mm-30) REVERT: PP 66 ARG cc_start: 0.9215 (mpp-170) cc_final: 0.8982 (mtt180) REVERT: PQ 108 THR cc_start: 0.8612 (m) cc_final: 0.8106 (p) REVERT: PR 13 ASP cc_start: 0.9058 (m-30) cc_final: 0.8849 (m-30) REVERT: PR 66 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8540 (mtp180) REVERT: PR 100 GLU cc_start: 0.5810 (mt-10) cc_final: 0.5164 (mm-30) REVERT: PS 13 ASP cc_start: 0.9005 (m-30) cc_final: 0.8746 (m-30) REVERT: PS 66 ARG cc_start: 0.9201 (mtt90) cc_final: 0.8932 (mtt180) REVERT: PU 66 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8601 (mtp180) REVERT: PU 100 GLU cc_start: 0.5785 (mt-10) cc_final: 0.5170 (mm-30) REVERT: PV 66 ARG cc_start: 0.9316 (mpp-170) cc_final: 0.9104 (mtt180) outliers start: 185 outliers final: 36 residues processed: 1906 average time/residue: 1.4015 time to fit residues: 3282.3961 Evaluate side-chains 1621 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1573 time to evaluate : 4.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PA residue 146 ILE Chi-restraints excluded: chain PA residue 164 GLU Chi-restraints excluded: chain PA residue 210 ILE Chi-restraints excluded: chain PA residue 261 ARG Chi-restraints excluded: chain PA residue 376 GLU Chi-restraints excluded: chain PA residue 386 GLU Chi-restraints excluded: chain PB residue 69 SER Chi-restraints excluded: chain PB residue 249 GLU Chi-restraints excluded: chain PC residue 34 THR Chi-restraints excluded: chain PC residue 146 ILE Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PC residue 391 ILE Chi-restraints excluded: chain PD residue 34 THR Chi-restraints excluded: chain PD residue 365 SER Chi-restraints excluded: chain PD residue 386 GLU Chi-restraints excluded: chain PD residue 391 ILE Chi-restraints excluded: chain PE residue 34 THR Chi-restraints excluded: chain PE residue 69 SER Chi-restraints excluded: chain PE residue 249 GLU Chi-restraints excluded: chain PE residue 386 GLU Chi-restraints excluded: chain PF residue 69 SER Chi-restraints excluded: chain PF residue 144 GLU Chi-restraints excluded: chain PF residue 146 ILE Chi-restraints excluded: chain PG residue 106 GLU Chi-restraints excluded: chain PG residue 261 ARG Chi-restraints excluded: chain PG residue 365 SER Chi-restraints excluded: chain PH residue 69 SER Chi-restraints excluded: chain PH residue 249 GLU Chi-restraints excluded: chain PH residue 386 GLU Chi-restraints excluded: chain PI residue 146 ILE Chi-restraints excluded: chain PI residue 221 GLN Chi-restraints excluded: chain PJ residue 261 ARG Chi-restraints excluded: chain PJ residue 365 SER Chi-restraints excluded: chain PJ residue 386 GLU Chi-restraints excluded: chain PJ residue 423 SER Chi-restraints excluded: chain PK residue 69 SER Chi-restraints excluded: chain PK residue 249 GLU Chi-restraints excluded: chain PK residue 386 GLU Chi-restraints excluded: chain PL residue 146 ILE Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PM residue 96 SER Chi-restraints excluded: chain PN residue 18 THR Chi-restraints excluded: chain PO residue 132 ASP Chi-restraints excluded: chain PP residue 96 SER Chi-restraints excluded: chain PR residue 66 ARG Chi-restraints excluded: chain PS residue 96 SER Chi-restraints excluded: chain PU residue 66 ARG Chi-restraints excluded: chain PV residue 96 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 320 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 480 optimal weight: 2.9990 chunk 393 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 578 optimal weight: 9.9990 chunk 625 optimal weight: 9.9990 chunk 515 optimal weight: 10.0000 chunk 573 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 464 optimal weight: 10.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PX 39 ASN PX 117 GLN PA 181 HIS PA 226 ASN PA 257 ASN PA 393 GLN PB 143 GLN PB 200 ASN PD 92 HIS ** PD 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PD 181 HIS PD 226 ASN PD 257 ASN PD 393 GLN PE 143 GLN PF 101 GLN PF 393 GLN PG 257 ASN PG 393 GLN PI 92 HIS PI 185 GLN PI 393 GLN ** PJ 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PJ 257 ASN PJ 393 GLN PL 143 GLN PL 181 HIS PL 393 GLN PM 39 ASN PN 20 GLN PN 28 GLN PN 117 GLN PN 133 ASN PO 28 GLN PO 39 ASN PO 117 GLN PO 133 ASN PP 39 ASN PQ 28 GLN PR 39 ASN PR 117 GLN PR 133 ASN PS 39 ASN PT 28 GLN PU 117 GLN PV 39 ASN PW 28 GLN PW 133 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 51240 Z= 0.464 Angle : 0.663 8.989 69576 Z= 0.342 Chirality : 0.044 0.140 7536 Planarity : 0.005 0.049 9348 Dihedral : 7.930 86.471 6998 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.06 % Allowed : 15.97 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.10), residues: 6252 helix: 1.86 (0.09), residues: 3168 sheet: 0.82 (0.20), residues: 540 loop : -0.37 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPPJ 134 HIS 0.004 0.001 HISPD 175 PHE 0.025 0.003 PHEPD 334 TYR 0.026 0.002 TYRPM 76 ARG 0.007 0.001 ARGPK 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1844 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1628 time to evaluate : 4.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PX 66 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8301 (mtp180) REVERT: PA 59 ASP cc_start: 0.9048 (m-30) cc_final: 0.8790 (m-30) REVERT: PA 67 ARG cc_start: 0.9285 (tpp80) cc_final: 0.8525 (tpt90) REVERT: PA 68 ASP cc_start: 0.8354 (p0) cc_final: 0.7971 (p0) REVERT: PA 98 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8612 (mp0) REVERT: PA 112 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8660 (mt-10) REVERT: PA 144 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8097 (mt-10) REVERT: PA 164 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: PA 170 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8618 (mmmm) REVERT: PA 179 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8685 (mtmp) REVERT: PA 261 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8121 (mmm-85) REVERT: PA 379 ASP cc_start: 0.8812 (t0) cc_final: 0.8609 (t0) REVERT: PA 426 ASP cc_start: 0.8958 (m-30) cc_final: 0.8536 (m-30) REVERT: PB 42 MET cc_start: 0.7707 (tpt) cc_final: 0.7277 (tpp) REVERT: PB 59 ASP cc_start: 0.8933 (m-30) cc_final: 0.8710 (m-30) REVERT: PB 149 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8232 (mm-30) REVERT: PB 261 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8417 (mmm-85) REVERT: PB 383 ASP cc_start: 0.8920 (t0) cc_final: 0.8646 (t0) REVERT: PC 112 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8624 (mt-10) REVERT: PC 144 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8187 (mt-10) REVERT: PC 149 GLU cc_start: 0.8627 (mp0) cc_final: 0.8410 (mm-30) REVERT: PC 261 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8627 (mmm-85) REVERT: PC 370 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8822 (mp0) REVERT: PC 372 ASP cc_start: 0.8557 (t70) cc_final: 0.8331 (t70) REVERT: PC 427 MET cc_start: 0.8975 (mtp) cc_final: 0.8757 (mtm) REVERT: PC 428 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8677 (mt-10) REVERT: PD 68 ASP cc_start: 0.8401 (p0) cc_final: 0.8125 (p0) REVERT: PD 87 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8411 (mm-30) REVERT: PD 112 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8554 (mt-10) REVERT: PD 144 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7633 (mt-10) REVERT: PD 164 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7688 (mm-30) REVERT: PD 261 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8081 (mmm-85) REVERT: PD 379 ASP cc_start: 0.8860 (t0) cc_final: 0.8487 (t0) REVERT: PD 408 ASP cc_start: 0.8898 (t0) cc_final: 0.8584 (t0) REVERT: PE 59 ASP cc_start: 0.8967 (m-30) cc_final: 0.8729 (m-30) REVERT: PE 67 ARG cc_start: 0.9289 (tpp80) cc_final: 0.9059 (tpp80) REVERT: PE 112 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8512 (mt-10) REVERT: PE 144 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8099 (mt-10) REVERT: PE 261 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8226 (mmm-85) REVERT: PE 364 TYR cc_start: 0.9286 (m-80) cc_final: 0.8971 (m-80) REVERT: PE 383 ASP cc_start: 0.8884 (t0) cc_final: 0.8296 (t0) REVERT: PE 386 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: PE 428 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8567 (mt-10) REVERT: PF 112 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8549 (mt-10) REVERT: PF 144 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8496 (mp0) REVERT: PF 170 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8595 (mmmm) REVERT: PF 261 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8441 (mmm-85) REVERT: PF 315 GLU cc_start: 0.9036 (mp0) cc_final: 0.8666 (mp0) REVERT: PF 374 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8581 (ttp80) REVERT: PF 392 GLN cc_start: 0.9110 (tt0) cc_final: 0.8891 (mt0) REVERT: PF 423 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8810 (p) REVERT: PF 430 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8563 (p0) REVERT: PF 431 GLU cc_start: 0.9133 (tt0) cc_final: 0.8926 (tt0) REVERT: PG 68 ASP cc_start: 0.8350 (p0) cc_final: 0.8057 (p0) REVERT: PG 98 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8643 (mp0) REVERT: PG 144 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8284 (mt-10) REVERT: PG 261 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8280 (mmm-85) REVERT: PG 272 ASP cc_start: 0.8756 (p0) cc_final: 0.8498 (p0) REVERT: PG 315 GLU cc_start: 0.9040 (mp0) cc_final: 0.8834 (mp0) REVERT: PG 370 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8936 (mp0) REVERT: PG 379 ASP cc_start: 0.8790 (t0) cc_final: 0.8453 (t0) REVERT: PG 426 ASP cc_start: 0.9041 (m-30) cc_final: 0.8818 (m-30) REVERT: PG 431 GLU cc_start: 0.9044 (tt0) cc_final: 0.8834 (tm-30) REVERT: PH 59 ASP cc_start: 0.8979 (m-30) cc_final: 0.8742 (m-30) REVERT: PH 112 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8249 (mt-10) REVERT: PH 144 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8273 (mt-10) REVERT: PH 261 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8321 (mmm-85) REVERT: PH 370 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8771 (mp0) REVERT: PH 383 ASP cc_start: 0.8879 (t0) cc_final: 0.8236 (t0) REVERT: PH 386 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: PH 428 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8560 (mt-10) REVERT: PH 431 GLU cc_start: 0.9028 (tt0) cc_final: 0.8795 (tm-30) REVERT: PI 42 MET cc_start: 0.7698 (tpt) cc_final: 0.7227 (tpp) REVERT: PI 59 ASP cc_start: 0.8973 (m-30) cc_final: 0.8767 (m-30) REVERT: PI 67 ARG cc_start: 0.9336 (tpp80) cc_final: 0.8571 (tpt90) REVERT: PI 144 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8152 (mt-10) REVERT: PI 261 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8507 (mmm-85) REVERT: PI 315 GLU cc_start: 0.9080 (mp0) cc_final: 0.8831 (mp0) REVERT: PI 370 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8714 (mp0) REVERT: PI 389 ASP cc_start: 0.8883 (m-30) cc_final: 0.8583 (m-30) REVERT: PJ 68 ASP cc_start: 0.8361 (p0) cc_final: 0.8079 (p0) REVERT: PJ 115 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8682 (mt-10) REVERT: PJ 144 GLU cc_start: 0.8686 (mt-10) cc_final: 0.7705 (mt-10) REVERT: PJ 149 GLU cc_start: 0.8716 (mp0) cc_final: 0.8452 (mm-30) REVERT: PJ 261 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8370 (mmm-85) REVERT: PJ 315 GLU cc_start: 0.9024 (mp0) cc_final: 0.8797 (mp0) REVERT: PJ 364 TYR cc_start: 0.9270 (m-80) cc_final: 0.8950 (m-80) REVERT: PJ 379 ASP cc_start: 0.8830 (t0) cc_final: 0.8569 (t0) REVERT: PJ 419 ASP cc_start: 0.9131 (m-30) cc_final: 0.8715 (m-30) REVERT: PJ 426 ASP cc_start: 0.8990 (m-30) cc_final: 0.8539 (m-30) REVERT: PJ 428 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8622 (mt-10) REVERT: PK 42 MET cc_start: 0.7511 (tpt) cc_final: 0.7079 (tpp) REVERT: PK 59 ASP cc_start: 0.9020 (m-30) cc_final: 0.8776 (m-30) REVERT: PK 67 ARG cc_start: 0.9240 (tpp80) cc_final: 0.8625 (tpt90) REVERT: PK 112 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8531 (mt-10) REVERT: PK 144 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8276 (mt-10) REVERT: PK 261 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8292 (mmm-85) REVERT: PK 315 GLU cc_start: 0.9014 (mp0) cc_final: 0.8794 (mp0) REVERT: PK 383 ASP cc_start: 0.8879 (t0) cc_final: 0.8614 (t0) REVERT: PK 428 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8669 (mt-10) REVERT: PL 59 ASP cc_start: 0.8974 (m-30) cc_final: 0.8754 (m-30) REVERT: PL 112 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8519 (mt-10) REVERT: PL 144 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8130 (mt-10) REVERT: PL 170 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8650 (mmmm) REVERT: PL 261 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8585 (mmm-85) REVERT: PL 389 ASP cc_start: 0.8844 (m-30) cc_final: 0.8513 (m-30) REVERT: PL 392 GLN cc_start: 0.9112 (tt0) cc_final: 0.8873 (mt0) REVERT: PL 409 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9177 (mm) REVERT: PM 13 ASP cc_start: 0.9123 (m-30) cc_final: 0.8832 (m-30) REVERT: PM 47 GLU cc_start: 0.8973 (tp30) cc_final: 0.8734 (tp30) REVERT: PM 66 ARG cc_start: 0.9292 (mtt90) cc_final: 0.9072 (mpp-170) REVERT: PM 132 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8869 (t0) REVERT: PN 20 GLN cc_start: 0.8972 (tp40) cc_final: 0.8762 (tp40) REVERT: PN 66 ARG cc_start: 0.9349 (mtt90) cc_final: 0.9086 (mpp-170) REVERT: PN 107 SER cc_start: 0.9007 (t) cc_final: 0.8763 (t) REVERT: PN 132 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8782 (t0) REVERT: PO 13 ASP cc_start: 0.9116 (m-30) cc_final: 0.8777 (m-30) REVERT: PO 66 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8355 (mtp180) REVERT: PQ 66 ARG cc_start: 0.9293 (mtt90) cc_final: 0.8909 (mtt180) REVERT: PR 13 ASP cc_start: 0.9156 (m-30) cc_final: 0.8923 (m-30) REVERT: PR 66 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8345 (mtp180) REVERT: PS 13 ASP cc_start: 0.9115 (m-30) cc_final: 0.8811 (m-30) REVERT: PS 47 GLU cc_start: 0.8944 (tp30) cc_final: 0.8684 (tp30) REVERT: PS 66 ARG cc_start: 0.9293 (mtt90) cc_final: 0.9050 (mtt180) REVERT: PT 66 ARG cc_start: 0.9384 (OUTLIER) cc_final: 0.8947 (mtt180) REVERT: PU 64 MET cc_start: 0.9174 (mtm) cc_final: 0.8953 (mtp) REVERT: PV 66 ARG cc_start: 0.9393 (mpp-170) cc_final: 0.9126 (mtt180) outliers start: 216 outliers final: 70 residues processed: 1743 average time/residue: 1.4494 time to fit residues: 3106.6130 Evaluate side-chains 1508 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1413 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PX residue 34 SER Chi-restraints excluded: chain PX residue 66 ARG Chi-restraints excluded: chain PX residue 138 LEU Chi-restraints excluded: chain PA residue 69 SER Chi-restraints excluded: chain PA residue 164 GLU Chi-restraints excluded: chain PA residue 249 GLU Chi-restraints excluded: chain PA residue 261 ARG Chi-restraints excluded: chain PA residue 365 SER Chi-restraints excluded: chain PA residue 423 SER Chi-restraints excluded: chain PB residue 34 THR Chi-restraints excluded: chain PB residue 36 GLN Chi-restraints excluded: chain PB residue 69 SER Chi-restraints excluded: chain PB residue 250 ASP Chi-restraints excluded: chain PB residue 261 ARG Chi-restraints excluded: chain PC residue 34 THR Chi-restraints excluded: chain PC residue 69 SER Chi-restraints excluded: chain PC residue 104 ASP Chi-restraints excluded: chain PC residue 146 ILE Chi-restraints excluded: chain PC residue 249 GLU Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PD residue 34 THR Chi-restraints excluded: chain PD residue 69 SER Chi-restraints excluded: chain PD residue 164 GLU Chi-restraints excluded: chain PD residue 249 GLU Chi-restraints excluded: chain PD residue 261 ARG Chi-restraints excluded: chain PD residue 365 SER Chi-restraints excluded: chain PD residue 376 GLU Chi-restraints excluded: chain PD residue 391 ILE Chi-restraints excluded: chain PE residue 36 GLN Chi-restraints excluded: chain PE residue 69 SER Chi-restraints excluded: chain PE residue 76 LEU Chi-restraints excluded: chain PE residue 249 GLU Chi-restraints excluded: chain PE residue 250 ASP Chi-restraints excluded: chain PE residue 261 ARG Chi-restraints excluded: chain PE residue 333 ARG Chi-restraints excluded: chain PE residue 386 GLU Chi-restraints excluded: chain PF residue 69 SER Chi-restraints excluded: chain PF residue 104 ASP Chi-restraints excluded: chain PF residue 146 ILE Chi-restraints excluded: chain PF residue 261 ARG Chi-restraints excluded: chain PF residue 423 SER Chi-restraints excluded: chain PF residue 430 ASP Chi-restraints excluded: chain PG residue 261 ARG Chi-restraints excluded: chain PG residue 365 SER Chi-restraints excluded: chain PG residue 386 GLU Chi-restraints excluded: chain PG residue 391 ILE Chi-restraints excluded: chain PH residue 34 THR Chi-restraints excluded: chain PH residue 69 SER Chi-restraints excluded: chain PH residue 249 GLU Chi-restraints excluded: chain PH residue 250 ASP Chi-restraints excluded: chain PH residue 261 ARG Chi-restraints excluded: chain PH residue 386 GLU Chi-restraints excluded: chain PH residue 429 LYS Chi-restraints excluded: chain PI residue 104 ASP Chi-restraints excluded: chain PI residue 146 ILE Chi-restraints excluded: chain PI residue 221 GLN Chi-restraints excluded: chain PI residue 261 ARG Chi-restraints excluded: chain PJ residue 147 THR Chi-restraints excluded: chain PJ residue 261 ARG Chi-restraints excluded: chain PJ residue 365 SER Chi-restraints excluded: chain PJ residue 386 GLU Chi-restraints excluded: chain PJ residue 391 ILE Chi-restraints excluded: chain PK residue 69 SER Chi-restraints excluded: chain PK residue 249 GLU Chi-restraints excluded: chain PK residue 250 ASP Chi-restraints excluded: chain PK residue 261 ARG Chi-restraints excluded: chain PK residue 386 GLU Chi-restraints excluded: chain PK residue 407 LEU Chi-restraints excluded: chain PK residue 409 LEU Chi-restraints excluded: chain PK residue 429 LYS Chi-restraints excluded: chain PL residue 69 SER Chi-restraints excluded: chain PL residue 146 ILE Chi-restraints excluded: chain PL residue 221 GLN Chi-restraints excluded: chain PL residue 249 GLU Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PL residue 409 LEU Chi-restraints excluded: chain PL residue 416 GLU Chi-restraints excluded: chain PM residue 100 GLU Chi-restraints excluded: chain PM residue 132 ASP Chi-restraints excluded: chain PN residue 18 THR Chi-restraints excluded: chain PN residue 96 SER Chi-restraints excluded: chain PN residue 132 ASP Chi-restraints excluded: chain PO residue 66 ARG Chi-restraints excluded: chain PP residue 96 SER Chi-restraints excluded: chain PQ residue 96 SER Chi-restraints excluded: chain PR residue 66 ARG Chi-restraints excluded: chain PR residue 138 LEU Chi-restraints excluded: chain PS residue 100 GLU Chi-restraints excluded: chain PS residue 138 LEU Chi-restraints excluded: chain PT residue 66 ARG Chi-restraints excluded: chain PT residue 96 SER Chi-restraints excluded: chain PT residue 100 GLU Chi-restraints excluded: chain PU residue 138 LEU Chi-restraints excluded: chain PV residue 96 SER Chi-restraints excluded: chain PV residue 100 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 571 optimal weight: 0.9990 chunk 435 optimal weight: 0.0270 chunk 300 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 276 optimal weight: 0.0870 chunk 388 optimal weight: 6.9990 chunk 580 optimal weight: 8.9990 chunk 614 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 550 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PX 20 GLN PX 39 ASN PA 257 ASN PA 393 GLN PC 38 ASN PC 185 GLN PC 393 GLN PD 92 HIS PD 101 GLN PD 257 ASN PD 393 GLN PE 181 HIS PE 185 GLN PG 257 ASN PG 393 GLN PH 185 GLN PI 185 GLN PJ 257 ASN PJ 393 GLN PL 181 HIS PL 185 GLN PM 39 ASN PN 117 GLN PO 20 GLN PO 39 ASN PO 133 ASN PQ 117 GLN PR 39 ASN PR 133 ASN PS 39 ASN PT 117 GLN PU 39 ASN PV 39 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 51240 Z= 0.157 Angle : 0.552 9.337 69576 Z= 0.284 Chirality : 0.039 0.132 7536 Planarity : 0.003 0.045 9348 Dihedral : 7.602 83.410 6996 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.71 % Allowed : 18.59 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.10), residues: 6252 helix: 2.06 (0.09), residues: 3168 sheet: 1.79 (0.23), residues: 396 loop : -0.39 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPPD 134 HIS 0.003 0.001 HISPG 175 PHE 0.007 0.001 PHEPJ 334 TYR 0.011 0.001 TYRPB 137 ARG 0.006 0.000 ARGPC 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1846 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1702 time to evaluate : 4.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PX 20 GLN cc_start: 0.8764 (tp40) cc_final: 0.8476 (tp40) REVERT: PX 24 ASP cc_start: 0.8771 (m-30) cc_final: 0.8534 (m-30) REVERT: PA 59 ASP cc_start: 0.9051 (m-30) cc_final: 0.8794 (m-30) REVERT: PA 67 ARG cc_start: 0.9269 (tpp80) cc_final: 0.8706 (tpt90) REVERT: PA 68 ASP cc_start: 0.8195 (p0) cc_final: 0.7842 (p0) REVERT: PA 98 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8581 (mp0) REVERT: PA 164 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: PA 179 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8535 (mtmp) REVERT: PA 261 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8130 (mmm-85) REVERT: PA 379 ASP cc_start: 0.8830 (t0) cc_final: 0.8468 (t0) REVERT: PA 408 ASP cc_start: 0.8861 (t0) cc_final: 0.8465 (t0) REVERT: PA 429 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8490 (ttmm) REVERT: PB 42 MET cc_start: 0.7452 (tpt) cc_final: 0.7158 (tpp) REVERT: PB 59 ASP cc_start: 0.8960 (m-30) cc_final: 0.8739 (m-30) REVERT: PB 98 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8574 (mp0) REVERT: PB 149 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8257 (mm-30) REVERT: PB 206 ASP cc_start: 0.9189 (t0) cc_final: 0.8880 (t0) REVERT: PB 261 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8397 (mmm-85) REVERT: PB 389 ASP cc_start: 0.8726 (m-30) cc_final: 0.8454 (m-30) REVERT: PC 144 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8185 (mt-10) REVERT: PC 149 GLU cc_start: 0.8649 (mp0) cc_final: 0.8395 (mm-30) REVERT: PC 261 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8485 (mmm-85) REVERT: PC 379 ASP cc_start: 0.8822 (t0) cc_final: 0.8512 (t0) REVERT: PD 67 ARG cc_start: 0.9240 (tpp80) cc_final: 0.8723 (tpt90) REVERT: PD 68 ASP cc_start: 0.8284 (p0) cc_final: 0.7975 (p0) REVERT: PD 112 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8515 (mt-10) REVERT: PD 164 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: PD 372 ASP cc_start: 0.8716 (t70) cc_final: 0.8387 (t0) REVERT: PD 379 ASP cc_start: 0.8838 (t0) cc_final: 0.8437 (t0) REVERT: PD 408 ASP cc_start: 0.8875 (t0) cc_final: 0.8567 (t0) REVERT: PE 59 ASP cc_start: 0.8964 (m-30) cc_final: 0.8729 (m-30) REVERT: PE 112 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8272 (mt-10) REVERT: PE 144 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8085 (mt-10) REVERT: PE 261 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8267 (mmm-85) REVERT: PE 364 TYR cc_start: 0.9269 (m-80) cc_final: 0.8894 (m-80) REVERT: PE 386 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: PE 389 ASP cc_start: 0.8731 (m-30) cc_final: 0.8384 (m-30) REVERT: PE 428 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8580 (mt-10) REVERT: PF 67 ARG cc_start: 0.9227 (tpp80) cc_final: 0.8554 (tpt90) REVERT: PF 144 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8542 (mp0) REVERT: PF 430 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8442 (p0) REVERT: PF 431 GLU cc_start: 0.9127 (tt0) cc_final: 0.8923 (tt0) REVERT: PG 59 ASP cc_start: 0.9058 (m-30) cc_final: 0.8801 (m-30) REVERT: PG 68 ASP cc_start: 0.8303 (p0) cc_final: 0.8023 (p0) REVERT: PG 98 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8555 (mp0) REVERT: PG 370 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8847 (mp0) REVERT: PG 379 ASP cc_start: 0.8796 (t0) cc_final: 0.8401 (t0) REVERT: PG 426 ASP cc_start: 0.8932 (m-30) cc_final: 0.8696 (m-30) REVERT: PG 431 GLU cc_start: 0.9072 (tt0) cc_final: 0.8844 (tm-30) REVERT: PH 42 MET cc_start: 0.7462 (tpt) cc_final: 0.6388 (tmm) REVERT: PH 59 ASP cc_start: 0.8984 (m-30) cc_final: 0.8758 (m-30) REVERT: PH 112 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8224 (mt-10) REVERT: PH 144 GLU cc_start: 0.8673 (mt-10) cc_final: 0.7998 (mt-10) REVERT: PH 386 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: PH 389 ASP cc_start: 0.8732 (m-30) cc_final: 0.8483 (m-30) REVERT: PH 428 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8438 (mt-10) REVERT: PI 59 ASP cc_start: 0.8981 (m-30) cc_final: 0.8772 (m-30) REVERT: PI 112 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8489 (mt-10) REVERT: PI 144 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8128 (mt-10) REVERT: PI 149 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8349 (mm-30) REVERT: PI 261 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8345 (mmm-85) REVERT: PI 379 ASP cc_start: 0.8846 (t0) cc_final: 0.8541 (t0) REVERT: PI 389 ASP cc_start: 0.8875 (m-30) cc_final: 0.8569 (m-30) REVERT: PI 426 ASP cc_start: 0.8983 (m-30) cc_final: 0.8676 (m-30) REVERT: PJ 59 ASP cc_start: 0.9051 (m-30) cc_final: 0.8802 (m-30) REVERT: PJ 67 ARG cc_start: 0.9238 (tpp80) cc_final: 0.8760 (tpt90) REVERT: PJ 68 ASP cc_start: 0.8311 (p0) cc_final: 0.7964 (p0) REVERT: PJ 149 GLU cc_start: 0.8691 (mp0) cc_final: 0.8364 (mm-30) REVERT: PJ 370 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8801 (mp0) REVERT: PJ 379 ASP cc_start: 0.8857 (t0) cc_final: 0.8409 (t0) REVERT: PJ 419 ASP cc_start: 0.9083 (m-30) cc_final: 0.8712 (m-30) REVERT: PK 42 MET cc_start: 0.7036 (tpt) cc_final: 0.6784 (tpp) REVERT: PK 59 ASP cc_start: 0.8961 (m-30) cc_final: 0.8736 (m-30) REVERT: PK 144 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8171 (mt-10) REVERT: PK 428 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8548 (mt-10) REVERT: PL 42 MET cc_start: 0.7417 (tpt) cc_final: 0.7158 (tpp) REVERT: PL 59 ASP cc_start: 0.8975 (m-30) cc_final: 0.8749 (m-30) REVERT: PL 144 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8127 (mt-10) REVERT: PL 261 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8472 (mmm-85) REVERT: PL 364 TYR cc_start: 0.9205 (m-80) cc_final: 0.8818 (m-80) REVERT: PL 389 ASP cc_start: 0.8824 (m-30) cc_final: 0.8517 (m-30) REVERT: PL 409 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9139 (mm) REVERT: PM 13 ASP cc_start: 0.9080 (m-30) cc_final: 0.8799 (m-30) REVERT: PO 13 ASP cc_start: 0.8996 (m-30) cc_final: 0.8687 (m-30) REVERT: PO 20 GLN cc_start: 0.8747 (tp40) cc_final: 0.8423 (tp40) REVERT: PO 24 ASP cc_start: 0.8753 (m-30) cc_final: 0.8481 (m-30) REVERT: PP 107 SER cc_start: 0.9163 (m) cc_final: 0.8960 (p) REVERT: PQ 20 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8572 (tp40) REVERT: PR 13 ASP cc_start: 0.9022 (m-30) cc_final: 0.8818 (m-30) REVERT: PR 20 GLN cc_start: 0.8790 (tp40) cc_final: 0.8471 (tp40) REVERT: PR 24 ASP cc_start: 0.8761 (m-30) cc_final: 0.8498 (m-30) REVERT: PR 66 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8537 (mtp180) REVERT: PS 11 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8896 (ttmt) REVERT: PS 13 ASP cc_start: 0.9045 (m-30) cc_final: 0.8756 (m-30) REVERT: PT 66 ARG cc_start: 0.9328 (mpp-170) cc_final: 0.9067 (mpp-170) REVERT: PU 64 MET cc_start: 0.9192 (mtm) cc_final: 0.8979 (mtp) REVERT: PV 8 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8716 (pt0) REVERT: PV 66 ARG cc_start: 0.9365 (mpp-170) cc_final: 0.9042 (mtt180) REVERT: PW 20 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8561 (tp40) outliers start: 144 outliers final: 50 residues processed: 1764 average time/residue: 1.3968 time to fit residues: 3053.6305 Evaluate side-chains 1535 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1471 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PA residue 164 GLU Chi-restraints excluded: chain PA residue 249 GLU Chi-restraints excluded: chain PA residue 261 ARG Chi-restraints excluded: chain PA residue 365 SER Chi-restraints excluded: chain PA residue 376 GLU Chi-restraints excluded: chain PA residue 386 GLU Chi-restraints excluded: chain PA residue 407 LEU Chi-restraints excluded: chain PA residue 423 SER Chi-restraints excluded: chain PA residue 429 LYS Chi-restraints excluded: chain PB residue 261 ARG Chi-restraints excluded: chain PC residue 34 THR Chi-restraints excluded: chain PC residue 146 ILE Chi-restraints excluded: chain PC residue 249 GLU Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PC residue 391 ILE Chi-restraints excluded: chain PD residue 34 THR Chi-restraints excluded: chain PD residue 164 GLU Chi-restraints excluded: chain PD residue 249 GLU Chi-restraints excluded: chain PD residue 365 SER Chi-restraints excluded: chain PD residue 376 GLU Chi-restraints excluded: chain PD residue 386 GLU Chi-restraints excluded: chain PD residue 423 SER Chi-restraints excluded: chain PE residue 36 GLN Chi-restraints excluded: chain PE residue 249 GLU Chi-restraints excluded: chain PE residue 261 ARG Chi-restraints excluded: chain PE residue 386 GLU Chi-restraints excluded: chain PE residue 409 LEU Chi-restraints excluded: chain PE residue 429 LYS Chi-restraints excluded: chain PF residue 104 ASP Chi-restraints excluded: chain PF residue 146 ILE Chi-restraints excluded: chain PF residue 249 GLU Chi-restraints excluded: chain PF residue 423 SER Chi-restraints excluded: chain PF residue 430 ASP Chi-restraints excluded: chain PG residue 34 THR Chi-restraints excluded: chain PG residue 365 SER Chi-restraints excluded: chain PG residue 376 GLU Chi-restraints excluded: chain PH residue 36 GLN Chi-restraints excluded: chain PH residue 249 GLU Chi-restraints excluded: chain PH residue 386 GLU Chi-restraints excluded: chain PH residue 409 LEU Chi-restraints excluded: chain PI residue 146 ILE Chi-restraints excluded: chain PI residue 249 GLU Chi-restraints excluded: chain PI residue 261 ARG Chi-restraints excluded: chain PI residue 326 SER Chi-restraints excluded: chain PI residue 429 LYS Chi-restraints excluded: chain PJ residue 365 SER Chi-restraints excluded: chain PJ residue 386 GLU Chi-restraints excluded: chain PK residue 36 GLN Chi-restraints excluded: chain PK residue 249 GLU Chi-restraints excluded: chain PK residue 386 GLU Chi-restraints excluded: chain PK residue 409 LEU Chi-restraints excluded: chain PL residue 146 ILE Chi-restraints excluded: chain PL residue 249 GLU Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PL residue 409 LEU Chi-restraints excluded: chain PL residue 416 GLU Chi-restraints excluded: chain PM residue 96 SER Chi-restraints excluded: chain PN residue 18 THR Chi-restraints excluded: chain PN residue 32 LEU Chi-restraints excluded: chain PQ residue 32 LEU Chi-restraints excluded: chain PR residue 66 ARG Chi-restraints excluded: chain PS residue 96 SER Chi-restraints excluded: chain PS residue 113 GLU Chi-restraints excluded: chain PT residue 32 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 511 optimal weight: 9.9990 chunk 348 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 457 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 524 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 313 optimal weight: 9.9990 chunk 551 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PX 28 GLN PX 39 ASN PX 117 GLN PA 257 ASN PA 393 GLN PC 38 ASN PC 92 HIS PC 185 GLN PD 92 HIS PD 257 ASN PF 92 HIS PG 257 ASN PG 393 GLN PH 143 GLN PH 318 ASN PI 92 HIS ** PJ 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PJ 226 ASN PJ 393 GLN PK 143 GLN PL 92 HIS PL 200 ASN PM 39 ASN PO 28 GLN PO 39 ASN PO 117 GLN PO 133 ASN PP 39 ASN PR 28 GLN PR 39 ASN PR 117 GLN PR 133 ASN PS 39 ASN PU 28 GLN PU 117 GLN PU 133 ASN PV 39 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 51240 Z= 0.338 Angle : 0.611 8.948 69576 Z= 0.312 Chirality : 0.041 0.129 7536 Planarity : 0.004 0.045 9348 Dihedral : 7.497 85.498 6996 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.63 % Allowed : 19.00 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.10), residues: 6252 helix: 2.04 (0.09), residues: 3168 sheet: 1.63 (0.22), residues: 396 loop : -0.43 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPPE 134 HIS 0.004 0.001 HISPT 84 PHE 0.022 0.002 PHEPD 334 TYR 0.021 0.002 TYRPM 76 ARG 0.006 0.001 ARGPG 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1717 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 1524 time to evaluate : 4.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PX 20 GLN cc_start: 0.8854 (tp40) cc_final: 0.8499 (tp40) REVERT: PX 24 ASP cc_start: 0.8826 (m-30) cc_final: 0.8535 (m-30) REVERT: PX 66 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8340 (mtp180) REVERT: PA 59 ASP cc_start: 0.9084 (m-30) cc_final: 0.8816 (m-30) REVERT: PA 98 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8564 (mp0) REVERT: PA 164 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: PA 261 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8077 (mmm-85) REVERT: PA 370 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8897 (mp0) REVERT: PA 379 ASP cc_start: 0.8848 (t0) cc_final: 0.8478 (t0) REVERT: PA 408 ASP cc_start: 0.8842 (t0) cc_final: 0.8481 (t0) REVERT: PA 426 ASP cc_start: 0.8879 (m-30) cc_final: 0.8492 (m-30) REVERT: PA 429 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8677 (ttmm) REVERT: PB 42 MET cc_start: 0.7297 (tpt) cc_final: 0.7007 (tpp) REVERT: PB 149 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8342 (mm-30) REVERT: PB 261 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8398 (mmm-85) REVERT: PB 389 ASP cc_start: 0.8789 (m-30) cc_final: 0.8493 (m-30) REVERT: PC 112 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8602 (mt-10) REVERT: PC 144 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8156 (mt-10) REVERT: PC 149 GLU cc_start: 0.8738 (mp0) cc_final: 0.8361 (mm-30) REVERT: PC 210 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9183 (mp) REVERT: PC 261 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8578 (mmm-85) REVERT: PC 426 ASP cc_start: 0.8907 (m-30) cc_final: 0.8697 (m-30) REVERT: PD 98 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8895 (mp0) REVERT: PD 112 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8549 (mt-10) REVERT: PD 144 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8034 (mt-10) REVERT: PD 164 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: PD 261 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8112 (mmm-85) REVERT: PD 372 ASP cc_start: 0.8716 (t70) cc_final: 0.8408 (t0) REVERT: PD 379 ASP cc_start: 0.8852 (t0) cc_final: 0.8581 (t0) REVERT: PD 408 ASP cc_start: 0.8798 (t0) cc_final: 0.8545 (t0) REVERT: PD 419 ASP cc_start: 0.9056 (m-30) cc_final: 0.8801 (m-30) REVERT: PD 426 ASP cc_start: 0.8911 (m-30) cc_final: 0.8480 (m-30) REVERT: PD 429 LYS cc_start: 0.8977 (ptmm) cc_final: 0.8485 (ttmm) REVERT: PE 98 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8646 (mp0) REVERT: PE 112 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8318 (mt-10) REVERT: PE 144 GLU cc_start: 0.8662 (mt-10) cc_final: 0.7953 (mt-10) REVERT: PE 149 GLU cc_start: 0.8700 (mp0) cc_final: 0.8432 (mm-30) REVERT: PE 227 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8753 (mm-30) REVERT: PE 261 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8244 (mmm-85) REVERT: PE 383 ASP cc_start: 0.8767 (t0) cc_final: 0.8387 (t0) REVERT: PE 386 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: PE 389 ASP cc_start: 0.8661 (m-30) cc_final: 0.8395 (m-30) REVERT: PE 428 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8613 (mt-10) REVERT: PF 98 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8488 (mp0) REVERT: PF 112 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8588 (mt-10) REVERT: PF 144 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8497 (mp0) REVERT: PF 149 GLU cc_start: 0.8613 (mp0) cc_final: 0.8347 (mm-30) REVERT: PF 261 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8439 (mmm-85) REVERT: PF 370 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8658 (mp0) REVERT: PF 383 ASP cc_start: 0.8908 (t0) cc_final: 0.8687 (t0) REVERT: PG 67 ARG cc_start: 0.9305 (tpp80) cc_final: 0.8620 (tpt90) REVERT: PG 98 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8592 (mp0) REVERT: PG 261 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8178 (mmm-85) REVERT: PG 370 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8856 (mp0) REVERT: PG 379 ASP cc_start: 0.8837 (t0) cc_final: 0.8603 (t0) REVERT: PG 426 ASP cc_start: 0.8980 (m-30) cc_final: 0.8723 (m-30) REVERT: PG 431 GLU cc_start: 0.9035 (tt0) cc_final: 0.8794 (tm-30) REVERT: PH 42 MET cc_start: 0.7322 (tpt) cc_final: 0.6362 (tmm) REVERT: PH 98 GLU cc_start: 0.9019 (mp0) cc_final: 0.8474 (mp0) REVERT: PH 112 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8276 (mt-10) REVERT: PH 144 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8204 (mt-10) REVERT: PH 261 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8326 (mmm-85) REVERT: PH 386 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: PH 389 ASP cc_start: 0.8747 (m-30) cc_final: 0.8451 (m-30) REVERT: PH 428 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8520 (mt-10) REVERT: PI 42 MET cc_start: 0.7483 (tpt) cc_final: 0.7000 (tpp) REVERT: PI 59 ASP cc_start: 0.8985 (m-30) cc_final: 0.8759 (m-30) REVERT: PI 112 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8447 (mt-10) REVERT: PI 144 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8065 (mt-10) REVERT: PI 149 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8347 (mm-30) REVERT: PI 261 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8449 (mmm-85) REVERT: PI 364 TYR cc_start: 0.9166 (m-80) cc_final: 0.8747 (m-80) REVERT: PI 389 ASP cc_start: 0.8845 (m-30) cc_final: 0.8555 (m-30) REVERT: PI 426 ASP cc_start: 0.9048 (m-30) cc_final: 0.8782 (m-30) REVERT: PI 429 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8651 (ttmm) REVERT: PJ 42 MET cc_start: 0.7494 (tpt) cc_final: 0.7174 (tpp) REVERT: PJ 59 ASP cc_start: 0.9083 (m-30) cc_final: 0.8837 (m-30) REVERT: PJ 98 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8846 (mp0) REVERT: PJ 112 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8591 (mt-10) REVERT: PJ 144 GLU cc_start: 0.8698 (mt-10) cc_final: 0.7912 (mt-10) REVERT: PJ 149 GLU cc_start: 0.8718 (mp0) cc_final: 0.8404 (mm-30) REVERT: PJ 164 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7666 (mt-10) REVERT: PJ 261 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8209 (mmm-85) REVERT: PJ 364 TYR cc_start: 0.9290 (m-80) cc_final: 0.8963 (m-80) REVERT: PJ 379 ASP cc_start: 0.8889 (t0) cc_final: 0.8611 (t0) REVERT: PJ 419 ASP cc_start: 0.9089 (m-30) cc_final: 0.8830 (m-30) REVERT: PJ 426 ASP cc_start: 0.8919 (m-30) cc_final: 0.8475 (m-30) REVERT: PK 42 MET cc_start: 0.6957 (tpt) cc_final: 0.6728 (tpp) REVERT: PK 59 ASP cc_start: 0.8981 (m-30) cc_final: 0.8752 (m-30) REVERT: PK 112 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8423 (mt-10) REVERT: PK 144 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8151 (mt-10) REVERT: PK 261 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7987 (mmm-85) REVERT: PK 376 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8253 (tm-30) REVERT: PK 428 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8651 (mt-10) REVERT: PL 59 ASP cc_start: 0.8983 (m-30) cc_final: 0.8771 (m-30) REVERT: PL 112 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8595 (mt-10) REVERT: PL 144 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8125 (mt-10) REVERT: PL 261 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8583 (mmm-85) REVERT: PL 389 ASP cc_start: 0.8819 (m-30) cc_final: 0.8532 (m-30) REVERT: PL 409 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9140 (mm) REVERT: PM 13 ASP cc_start: 0.9129 (m-30) cc_final: 0.8838 (m-30) REVERT: PM 132 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8784 (t0) REVERT: PN 66 ARG cc_start: 0.9437 (mpp-170) cc_final: 0.8990 (mtt180) REVERT: PN 100 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7372 (pm20) REVERT: PN 132 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8750 (t0) REVERT: PO 13 ASP cc_start: 0.9066 (m-30) cc_final: 0.8727 (m-30) REVERT: PO 20 GLN cc_start: 0.8834 (tp40) cc_final: 0.8485 (tp40) REVERT: PO 24 ASP cc_start: 0.8814 (m-30) cc_final: 0.8529 (m-30) REVERT: PP 66 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8642 (mtp180) REVERT: PQ 20 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8643 (tp40) REVERT: PQ 66 ARG cc_start: 0.9413 (mpp-170) cc_final: 0.8979 (mtt180) REVERT: PR 13 ASP cc_start: 0.9114 (m-30) cc_final: 0.8884 (m-30) REVERT: PR 20 GLN cc_start: 0.8870 (tp40) cc_final: 0.8516 (tp40) REVERT: PR 24 ASP cc_start: 0.8818 (m-30) cc_final: 0.8559 (m-30) REVERT: PR 66 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8146 (mtp180) REVERT: PS 13 ASP cc_start: 0.9101 (m-30) cc_final: 0.8815 (m-30) REVERT: PT 66 ARG cc_start: 0.9358 (OUTLIER) cc_final: 0.8906 (mtt180) REVERT: PU 13 ASP cc_start: 0.9095 (m-30) cc_final: 0.8848 (m-30) REVERT: PU 20 GLN cc_start: 0.8813 (tp40) cc_final: 0.8420 (tp40) REVERT: PU 64 MET cc_start: 0.9205 (mtm) cc_final: 0.8946 (mtp) REVERT: PV 66 ARG cc_start: 0.9394 (mpp-170) cc_final: 0.9093 (mtt180) REVERT: PW 20 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8638 (tp40) REVERT: PW 100 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7382 (pm20) outliers start: 193 outliers final: 92 residues processed: 1630 average time/residue: 1.3603 time to fit residues: 2740.4325 Evaluate side-chains 1511 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1393 time to evaluate : 4.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PX residue 66 ARG Chi-restraints excluded: chain PA residue 69 SER Chi-restraints excluded: chain PA residue 164 GLU Chi-restraints excluded: chain PA residue 249 GLU Chi-restraints excluded: chain PA residue 261 ARG Chi-restraints excluded: chain PA residue 365 SER Chi-restraints excluded: chain PA residue 376 GLU Chi-restraints excluded: chain PA residue 386 GLU Chi-restraints excluded: chain PA residue 391 ILE Chi-restraints excluded: chain PA residue 429 LYS Chi-restraints excluded: chain PB residue 69 SER Chi-restraints excluded: chain PB residue 76 LEU Chi-restraints excluded: chain PB residue 108 MET Chi-restraints excluded: chain PB residue 250 ASP Chi-restraints excluded: chain PB residue 261 ARG Chi-restraints excluded: chain PB residue 271 THR Chi-restraints excluded: chain PB residue 303 MET Chi-restraints excluded: chain PB residue 386 GLU Chi-restraints excluded: chain PC residue 69 SER Chi-restraints excluded: chain PC residue 104 ASP Chi-restraints excluded: chain PC residue 141 GLU Chi-restraints excluded: chain PC residue 146 ILE Chi-restraints excluded: chain PC residue 210 ILE Chi-restraints excluded: chain PC residue 249 GLU Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PC residue 391 ILE Chi-restraints excluded: chain PC residue 401 GLU Chi-restraints excluded: chain PD residue 34 THR Chi-restraints excluded: chain PD residue 69 SER Chi-restraints excluded: chain PD residue 104 ASP Chi-restraints excluded: chain PD residue 164 GLU Chi-restraints excluded: chain PD residue 236 LEU Chi-restraints excluded: chain PD residue 249 GLU Chi-restraints excluded: chain PD residue 261 ARG Chi-restraints excluded: chain PD residue 365 SER Chi-restraints excluded: chain PD residue 376 GLU Chi-restraints excluded: chain PD residue 386 GLU Chi-restraints excluded: chain PE residue 69 SER Chi-restraints excluded: chain PE residue 249 GLU Chi-restraints excluded: chain PE residue 250 ASP Chi-restraints excluded: chain PE residue 261 ARG Chi-restraints excluded: chain PE residue 271 THR Chi-restraints excluded: chain PE residue 386 GLU Chi-restraints excluded: chain PE residue 401 GLU Chi-restraints excluded: chain PE residue 409 LEU Chi-restraints excluded: chain PE residue 429 LYS Chi-restraints excluded: chain PF residue 56 THR Chi-restraints excluded: chain PF residue 69 SER Chi-restraints excluded: chain PF residue 104 ASP Chi-restraints excluded: chain PF residue 141 GLU Chi-restraints excluded: chain PF residue 146 ILE Chi-restraints excluded: chain PF residue 249 GLU Chi-restraints excluded: chain PF residue 261 ARG Chi-restraints excluded: chain PG residue 34 THR Chi-restraints excluded: chain PG residue 69 SER Chi-restraints excluded: chain PG residue 236 LEU Chi-restraints excluded: chain PG residue 249 GLU Chi-restraints excluded: chain PG residue 261 ARG Chi-restraints excluded: chain PG residue 346 ARG Chi-restraints excluded: chain PG residue 365 SER Chi-restraints excluded: chain PG residue 376 GLU Chi-restraints excluded: chain PG residue 386 GLU Chi-restraints excluded: chain PG residue 391 ILE Chi-restraints excluded: chain PH residue 69 SER Chi-restraints excluded: chain PH residue 141 GLU Chi-restraints excluded: chain PH residue 249 GLU Chi-restraints excluded: chain PH residue 261 ARG Chi-restraints excluded: chain PH residue 271 THR Chi-restraints excluded: chain PH residue 386 GLU Chi-restraints excluded: chain PH residue 409 LEU Chi-restraints excluded: chain PH residue 416 GLU Chi-restraints excluded: chain PI residue 69 SER Chi-restraints excluded: chain PI residue 104 ASP Chi-restraints excluded: chain PI residue 141 GLU Chi-restraints excluded: chain PI residue 146 ILE Chi-restraints excluded: chain PI residue 249 GLU Chi-restraints excluded: chain PI residue 261 ARG Chi-restraints excluded: chain PI residue 386 GLU Chi-restraints excluded: chain PI residue 429 LYS Chi-restraints excluded: chain PJ residue 236 LEU Chi-restraints excluded: chain PJ residue 249 GLU Chi-restraints excluded: chain PJ residue 261 ARG Chi-restraints excluded: chain PJ residue 365 SER Chi-restraints excluded: chain PJ residue 386 GLU Chi-restraints excluded: chain PJ residue 391 ILE Chi-restraints excluded: chain PJ residue 423 SER Chi-restraints excluded: chain PK residue 69 SER Chi-restraints excluded: chain PK residue 141 GLU Chi-restraints excluded: chain PK residue 249 GLU Chi-restraints excluded: chain PK residue 250 ASP Chi-restraints excluded: chain PK residue 261 ARG Chi-restraints excluded: chain PK residue 271 THR Chi-restraints excluded: chain PK residue 386 GLU Chi-restraints excluded: chain PK residue 401 GLU Chi-restraints excluded: chain PK residue 409 LEU Chi-restraints excluded: chain PL residue 60 LEU Chi-restraints excluded: chain PL residue 69 SER Chi-restraints excluded: chain PL residue 146 ILE Chi-restraints excluded: chain PL residue 249 GLU Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PL residue 409 LEU Chi-restraints excluded: chain PM residue 132 ASP Chi-restraints excluded: chain PN residue 18 THR Chi-restraints excluded: chain PN residue 96 SER Chi-restraints excluded: chain PN residue 132 ASP Chi-restraints excluded: chain PO residue 138 LEU Chi-restraints excluded: chain PP residue 66 ARG Chi-restraints excluded: chain PP residue 96 SER Chi-restraints excluded: chain PQ residue 96 SER Chi-restraints excluded: chain PR residue 66 ARG Chi-restraints excluded: chain PR residue 138 LEU Chi-restraints excluded: chain PS residue 113 GLU Chi-restraints excluded: chain PT residue 66 ARG Chi-restraints excluded: chain PT residue 90 GLU Chi-restraints excluded: chain PT residue 96 SER Chi-restraints excluded: chain PU residue 138 LEU Chi-restraints excluded: chain PV residue 96 SER Chi-restraints excluded: chain PV residue 113 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 206 optimal weight: 3.9990 chunk 553 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 360 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 615 optimal weight: 4.9990 chunk 510 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PX 39 ASN PX 117 GLN PA 257 ASN PC 92 HIS PD 92 HIS PD 257 ASN PF 92 HIS PG 257 ASN PI 92 HIS PI 232 GLN PJ 36 GLN ** PJ 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PJ 393 GLN PL 92 HIS PM 39 ASN PO 28 GLN PO 39 ASN PO 117 GLN PP 39 ASN PQ 117 GLN PR 39 ASN PS 39 ASN PT 117 GLN PV 39 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 51240 Z= 0.297 Angle : 0.600 8.840 69576 Z= 0.306 Chirality : 0.041 0.133 7536 Planarity : 0.004 0.045 9348 Dihedral : 7.367 85.193 6996 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.78 % Allowed : 19.34 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.10), residues: 6252 helix: 2.03 (0.09), residues: 3168 sheet: 1.52 (0.22), residues: 396 loop : -0.42 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPPJ 134 HIS 0.004 0.001 HISPN 84 PHE 0.015 0.002 PHEPF 334 TYR 0.015 0.001 TYRPV 76 ARG 0.006 0.000 ARGPG 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1699 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 1498 time to evaluate : 4.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PA 59 ASP cc_start: 0.9082 (m-30) cc_final: 0.8782 (m-30) REVERT: PA 98 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8554 (mp0) REVERT: PA 164 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: PA 261 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8109 (mmm-85) REVERT: PA 315 GLU cc_start: 0.8932 (mp0) cc_final: 0.8580 (mp0) REVERT: PA 370 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8893 (mp0) REVERT: PA 408 ASP cc_start: 0.8825 (t0) cc_final: 0.8498 (t0) REVERT: PA 426 ASP cc_start: 0.8876 (m-30) cc_final: 0.8407 (m-30) REVERT: PB 42 MET cc_start: 0.7247 (tpt) cc_final: 0.6963 (tpp) REVERT: PB 149 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8359 (mm-30) REVERT: PB 261 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8401 (mmm-85) REVERT: PB 389 ASP cc_start: 0.8772 (m-30) cc_final: 0.8456 (m-30) REVERT: PC 67 ARG cc_start: 0.9265 (tpp80) cc_final: 0.8618 (tpt90) REVERT: PC 149 GLU cc_start: 0.8787 (mp0) cc_final: 0.8465 (mm-30) REVERT: PC 170 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8703 (mmmm) REVERT: PC 210 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9177 (mp) REVERT: PC 261 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8582 (mmm-85) REVERT: PC 370 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8695 (mp0) REVERT: PD 98 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8872 (mp0) REVERT: PD 112 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8581 (mt-10) REVERT: PD 164 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: PD 261 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8082 (mmm-85) REVERT: PD 370 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8812 (mp0) REVERT: PD 379 ASP cc_start: 0.8837 (t0) cc_final: 0.8624 (t0) REVERT: PD 408 ASP cc_start: 0.8762 (t0) cc_final: 0.8489 (t0) REVERT: PD 426 ASP cc_start: 0.8892 (m-30) cc_final: 0.8412 (m-30) REVERT: PE 98 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8597 (mp0) REVERT: PE 100 LYS cc_start: 0.9283 (mmmt) cc_final: 0.9060 (tmtt) REVERT: PE 112 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8308 (mt-10) REVERT: PE 144 GLU cc_start: 0.8658 (mt-10) cc_final: 0.7954 (mt-10) REVERT: PE 149 GLU cc_start: 0.8748 (mp0) cc_final: 0.8468 (mm-30) REVERT: PE 261 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8300 (mmm-85) REVERT: PE 376 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8228 (tm-30) REVERT: PE 383 ASP cc_start: 0.8768 (t0) cc_final: 0.8280 (t0) REVERT: PE 386 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: PE 389 ASP cc_start: 0.8648 (m-30) cc_final: 0.8367 (m-30) REVERT: PE 428 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8573 (mt-10) REVERT: PF 67 ARG cc_start: 0.9251 (tpp80) cc_final: 0.8621 (tpt90) REVERT: PF 98 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8508 (mp0) REVERT: PF 112 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8506 (mt-10) REVERT: PF 144 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8541 (mp0) REVERT: PF 149 GLU cc_start: 0.8622 (mp0) cc_final: 0.8380 (mm-30) REVERT: PF 261 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8384 (mmm-85) REVERT: PF 370 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8649 (mp0) REVERT: PF 383 ASP cc_start: 0.8908 (t0) cc_final: 0.8641 (t0) REVERT: PG 42 MET cc_start: 0.7788 (tpp) cc_final: 0.6637 (tmm) REVERT: PG 98 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8589 (mp0) REVERT: PG 370 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8851 (mp0) REVERT: PG 379 ASP cc_start: 0.8832 (t0) cc_final: 0.8593 (t0) REVERT: PH 42 MET cc_start: 0.7260 (tpt) cc_final: 0.6225 (tmm) REVERT: PH 98 GLU cc_start: 0.8990 (mp0) cc_final: 0.8507 (mp0) REVERT: PH 112 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8278 (mt-10) REVERT: PH 144 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8195 (mt-10) REVERT: PH 261 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8322 (mmm-85) REVERT: PH 386 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: PH 389 ASP cc_start: 0.8737 (m-30) cc_final: 0.8439 (m-30) REVERT: PH 428 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8581 (mt-10) REVERT: PI 42 MET cc_start: 0.7405 (tpt) cc_final: 0.6955 (tpp) REVERT: PI 59 ASP cc_start: 0.8971 (m-30) cc_final: 0.8771 (m-30) REVERT: PI 67 ARG cc_start: 0.9268 (tpp80) cc_final: 0.8636 (tpt90) REVERT: PI 149 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8304 (mm-30) REVERT: PI 261 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8478 (mmm-85) REVERT: PI 331 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8403 (mt-10) REVERT: PI 370 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8709 (mp0) REVERT: PI 379 ASP cc_start: 0.8850 (t0) cc_final: 0.8593 (t70) REVERT: PI 383 ASP cc_start: 0.8925 (t0) cc_final: 0.8691 (t0) REVERT: PI 389 ASP cc_start: 0.8839 (m-30) cc_final: 0.8556 (m-30) REVERT: PI 426 ASP cc_start: 0.9043 (m-30) cc_final: 0.8769 (m-30) REVERT: PI 429 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8810 (ttmm) REVERT: PJ 42 MET cc_start: 0.7383 (tpt) cc_final: 0.7130 (tpp) REVERT: PJ 98 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8838 (mp0) REVERT: PJ 149 GLU cc_start: 0.8732 (mp0) cc_final: 0.8362 (mm-30) REVERT: PJ 261 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8215 (mmm-85) REVERT: PJ 379 ASP cc_start: 0.8891 (t0) cc_final: 0.8609 (t0) REVERT: PJ 426 ASP cc_start: 0.8862 (m-30) cc_final: 0.8426 (m-30) REVERT: PK 42 MET cc_start: 0.6914 (tpt) cc_final: 0.6713 (tpp) REVERT: PK 59 ASP cc_start: 0.8981 (m-30) cc_final: 0.8757 (m-30) REVERT: PK 67 ARG cc_start: 0.9243 (tpp80) cc_final: 0.9026 (tpp80) REVERT: PK 149 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8229 (mm-30) REVERT: PK 261 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8258 (mmm-85) REVERT: PK 389 ASP cc_start: 0.8622 (m-30) cc_final: 0.8371 (m-30) REVERT: PL 56 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8684 (t) REVERT: PL 59 ASP cc_start: 0.8976 (m-30) cc_final: 0.8725 (m-30) REVERT: PL 67 ARG cc_start: 0.9261 (tpp80) cc_final: 0.8626 (tpt90) REVERT: PL 112 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8521 (mt-10) REVERT: PL 144 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8175 (mt-10) REVERT: PL 261 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8576 (mmm-85) REVERT: PL 315 GLU cc_start: 0.8928 (mp0) cc_final: 0.8675 (mp0) REVERT: PL 383 ASP cc_start: 0.8777 (t0) cc_final: 0.8570 (t0) REVERT: PL 389 ASP cc_start: 0.8794 (m-30) cc_final: 0.8530 (m-30) REVERT: PL 409 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9151 (mm) REVERT: PL 426 ASP cc_start: 0.8940 (m-30) cc_final: 0.8731 (m-30) REVERT: PM 13 ASP cc_start: 0.9129 (m-30) cc_final: 0.8835 (m-30) REVERT: PO 13 ASP cc_start: 0.9058 (m-30) cc_final: 0.8728 (m-30) REVERT: PO 20 GLN cc_start: 0.8862 (tp40) cc_final: 0.8534 (tp40) REVERT: PO 24 ASP cc_start: 0.8808 (m-30) cc_final: 0.8563 (m-30) REVERT: PP 66 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.8671 (mtp180) REVERT: PQ 66 ARG cc_start: 0.9419 (mpp-170) cc_final: 0.8983 (mtt180) REVERT: PQ 100 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7240 (pm20) REVERT: PR 13 ASP cc_start: 0.9106 (m-30) cc_final: 0.8871 (m-30) REVERT: PR 20 GLN cc_start: 0.8904 (tp40) cc_final: 0.8556 (tp40) REVERT: PR 24 ASP cc_start: 0.8799 (m-30) cc_final: 0.8568 (m-30) REVERT: PR 66 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8274 (mtp180) REVERT: PS 13 ASP cc_start: 0.9103 (m-30) cc_final: 0.8833 (m-30) REVERT: PS 66 ARG cc_start: 0.9306 (mtt90) cc_final: 0.9009 (mtt180) REVERT: PT 66 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.8899 (mtt180) REVERT: PU 20 GLN cc_start: 0.8812 (tp40) cc_final: 0.8431 (tp40) REVERT: PU 64 MET cc_start: 0.9211 (mtm) cc_final: 0.8953 (mtp) REVERT: PV 66 ARG cc_start: 0.9385 (mpp-170) cc_final: 0.9070 (mtt180) outliers start: 201 outliers final: 95 residues processed: 1603 average time/residue: 1.3352 time to fit residues: 2651.7770 Evaluate side-chains 1537 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1420 time to evaluate : 4.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PA residue 69 SER Chi-restraints excluded: chain PA residue 164 GLU Chi-restraints excluded: chain PA residue 215 ARG Chi-restraints excluded: chain PA residue 249 GLU Chi-restraints excluded: chain PA residue 261 ARG Chi-restraints excluded: chain PA residue 365 SER Chi-restraints excluded: chain PA residue 376 GLU Chi-restraints excluded: chain PA residue 386 GLU Chi-restraints excluded: chain PA residue 391 ILE Chi-restraints excluded: chain PA residue 423 SER Chi-restraints excluded: chain PB residue 69 SER Chi-restraints excluded: chain PB residue 76 LEU Chi-restraints excluded: chain PB residue 261 ARG Chi-restraints excluded: chain PB residue 271 THR Chi-restraints excluded: chain PB residue 303 MET Chi-restraints excluded: chain PB residue 386 GLU Chi-restraints excluded: chain PB residue 429 LYS Chi-restraints excluded: chain PC residue 56 THR Chi-restraints excluded: chain PC residue 69 SER Chi-restraints excluded: chain PC residue 104 ASP Chi-restraints excluded: chain PC residue 146 ILE Chi-restraints excluded: chain PC residue 210 ILE Chi-restraints excluded: chain PC residue 249 GLU Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PC residue 391 ILE Chi-restraints excluded: chain PC residue 401 GLU Chi-restraints excluded: chain PD residue 34 THR Chi-restraints excluded: chain PD residue 69 SER Chi-restraints excluded: chain PD residue 164 GLU Chi-restraints excluded: chain PD residue 249 GLU Chi-restraints excluded: chain PD residue 261 ARG Chi-restraints excluded: chain PD residue 365 SER Chi-restraints excluded: chain PD residue 376 GLU Chi-restraints excluded: chain PD residue 386 GLU Chi-restraints excluded: chain PD residue 391 ILE Chi-restraints excluded: chain PD residue 423 SER Chi-restraints excluded: chain PE residue 34 THR Chi-restraints excluded: chain PE residue 69 SER Chi-restraints excluded: chain PE residue 249 GLU Chi-restraints excluded: chain PE residue 250 ASP Chi-restraints excluded: chain PE residue 261 ARG Chi-restraints excluded: chain PE residue 271 THR Chi-restraints excluded: chain PE residue 386 GLU Chi-restraints excluded: chain PE residue 401 GLU Chi-restraints excluded: chain PE residue 409 LEU Chi-restraints excluded: chain PE residue 429 LYS Chi-restraints excluded: chain PF residue 56 THR Chi-restraints excluded: chain PF residue 60 LEU Chi-restraints excluded: chain PF residue 69 SER Chi-restraints excluded: chain PF residue 104 ASP Chi-restraints excluded: chain PF residue 146 ILE Chi-restraints excluded: chain PF residue 249 GLU Chi-restraints excluded: chain PF residue 261 ARG Chi-restraints excluded: chain PF residue 401 GLU Chi-restraints excluded: chain PG residue 34 THR Chi-restraints excluded: chain PG residue 236 LEU Chi-restraints excluded: chain PG residue 249 GLU Chi-restraints excluded: chain PG residue 365 SER Chi-restraints excluded: chain PG residue 376 GLU Chi-restraints excluded: chain PG residue 386 GLU Chi-restraints excluded: chain PG residue 391 ILE Chi-restraints excluded: chain PH residue 141 GLU Chi-restraints excluded: chain PH residue 146 ILE Chi-restraints excluded: chain PH residue 249 GLU Chi-restraints excluded: chain PH residue 250 ASP Chi-restraints excluded: chain PH residue 261 ARG Chi-restraints excluded: chain PH residue 271 THR Chi-restraints excluded: chain PH residue 386 GLU Chi-restraints excluded: chain PH residue 401 GLU Chi-restraints excluded: chain PH residue 416 GLU Chi-restraints excluded: chain PI residue 60 LEU Chi-restraints excluded: chain PI residue 69 SER Chi-restraints excluded: chain PI residue 104 ASP Chi-restraints excluded: chain PI residue 146 ILE Chi-restraints excluded: chain PI residue 249 GLU Chi-restraints excluded: chain PI residue 261 ARG Chi-restraints excluded: chain PI residue 386 GLU Chi-restraints excluded: chain PI residue 409 LEU Chi-restraints excluded: chain PI residue 429 LYS Chi-restraints excluded: chain PJ residue 56 THR Chi-restraints excluded: chain PJ residue 146 ILE Chi-restraints excluded: chain PJ residue 236 LEU Chi-restraints excluded: chain PJ residue 249 GLU Chi-restraints excluded: chain PJ residue 261 ARG Chi-restraints excluded: chain PJ residue 365 SER Chi-restraints excluded: chain PJ residue 386 GLU Chi-restraints excluded: chain PJ residue 391 ILE Chi-restraints excluded: chain PJ residue 423 SER Chi-restraints excluded: chain PK residue 250 ASP Chi-restraints excluded: chain PK residue 261 ARG Chi-restraints excluded: chain PK residue 271 THR Chi-restraints excluded: chain PK residue 333 ARG Chi-restraints excluded: chain PK residue 386 GLU Chi-restraints excluded: chain PK residue 401 GLU Chi-restraints excluded: chain PK residue 409 LEU Chi-restraints excluded: chain PL residue 56 THR Chi-restraints excluded: chain PL residue 60 LEU Chi-restraints excluded: chain PL residue 69 SER Chi-restraints excluded: chain PL residue 146 ILE Chi-restraints excluded: chain PL residue 249 GLU Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PL residue 409 LEU Chi-restraints excluded: chain PL residue 429 LYS Chi-restraints excluded: chain PM residue 139 ARG Chi-restraints excluded: chain PN residue 18 THR Chi-restraints excluded: chain PN residue 96 SER Chi-restraints excluded: chain PP residue 66 ARG Chi-restraints excluded: chain PP residue 96 SER Chi-restraints excluded: chain PQ residue 96 SER Chi-restraints excluded: chain PR residue 66 ARG Chi-restraints excluded: chain PR residue 138 LEU Chi-restraints excluded: chain PS residue 113 GLU Chi-restraints excluded: chain PT residue 66 ARG Chi-restraints excluded: chain PT residue 96 SER Chi-restraints excluded: chain PU residue 138 LEU Chi-restraints excluded: chain PV residue 96 SER Chi-restraints excluded: chain PV residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 593 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 350 optimal weight: 7.9990 chunk 449 optimal weight: 6.9990 chunk 348 optimal weight: 0.9990 chunk 518 optimal weight: 6.9990 chunk 343 optimal weight: 10.0000 chunk 613 optimal weight: 8.9990 chunk 383 optimal weight: 0.6980 chunk 373 optimal weight: 0.5980 chunk 283 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PX 28 GLN PX 39 ASN PX 117 GLN PA 257 ASN PC 92 HIS PD 257 ASN PF 92 HIS PG 225 GLN PG 257 ASN PI 92 HIS PJ 36 GLN PL 92 HIS PM 39 ASN PO 39 ASN PP 39 ASN PR 39 ASN PR 117 GLN PS 39 ASN PU 117 GLN PV 39 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 51240 Z= 0.171 Angle : 0.568 9.651 69576 Z= 0.288 Chirality : 0.039 0.145 7536 Planarity : 0.003 0.044 9348 Dihedral : 7.242 83.719 6996 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.43 % Allowed : 21.46 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 6252 helix: 2.09 (0.09), residues: 3168 sheet: 1.66 (0.23), residues: 396 loop : -0.36 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPPB 134 HIS 0.003 0.001 HISPA 175 PHE 0.014 0.001 PHEPI 334 TYR 0.011 0.001 TYRPG 135 ARG 0.007 0.000 ARGPA 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1731 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1602 time to evaluate : 4.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PX 20 GLN cc_start: 0.8794 (tp40) cc_final: 0.8508 (tp40) REVERT: PX 66 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8510 (mtp180) REVERT: PA 67 ARG cc_start: 0.9185 (tpp80) cc_final: 0.8844 (tpt90) REVERT: PA 98 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8523 (mp0) REVERT: PA 164 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: PA 261 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8090 (mmm-85) REVERT: PA 408 ASP cc_start: 0.8751 (t0) cc_final: 0.8441 (t0) REVERT: PB 42 MET cc_start: 0.7069 (tpt) cc_final: 0.6850 (tpp) REVERT: PB 149 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8417 (mm-30) REVERT: PB 261 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8358 (mmm-85) REVERT: PB 389 ASP cc_start: 0.8761 (m-30) cc_final: 0.8448 (m-30) REVERT: PC 67 ARG cc_start: 0.9225 (tpp80) cc_final: 0.8743 (tpt90) REVERT: PC 98 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8677 (mp0) REVERT: PC 112 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8508 (mt-10) REVERT: PC 144 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8125 (mt-10) REVERT: PC 149 GLU cc_start: 0.8772 (mp0) cc_final: 0.8455 (mm-30) REVERT: PC 170 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8664 (mmmm) REVERT: PC 261 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8533 (mmm-85) REVERT: PC 379 ASP cc_start: 0.8816 (t0) cc_final: 0.8390 (t0) REVERT: PC 383 ASP cc_start: 0.8818 (t0) cc_final: 0.8509 (t0) REVERT: PD 67 ARG cc_start: 0.9223 (tpp80) cc_final: 0.8878 (tpt90) REVERT: PD 98 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8845 (mp0) REVERT: PD 112 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8501 (mt-10) REVERT: PD 144 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8051 (mt-10) REVERT: PD 261 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8117 (mmm-85) REVERT: PD 372 ASP cc_start: 0.8722 (t70) cc_final: 0.8427 (t0) REVERT: PD 379 ASP cc_start: 0.8772 (t0) cc_final: 0.8421 (t0) REVERT: PD 408 ASP cc_start: 0.8706 (t0) cc_final: 0.8414 (t0) REVERT: PE 67 ARG cc_start: 0.9208 (tpp80) cc_final: 0.8997 (tpp80) REVERT: PE 98 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8539 (mp0) REVERT: PE 112 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8278 (mt-10) REVERT: PE 144 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7978 (mt-10) REVERT: PE 149 GLU cc_start: 0.8758 (mp0) cc_final: 0.8495 (mm-30) REVERT: PE 207 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8420 (mp0) REVERT: PE 215 ARG cc_start: 0.9027 (ttp-170) cc_final: 0.8781 (mtp-110) REVERT: PE 383 ASP cc_start: 0.8745 (t0) cc_final: 0.8178 (t0) REVERT: PE 386 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: PE 389 ASP cc_start: 0.8634 (m-30) cc_final: 0.8298 (m-30) REVERT: PE 428 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8464 (mt-10) REVERT: PF 67 ARG cc_start: 0.9267 (tpp80) cc_final: 0.8720 (tpt90) REVERT: PF 98 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8570 (mp0) REVERT: PF 149 GLU cc_start: 0.8607 (mp0) cc_final: 0.8375 (mm-30) REVERT: PF 261 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8359 (mmm-85) REVERT: PF 370 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8689 (mp0) REVERT: PF 379 ASP cc_start: 0.8787 (t0) cc_final: 0.8358 (t0) REVERT: PF 383 ASP cc_start: 0.8863 (t0) cc_final: 0.8497 (t0) REVERT: PG 42 MET cc_start: 0.7838 (tpp) cc_final: 0.6710 (tmm) REVERT: PG 67 ARG cc_start: 0.9241 (tpp80) cc_final: 0.8785 (tpt90) REVERT: PG 98 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8561 (mp0) REVERT: PG 112 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8462 (mt-10) REVERT: PG 144 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8064 (mt-10) REVERT: PG 149 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8279 (mm-30) REVERT: PG 346 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8874 (tpt-90) REVERT: PG 379 ASP cc_start: 0.8800 (t0) cc_final: 0.8549 (t0) REVERT: PG 408 ASP cc_start: 0.8716 (t0) cc_final: 0.8291 (t0) REVERT: PG 426 ASP cc_start: 0.8748 (m-30) cc_final: 0.8519 (m-30) REVERT: PH 42 MET cc_start: 0.7114 (tpt) cc_final: 0.6190 (tmm) REVERT: PH 112 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8400 (mt-10) REVERT: PH 144 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8328 (mt-10) REVERT: PH 149 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8349 (mm-30) REVERT: PH 164 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7979 (mt-10) REVERT: PH 261 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8366 (mmm-85) REVERT: PH 383 ASP cc_start: 0.8700 (t0) cc_final: 0.7945 (t0) REVERT: PH 386 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: PH 389 ASP cc_start: 0.8698 (m-30) cc_final: 0.8367 (m-30) REVERT: PH 428 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8486 (mt-10) REVERT: PH 429 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8376 (tptp) REVERT: PI 42 MET cc_start: 0.7277 (tpt) cc_final: 0.6807 (tpp) REVERT: PI 67 ARG cc_start: 0.9233 (tpp80) cc_final: 0.8755 (tpt90) REVERT: PI 102 LEU cc_start: 0.9397 (mm) cc_final: 0.8853 (tm) REVERT: PI 149 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8306 (mm-30) REVERT: PI 261 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8431 (mmm-85) REVERT: PI 326 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7898 (p) REVERT: PI 331 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8292 (mt-10) REVERT: PI 379 ASP cc_start: 0.8844 (t0) cc_final: 0.8537 (t0) REVERT: PI 383 ASP cc_start: 0.8873 (t0) cc_final: 0.8548 (t0) REVERT: PI 389 ASP cc_start: 0.8835 (m-30) cc_final: 0.8545 (m-30) REVERT: PI 426 ASP cc_start: 0.9015 (m-30) cc_final: 0.8742 (m-30) REVERT: PI 429 LYS cc_start: 0.9022 (ptmm) cc_final: 0.8650 (ttmm) REVERT: PJ 42 MET cc_start: 0.7151 (tpt) cc_final: 0.6203 (tmm) REVERT: PJ 59 ASP cc_start: 0.9050 (m-30) cc_final: 0.8799 (m-30) REVERT: PJ 67 ARG cc_start: 0.9201 (tpp80) cc_final: 0.8479 (tpt90) REVERT: PJ 149 GLU cc_start: 0.8699 (mp0) cc_final: 0.8323 (mm-30) REVERT: PJ 206 ASP cc_start: 0.9049 (t0) cc_final: 0.8847 (t0) REVERT: PJ 379 ASP cc_start: 0.8860 (t0) cc_final: 0.8620 (t0) REVERT: PJ 408 ASP cc_start: 0.8693 (t0) cc_final: 0.8297 (t0) REVERT: PK 42 MET cc_start: 0.6844 (tpt) cc_final: 0.6640 (tpp) REVERT: PK 59 ASP cc_start: 0.8973 (m-30) cc_final: 0.8762 (m-30) REVERT: PK 261 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8041 (mmm-85) REVERT: PK 389 ASP cc_start: 0.8597 (m-30) cc_final: 0.8272 (m-30) REVERT: PL 67 ARG cc_start: 0.9216 (tpp80) cc_final: 0.8731 (tpt90) REVERT: PL 102 LEU cc_start: 0.9407 (mm) cc_final: 0.8860 (tm) REVERT: PL 112 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8474 (mt-10) REVERT: PL 144 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8101 (mt-10) REVERT: PL 210 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9204 (mp) REVERT: PL 315 GLU cc_start: 0.8881 (mp0) cc_final: 0.8640 (mp0) REVERT: PL 383 ASP cc_start: 0.8726 (t0) cc_final: 0.8479 (t0) REVERT: PM 13 ASP cc_start: 0.9106 (m-30) cc_final: 0.8796 (m-30) REVERT: PO 13 ASP cc_start: 0.9005 (m-30) cc_final: 0.8691 (m-30) REVERT: PO 20 GLN cc_start: 0.8853 (tp40) cc_final: 0.8497 (tp40) REVERT: PO 24 ASP cc_start: 0.8755 (m-30) cc_final: 0.8461 (m-30) REVERT: PO 66 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8326 (mtp180) REVERT: PP 47 GLU cc_start: 0.8867 (tp30) cc_final: 0.8642 (tp30) REVERT: PP 66 ARG cc_start: 0.9372 (OUTLIER) cc_final: 0.8664 (mtp180) REVERT: PP 107 SER cc_start: 0.9167 (m) cc_final: 0.8906 (p) REVERT: PQ 100 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7359 (pm20) REVERT: PR 13 ASP cc_start: 0.9036 (m-30) cc_final: 0.8832 (m-30) REVERT: PR 20 GLN cc_start: 0.8842 (tp40) cc_final: 0.8470 (tp40) REVERT: PR 24 ASP cc_start: 0.8751 (m-30) cc_final: 0.8478 (m-30) REVERT: PR 66 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8215 (mtp180) REVERT: PS 11 LYS cc_start: 0.9168 (ttmt) cc_final: 0.8941 (ttmt) REVERT: PS 13 ASP cc_start: 0.9078 (m-30) cc_final: 0.8795 (m-30) REVERT: PS 66 ARG cc_start: 0.9268 (mtt90) cc_final: 0.9033 (mtt180) REVERT: PT 66 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.8905 (mtt180) REVERT: PU 20 GLN cc_start: 0.8792 (tp40) cc_final: 0.8402 (tp40) REVERT: PU 64 MET cc_start: 0.9206 (mtm) cc_final: 0.8964 (mtp) REVERT: PU 107 SER cc_start: 0.9183 (m) cc_final: 0.8973 (p) REVERT: PV 66 ARG cc_start: 0.9361 (mpp-170) cc_final: 0.9123 (mtt180) outliers start: 129 outliers final: 55 residues processed: 1664 average time/residue: 1.3344 time to fit residues: 2752.6231 Evaluate side-chains 1543 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 1468 time to evaluate : 4.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PX residue 34 SER Chi-restraints excluded: chain PX residue 66 ARG Chi-restraints excluded: chain PX residue 113 GLU Chi-restraints excluded: chain PA residue 69 SER Chi-restraints excluded: chain PA residue 164 GLU Chi-restraints excluded: chain PA residue 249 GLU Chi-restraints excluded: chain PA residue 261 ARG Chi-restraints excluded: chain PA residue 365 SER Chi-restraints excluded: chain PA residue 376 GLU Chi-restraints excluded: chain PA residue 386 GLU Chi-restraints excluded: chain PA residue 391 ILE Chi-restraints excluded: chain PA residue 423 SER Chi-restraints excluded: chain PB residue 261 ARG Chi-restraints excluded: chain PB residue 386 GLU Chi-restraints excluded: chain PC residue 56 THR Chi-restraints excluded: chain PC residue 69 SER Chi-restraints excluded: chain PC residue 146 ILE Chi-restraints excluded: chain PC residue 249 GLU Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PC residue 391 ILE Chi-restraints excluded: chain PD residue 34 THR Chi-restraints excluded: chain PD residue 236 LEU Chi-restraints excluded: chain PD residue 261 ARG Chi-restraints excluded: chain PD residue 365 SER Chi-restraints excluded: chain PD residue 376 GLU Chi-restraints excluded: chain PD residue 386 GLU Chi-restraints excluded: chain PD residue 423 SER Chi-restraints excluded: chain PE residue 69 SER Chi-restraints excluded: chain PE residue 249 GLU Chi-restraints excluded: chain PE residue 250 ASP Chi-restraints excluded: chain PE residue 386 GLU Chi-restraints excluded: chain PE residue 409 LEU Chi-restraints excluded: chain PE residue 429 LYS Chi-restraints excluded: chain PF residue 60 LEU Chi-restraints excluded: chain PF residue 69 SER Chi-restraints excluded: chain PF residue 249 GLU Chi-restraints excluded: chain PF residue 261 ARG Chi-restraints excluded: chain PF residue 409 LEU Chi-restraints excluded: chain PG residue 34 THR Chi-restraints excluded: chain PG residue 69 SER Chi-restraints excluded: chain PG residue 249 GLU Chi-restraints excluded: chain PG residue 346 ARG Chi-restraints excluded: chain PG residue 365 SER Chi-restraints excluded: chain PG residue 386 GLU Chi-restraints excluded: chain PH residue 146 ILE Chi-restraints excluded: chain PH residue 249 GLU Chi-restraints excluded: chain PH residue 261 ARG Chi-restraints excluded: chain PH residue 386 GLU Chi-restraints excluded: chain PH residue 429 LYS Chi-restraints excluded: chain PI residue 146 ILE Chi-restraints excluded: chain PI residue 249 GLU Chi-restraints excluded: chain PI residue 261 ARG Chi-restraints excluded: chain PI residue 326 SER Chi-restraints excluded: chain PI residue 386 GLU Chi-restraints excluded: chain PJ residue 365 SER Chi-restraints excluded: chain PJ residue 386 GLU Chi-restraints excluded: chain PJ residue 391 ILE Chi-restraints excluded: chain PJ residue 423 SER Chi-restraints excluded: chain PK residue 261 ARG Chi-restraints excluded: chain PK residue 386 GLU Chi-restraints excluded: chain PK residue 409 LEU Chi-restraints excluded: chain PL residue 141 GLU Chi-restraints excluded: chain PL residue 146 ILE Chi-restraints excluded: chain PL residue 210 ILE Chi-restraints excluded: chain PL residue 249 GLU Chi-restraints excluded: chain PN residue 18 THR Chi-restraints excluded: chain PO residue 66 ARG Chi-restraints excluded: chain PO residue 113 GLU Chi-restraints excluded: chain PP residue 66 ARG Chi-restraints excluded: chain PP residue 96 SER Chi-restraints excluded: chain PR residue 66 ARG Chi-restraints excluded: chain PS residue 113 GLU Chi-restraints excluded: chain PT residue 66 ARG Chi-restraints excluded: chain PV residue 96 SER Chi-restraints excluded: chain PV residue 113 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 379 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 366 optimal weight: 20.0000 chunk 184 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 389 optimal weight: 5.9990 chunk 417 optimal weight: 20.0000 chunk 303 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 481 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PX 28 GLN PX 39 ASN PX 117 GLN PX 133 ASN PA 200 ASN PC 92 HIS PC 393 GLN PD 36 GLN PD 92 HIS PF 92 HIS PG 200 ASN PG 257 ASN PI 92 HIS PI 143 GLN PJ 36 GLN PJ 92 HIS PJ 143 GLN PJ 200 ASN PK 393 GLN PL 92 HIS PM 28 GLN PM 39 ASN PO 28 GLN PO 39 ASN PO 117 GLN PP 39 ASN PR 28 GLN PR 39 ASN PR 117 GLN PS 28 GLN PS 39 ASN PU 28 GLN PU 117 GLN PV 28 GLN PV 39 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 51240 Z= 0.288 Angle : 0.617 9.624 69576 Z= 0.312 Chirality : 0.040 0.137 7536 Planarity : 0.004 0.044 9348 Dihedral : 7.241 85.017 6996 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.69 % Allowed : 22.05 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.10), residues: 6252 helix: 2.04 (0.09), residues: 3168 sheet: 1.51 (0.23), residues: 396 loop : -0.39 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPPH 134 HIS 0.004 0.001 HISPF 175 PHE 0.016 0.002 PHEPL 334 TYR 0.021 0.002 TYRPV 76 ARG 0.008 0.000 ARGPE 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1519 time to evaluate : 4.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PX 20 GLN cc_start: 0.8828 (tp40) cc_final: 0.8544 (tp40) REVERT: PX 24 ASP cc_start: 0.8797 (m-30) cc_final: 0.8536 (m-30) REVERT: PX 114 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8351 (mmtp) REVERT: PA 67 ARG cc_start: 0.9227 (tpp80) cc_final: 0.8796 (tpt90) REVERT: PA 98 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8610 (mp0) REVERT: PA 164 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: PA 261 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8139 (mmm-85) REVERT: PA 370 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8895 (mp0) REVERT: PA 408 ASP cc_start: 0.8741 (t0) cc_final: 0.8447 (t0) REVERT: PA 426 ASP cc_start: 0.8879 (m-30) cc_final: 0.8441 (m-30) REVERT: PB 149 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8448 (mm-30) REVERT: PB 215 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8058 (ttp-170) REVERT: PB 261 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8379 (mmm-85) REVERT: PB 301 MET cc_start: 0.8587 (ttt) cc_final: 0.8341 (ttt) REVERT: PB 389 ASP cc_start: 0.8780 (m-30) cc_final: 0.8455 (m-30) REVERT: PC 67 ARG cc_start: 0.9274 (tpp80) cc_final: 0.8571 (tpt90) REVERT: PC 107 PRO cc_start: 0.9225 (Cg_exo) cc_final: 0.8869 (Cg_endo) REVERT: PC 149 GLU cc_start: 0.8772 (mp0) cc_final: 0.8465 (mm-30) REVERT: PC 170 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8703 (mmmm) REVERT: PC 210 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9213 (mp) REVERT: PC 261 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8573 (mmm-85) REVERT: PC 370 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8607 (mp0) REVERT: PC 379 ASP cc_start: 0.8838 (t0) cc_final: 0.8538 (t0) REVERT: PC 383 ASP cc_start: 0.8847 (t0) cc_final: 0.8509 (t0) REVERT: PD 67 ARG cc_start: 0.9262 (tpp80) cc_final: 0.8760 (tpt90) REVERT: PD 112 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8563 (mt-10) REVERT: PD 261 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8135 (mmm-85) REVERT: PD 370 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8803 (mp0) REVERT: PD 379 ASP cc_start: 0.8825 (t0) cc_final: 0.8453 (t0) REVERT: PD 408 ASP cc_start: 0.8682 (t0) cc_final: 0.8399 (t0) REVERT: PD 426 ASP cc_start: 0.8904 (m-30) cc_final: 0.8410 (m-30) REVERT: PD 431 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8985 (tp30) REVERT: PE 98 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8590 (mp0) REVERT: PE 112 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8387 (mt-10) REVERT: PE 144 GLU cc_start: 0.8650 (mt-10) cc_final: 0.7964 (mt-10) REVERT: PE 149 GLU cc_start: 0.8760 (mp0) cc_final: 0.8486 (mm-30) REVERT: PE 207 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8413 (mp0) REVERT: PE 215 ARG cc_start: 0.9054 (ttp-170) cc_final: 0.8789 (mtp-110) REVERT: PE 261 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8344 (mmm-85) REVERT: PE 301 MET cc_start: 0.8583 (ttt) cc_final: 0.8370 (ttt) REVERT: PE 376 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8118 (tm-30) REVERT: PE 383 ASP cc_start: 0.8757 (t0) cc_final: 0.8166 (t0) REVERT: PE 386 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: PE 428 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8569 (mt-10) REVERT: PF 98 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8520 (mp0) REVERT: PF 102 LEU cc_start: 0.9392 (mm) cc_final: 0.8811 (tm) REVERT: PF 149 GLU cc_start: 0.8613 (mp0) cc_final: 0.8364 (mm-30) REVERT: PF 261 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8422 (mmm-85) REVERT: PF 331 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8446 (mt-10) REVERT: PF 370 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8706 (mp0) REVERT: PF 379 ASP cc_start: 0.8848 (t0) cc_final: 0.8529 (t0) REVERT: PF 383 ASP cc_start: 0.8877 (t0) cc_final: 0.8515 (t0) REVERT: PF 389 ASP cc_start: 0.8708 (m-30) cc_final: 0.8461 (m-30) REVERT: PF 416 GLU cc_start: 0.8517 (mp0) cc_final: 0.8314 (pm20) REVERT: PG 42 MET cc_start: 0.7821 (tpp) cc_final: 0.6644 (tmm) REVERT: PG 67 ARG cc_start: 0.9277 (tpp80) cc_final: 0.8712 (tpt90) REVERT: PG 98 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8579 (mp0) REVERT: PG 112 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8488 (mt-10) REVERT: PG 144 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8091 (mt-10) REVERT: PG 149 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8389 (mm-30) REVERT: PG 261 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8215 (mmm-85) REVERT: PG 301 MET cc_start: 0.8686 (ttt) cc_final: 0.8372 (ttt) REVERT: PG 379 ASP cc_start: 0.8824 (t0) cc_final: 0.8624 (t0) REVERT: PG 408 ASP cc_start: 0.8737 (t0) cc_final: 0.8331 (t0) REVERT: PH 42 MET cc_start: 0.7308 (tpt) cc_final: 0.6231 (tmm) REVERT: PH 67 ARG cc_start: 0.9255 (tpp80) cc_final: 0.9034 (tpp80) REVERT: PH 98 GLU cc_start: 0.8999 (mp0) cc_final: 0.8647 (mp0) REVERT: PH 112 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8250 (mt-10) REVERT: PH 144 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8287 (mt-10) REVERT: PH 149 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8349 (mm-30) REVERT: PH 227 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8887 (mm-30) REVERT: PH 261 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8355 (mmm-85) REVERT: PH 301 MET cc_start: 0.8571 (ttt) cc_final: 0.8363 (ttt) REVERT: PH 376 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8193 (tm-30) REVERT: PH 383 ASP cc_start: 0.8749 (t0) cc_final: 0.8008 (t0) REVERT: PH 386 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: PH 389 ASP cc_start: 0.8701 (m-30) cc_final: 0.8387 (m-30) REVERT: PH 428 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8531 (mt-10) REVERT: PH 429 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8402 (tptp) REVERT: PI 42 MET cc_start: 0.7082 (tpt) cc_final: 0.6611 (tpp) REVERT: PI 149 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8311 (mm-30) REVERT: PI 210 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9185 (mp) REVERT: PI 261 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8455 (mmm-85) REVERT: PI 370 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8669 (mp0) REVERT: PI 379 ASP cc_start: 0.8843 (t0) cc_final: 0.8574 (t0) REVERT: PI 383 ASP cc_start: 0.8890 (t0) cc_final: 0.8526 (t0) REVERT: PI 389 ASP cc_start: 0.8819 (m-30) cc_final: 0.8556 (m-30) REVERT: PI 426 ASP cc_start: 0.9035 (m-30) cc_final: 0.8769 (m-30) REVERT: PI 429 LYS cc_start: 0.9066 (ptmm) cc_final: 0.8690 (ttmm) REVERT: PJ 42 MET cc_start: 0.7120 (tpt) cc_final: 0.6914 (tpp) REVERT: PJ 59 ASP cc_start: 0.9083 (m-30) cc_final: 0.8837 (m-30) REVERT: PJ 67 ARG cc_start: 0.9233 (tpp80) cc_final: 0.8803 (tpt90) REVERT: PJ 149 GLU cc_start: 0.8715 (mp0) cc_final: 0.8346 (mm-30) REVERT: PJ 379 ASP cc_start: 0.8878 (t0) cc_final: 0.8632 (t0) REVERT: PJ 408 ASP cc_start: 0.8721 (t0) cc_final: 0.8354 (t0) REVERT: PJ 426 ASP cc_start: 0.8880 (m-30) cc_final: 0.8434 (m-30) REVERT: PK 42 MET cc_start: 0.6972 (tpt) cc_final: 0.6769 (tpp) REVERT: PK 261 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8006 (mmm-85) REVERT: PK 301 MET cc_start: 0.8507 (ttt) cc_final: 0.8288 (ttt) REVERT: PL 67 ARG cc_start: 0.9259 (tpp80) cc_final: 0.8559 (tpt90) REVERT: PL 102 LEU cc_start: 0.9451 (mm) cc_final: 0.8928 (tm) REVERT: PL 112 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8512 (mt-10) REVERT: PL 144 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8115 (mt-10) REVERT: PL 210 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9217 (mp) REVERT: PL 261 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8575 (mmm-85) REVERT: PL 315 GLU cc_start: 0.8930 (mp0) cc_final: 0.8642 (mp0) REVERT: PL 383 ASP cc_start: 0.8764 (t0) cc_final: 0.8479 (t0) REVERT: PL 389 ASP cc_start: 0.8801 (m-30) cc_final: 0.8585 (m-30) REVERT: PM 13 ASP cc_start: 0.9129 (m-30) cc_final: 0.8839 (m-30) REVERT: PM 132 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8799 (t0) REVERT: PN 100 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7390 (pm20) REVERT: PN 132 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8660 (t0) REVERT: PO 13 ASP cc_start: 0.9060 (m-30) cc_final: 0.8720 (m-30) REVERT: PO 66 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8288 (mtp180) REVERT: PP 66 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.9032 (mtt180) REVERT: PR 13 ASP cc_start: 0.9104 (m-30) cc_final: 0.8870 (m-30) REVERT: PR 20 GLN cc_start: 0.8924 (tp40) cc_final: 0.8502 (tp40) REVERT: PR 24 ASP cc_start: 0.8796 (m-30) cc_final: 0.8510 (m-30) REVERT: PR 66 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8157 (mtp180) REVERT: PS 11 LYS cc_start: 0.9191 (ttmt) cc_final: 0.8938 (ttmt) REVERT: PS 13 ASP cc_start: 0.9101 (m-30) cc_final: 0.8828 (m-30) REVERT: PS 66 ARG cc_start: 0.9306 (mtt90) cc_final: 0.9021 (mtt180) REVERT: PT 66 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.8912 (mtt180) REVERT: PU 20 GLN cc_start: 0.8830 (tp40) cc_final: 0.8538 (tp40) REVERT: PU 64 MET cc_start: 0.9197 (mtm) cc_final: 0.8978 (mtp) REVERT: PU 107 SER cc_start: 0.9223 (m) cc_final: 0.9008 (p) REVERT: PV 66 ARG cc_start: 0.9380 (mpp-170) cc_final: 0.9133 (mtt180) outliers start: 143 outliers final: 74 residues processed: 1592 average time/residue: 1.3337 time to fit residues: 2636.8062 Evaluate side-chains 1510 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1410 time to evaluate : 4.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PX residue 34 SER Chi-restraints excluded: chain PX residue 113 GLU Chi-restraints excluded: chain PX residue 114 LYS Chi-restraints excluded: chain PA residue 69 SER Chi-restraints excluded: chain PA residue 164 GLU Chi-restraints excluded: chain PA residue 236 LEU Chi-restraints excluded: chain PA residue 249 GLU Chi-restraints excluded: chain PA residue 261 ARG Chi-restraints excluded: chain PA residue 365 SER Chi-restraints excluded: chain PA residue 376 GLU Chi-restraints excluded: chain PA residue 386 GLU Chi-restraints excluded: chain PA residue 391 ILE Chi-restraints excluded: chain PA residue 423 SER Chi-restraints excluded: chain PB residue 69 SER Chi-restraints excluded: chain PB residue 215 ARG Chi-restraints excluded: chain PB residue 250 ASP Chi-restraints excluded: chain PB residue 261 ARG Chi-restraints excluded: chain PB residue 386 GLU Chi-restraints excluded: chain PB residue 429 LYS Chi-restraints excluded: chain PC residue 56 THR Chi-restraints excluded: chain PC residue 69 SER Chi-restraints excluded: chain PC residue 146 ILE Chi-restraints excluded: chain PC residue 210 ILE Chi-restraints excluded: chain PC residue 249 GLU Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PC residue 391 ILE Chi-restraints excluded: chain PC residue 401 GLU Chi-restraints excluded: chain PD residue 34 THR Chi-restraints excluded: chain PD residue 147 THR Chi-restraints excluded: chain PD residue 236 LEU Chi-restraints excluded: chain PD residue 249 GLU Chi-restraints excluded: chain PD residue 261 ARG Chi-restraints excluded: chain PD residue 365 SER Chi-restraints excluded: chain PD residue 376 GLU Chi-restraints excluded: chain PD residue 386 GLU Chi-restraints excluded: chain PD residue 391 ILE Chi-restraints excluded: chain PD residue 423 SER Chi-restraints excluded: chain PE residue 34 THR Chi-restraints excluded: chain PE residue 69 SER Chi-restraints excluded: chain PE residue 249 GLU Chi-restraints excluded: chain PE residue 250 ASP Chi-restraints excluded: chain PE residue 261 ARG Chi-restraints excluded: chain PE residue 386 GLU Chi-restraints excluded: chain PE residue 409 LEU Chi-restraints excluded: chain PF residue 60 LEU Chi-restraints excluded: chain PF residue 69 SER Chi-restraints excluded: chain PF residue 146 ILE Chi-restraints excluded: chain PF residue 249 GLU Chi-restraints excluded: chain PF residue 261 ARG Chi-restraints excluded: chain PG residue 34 THR Chi-restraints excluded: chain PG residue 69 SER Chi-restraints excluded: chain PG residue 236 LEU Chi-restraints excluded: chain PG residue 249 GLU Chi-restraints excluded: chain PG residue 261 ARG Chi-restraints excluded: chain PG residue 365 SER Chi-restraints excluded: chain PG residue 386 GLU Chi-restraints excluded: chain PG residue 413 GLU Chi-restraints excluded: chain PH residue 146 ILE Chi-restraints excluded: chain PH residue 249 GLU Chi-restraints excluded: chain PH residue 250 ASP Chi-restraints excluded: chain PH residue 261 ARG Chi-restraints excluded: chain PH residue 333 ARG Chi-restraints excluded: chain PH residue 386 GLU Chi-restraints excluded: chain PH residue 429 LYS Chi-restraints excluded: chain PI residue 146 ILE Chi-restraints excluded: chain PI residue 210 ILE Chi-restraints excluded: chain PI residue 249 GLU Chi-restraints excluded: chain PI residue 261 ARG Chi-restraints excluded: chain PJ residue 56 THR Chi-restraints excluded: chain PJ residue 236 LEU Chi-restraints excluded: chain PJ residue 365 SER Chi-restraints excluded: chain PJ residue 386 GLU Chi-restraints excluded: chain PJ residue 391 ILE Chi-restraints excluded: chain PJ residue 423 SER Chi-restraints excluded: chain PK residue 69 SER Chi-restraints excluded: chain PK residue 261 ARG Chi-restraints excluded: chain PK residue 386 GLU Chi-restraints excluded: chain PL residue 56 THR Chi-restraints excluded: chain PL residue 60 LEU Chi-restraints excluded: chain PL residue 69 SER Chi-restraints excluded: chain PL residue 141 GLU Chi-restraints excluded: chain PL residue 146 ILE Chi-restraints excluded: chain PL residue 210 ILE Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PM residue 132 ASP Chi-restraints excluded: chain PN residue 18 THR Chi-restraints excluded: chain PN residue 132 ASP Chi-restraints excluded: chain PO residue 66 ARG Chi-restraints excluded: chain PO residue 113 GLU Chi-restraints excluded: chain PP residue 66 ARG Chi-restraints excluded: chain PP residue 96 SER Chi-restraints excluded: chain PQ residue 96 SER Chi-restraints excluded: chain PR residue 66 ARG Chi-restraints excluded: chain PS residue 113 GLU Chi-restraints excluded: chain PS residue 138 LEU Chi-restraints excluded: chain PT residue 66 ARG Chi-restraints excluded: chain PT residue 96 SER Chi-restraints excluded: chain PT residue 113 GLU Chi-restraints excluded: chain PV residue 96 SER Chi-restraints excluded: chain PV residue 113 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 557 optimal weight: 2.9990 chunk 587 optimal weight: 2.9990 chunk 535 optimal weight: 3.9990 chunk 571 optimal weight: 6.9990 chunk 343 optimal weight: 8.9990 chunk 248 optimal weight: 0.0000 chunk 448 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 516 optimal weight: 5.9990 chunk 540 optimal weight: 0.9980 chunk 569 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PX 28 GLN PX 39 ASN PX 117 GLN PC 92 HIS PC 393 GLN PD 36 GLN PF 92 HIS PG 257 ASN PI 92 HIS PJ 36 GLN PJ 92 HIS PJ 393 GLN PL 92 HIS PM 39 ASN PO 28 GLN PO 39 ASN PO 117 GLN PP 39 ASN PR 28 GLN PR 39 ASN PR 117 GLN PS 39 ASN PU 28 GLN PU 117 GLN PV 39 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 51240 Z= 0.217 Angle : 0.610 12.402 69576 Z= 0.308 Chirality : 0.040 0.144 7536 Planarity : 0.003 0.045 9348 Dihedral : 7.156 84.258 6996 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.50 % Allowed : 22.78 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.10), residues: 6252 helix: 2.03 (0.09), residues: 3168 sheet: 1.58 (0.23), residues: 396 loop : -0.35 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPPK 134 HIS 0.004 0.001 HISPH 175 PHE 0.018 0.001 PHEPC 334 TYR 0.014 0.001 TYRPO 76 ARG 0.008 0.000 ARGPE 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1629 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1496 time to evaluate : 4.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PX 20 GLN cc_start: 0.8817 (tp40) cc_final: 0.8516 (tp40) REVERT: PX 24 ASP cc_start: 0.8781 (m-30) cc_final: 0.8504 (m-30) REVERT: PX 66 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8377 (mtp180) REVERT: PA 67 ARG cc_start: 0.9214 (tpp80) cc_final: 0.8792 (tpt90) REVERT: PA 98 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8587 (mp0) REVERT: PA 164 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: PA 261 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8109 (mmm-85) REVERT: PA 370 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8894 (mp0) REVERT: PA 408 ASP cc_start: 0.8706 (t0) cc_final: 0.8421 (t0) REVERT: PB 149 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8384 (mm-30) REVERT: PB 301 MET cc_start: 0.8538 (ttt) cc_final: 0.8326 (ttt) REVERT: PB 389 ASP cc_start: 0.8727 (m-30) cc_final: 0.8395 (m-30) REVERT: PC 149 GLU cc_start: 0.8740 (mp0) cc_final: 0.8407 (mm-30) REVERT: PC 170 LYS cc_start: 0.9093 (mmmm) cc_final: 0.8717 (mmmm) REVERT: PC 261 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8588 (mmm-85) REVERT: PC 370 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8640 (mp0) REVERT: PC 379 ASP cc_start: 0.8878 (t0) cc_final: 0.8556 (t0) REVERT: PC 383 ASP cc_start: 0.8791 (t0) cc_final: 0.8424 (t0) REVERT: PD 67 ARG cc_start: 0.9241 (tpp80) cc_final: 0.8805 (tpt90) REVERT: PD 112 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8542 (mt-10) REVERT: PD 261 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8126 (mmm-85) REVERT: PD 370 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8788 (mp0) REVERT: PD 379 ASP cc_start: 0.8776 (t0) cc_final: 0.8446 (t0) REVERT: PD 408 ASP cc_start: 0.8647 (t0) cc_final: 0.8351 (t0) REVERT: PD 431 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8983 (tp30) REVERT: PE 67 ARG cc_start: 0.9186 (tpp80) cc_final: 0.8536 (tpt90) REVERT: PE 98 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8518 (mp0) REVERT: PE 112 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8243 (mt-10) REVERT: PE 144 GLU cc_start: 0.8654 (mt-10) cc_final: 0.7970 (mt-10) REVERT: PE 149 GLU cc_start: 0.8765 (mp0) cc_final: 0.8488 (mm-30) REVERT: PE 215 ARG cc_start: 0.9026 (ttp-170) cc_final: 0.8767 (mtp-110) REVERT: PE 261 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8332 (mmm-85) REVERT: PE 301 MET cc_start: 0.8603 (ttt) cc_final: 0.8402 (ttt) REVERT: PE 376 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8099 (tm-30) REVERT: PE 383 ASP cc_start: 0.8729 (t0) cc_final: 0.8098 (t0) REVERT: PE 386 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8404 (mp0) REVERT: PE 428 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8461 (mt-10) REVERT: PF 67 ARG cc_start: 0.9180 (tpp80) cc_final: 0.8356 (tpt90) REVERT: PF 98 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8487 (mp0) REVERT: PF 102 LEU cc_start: 0.9378 (mm) cc_final: 0.8829 (tm) REVERT: PF 149 GLU cc_start: 0.8617 (mp0) cc_final: 0.8366 (mm-30) REVERT: PF 170 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8631 (mmmm) REVERT: PF 261 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8427 (mmm-85) REVERT: PF 331 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8394 (mt-10) REVERT: PF 370 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8766 (mp0) REVERT: PF 379 ASP cc_start: 0.8839 (t0) cc_final: 0.8527 (t0) REVERT: PF 383 ASP cc_start: 0.8842 (t0) cc_final: 0.8440 (t0) REVERT: PF 389 ASP cc_start: 0.8705 (m-30) cc_final: 0.8438 (m-30) REVERT: PG 42 MET cc_start: 0.7764 (tpp) cc_final: 0.6699 (tmm) REVERT: PG 67 ARG cc_start: 0.9267 (tpp80) cc_final: 0.8787 (tpt90) REVERT: PG 98 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8564 (mp0) REVERT: PG 261 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8241 (mmm-85) REVERT: PG 301 MET cc_start: 0.8672 (ttt) cc_final: 0.8348 (ttt) REVERT: PG 370 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8804 (mp0) REVERT: PG 408 ASP cc_start: 0.8713 (t0) cc_final: 0.8301 (t0) REVERT: PH 67 ARG cc_start: 0.9238 (tpp80) cc_final: 0.9027 (tpp80) REVERT: PH 98 GLU cc_start: 0.8987 (mp0) cc_final: 0.8548 (mp0) REVERT: PH 112 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8237 (mt-10) REVERT: PH 144 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8261 (mt-10) REVERT: PH 149 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8337 (mm-30) REVERT: PH 177 ARG cc_start: 0.8895 (ttt180) cc_final: 0.8016 (ttt90) REVERT: PH 215 ARG cc_start: 0.9029 (ttp-170) cc_final: 0.8774 (mtp-110) REVERT: PH 227 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8702 (mm-30) REVERT: PH 261 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8353 (mmm-85) REVERT: PH 376 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8113 (tm-30) REVERT: PH 379 ASP cc_start: 0.8918 (t0) cc_final: 0.8602 (t0) REVERT: PH 383 ASP cc_start: 0.8748 (t0) cc_final: 0.7988 (t0) REVERT: PH 386 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: PH 389 ASP cc_start: 0.8701 (m-30) cc_final: 0.8368 (m-30) REVERT: PH 428 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8601 (mt-10) REVERT: PH 429 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8411 (tptp) REVERT: PI 42 MET cc_start: 0.7063 (tpt) cc_final: 0.6701 (tpp) REVERT: PI 67 ARG cc_start: 0.9191 (tpp80) cc_final: 0.8604 (tpt90) REVERT: PI 98 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8752 (mp0) REVERT: PI 149 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8301 (mm-30) REVERT: PI 210 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9174 (mp) REVERT: PI 261 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8487 (mmm-85) REVERT: PI 326 SER cc_start: 0.8155 (OUTLIER) cc_final: 0.7936 (p) REVERT: PI 331 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8430 (mt-10) REVERT: PI 370 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8742 (mp0) REVERT: PI 379 ASP cc_start: 0.8864 (t0) cc_final: 0.8563 (t0) REVERT: PI 383 ASP cc_start: 0.8874 (t0) cc_final: 0.8478 (t0) REVERT: PI 389 ASP cc_start: 0.8823 (m-30) cc_final: 0.8561 (m-30) REVERT: PI 426 ASP cc_start: 0.9007 (m-30) cc_final: 0.8695 (m-30) REVERT: PJ 59 ASP cc_start: 0.9048 (m-30) cc_final: 0.8797 (m-30) REVERT: PJ 67 ARG cc_start: 0.9250 (tpp80) cc_final: 0.8815 (tpt90) REVERT: PJ 149 GLU cc_start: 0.8694 (mp0) cc_final: 0.8318 (mm-30) REVERT: PJ 379 ASP cc_start: 0.8868 (t0) cc_final: 0.8630 (t0) REVERT: PJ 391 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9053 (mt) REVERT: PJ 408 ASP cc_start: 0.8701 (t0) cc_final: 0.8323 (t0) REVERT: PK 261 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8044 (mmm-85) REVERT: PK 301 MET cc_start: 0.8542 (ttt) cc_final: 0.8326 (ttt) REVERT: PL 67 ARG cc_start: 0.9241 (tpp80) cc_final: 0.8698 (tpt90) REVERT: PL 102 LEU cc_start: 0.9444 (mm) cc_final: 0.8932 (tm) REVERT: PL 112 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8497 (mt-10) REVERT: PL 144 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8169 (mt-10) REVERT: PL 149 GLU cc_start: 0.8741 (mp0) cc_final: 0.8249 (mp0) REVERT: PL 210 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9215 (mp) REVERT: PL 261 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8539 (mmm-85) REVERT: PL 315 GLU cc_start: 0.8940 (mp0) cc_final: 0.8589 (mp0) REVERT: PL 383 ASP cc_start: 0.8720 (t0) cc_final: 0.8405 (t0) REVERT: PL 389 ASP cc_start: 0.8829 (m-30) cc_final: 0.8567 (m-30) REVERT: PM 13 ASP cc_start: 0.9122 (m-30) cc_final: 0.8829 (m-30) REVERT: PO 13 ASP cc_start: 0.9018 (m-30) cc_final: 0.8700 (m-30) REVERT: PO 20 GLN cc_start: 0.8809 (tp40) cc_final: 0.8513 (tp40) REVERT: PO 24 ASP cc_start: 0.8755 (m-30) cc_final: 0.8500 (m-30) REVERT: PO 66 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.8307 (mtp180) REVERT: PP 66 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8666 (mtp180) REVERT: PR 13 ASP cc_start: 0.9063 (m-30) cc_final: 0.8828 (m-30) REVERT: PR 20 GLN cc_start: 0.8863 (tp40) cc_final: 0.8437 (tp40) REVERT: PR 66 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8207 (mtp180) REVERT: PS 11 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8930 (ttmt) REVERT: PS 13 ASP cc_start: 0.9096 (m-30) cc_final: 0.8813 (m-30) REVERT: PS 66 ARG cc_start: 0.9288 (mtt90) cc_final: 0.8992 (mtt180) REVERT: PT 66 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.8897 (mtt180) REVERT: PU 20 GLN cc_start: 0.8772 (tp40) cc_final: 0.8414 (tp40) REVERT: PU 24 ASP cc_start: 0.8730 (m-30) cc_final: 0.8515 (m-30) REVERT: PU 64 MET cc_start: 0.9210 (mtm) cc_final: 0.8984 (mtp) REVERT: PU 90 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8490 (mp0) REVERT: PU 107 SER cc_start: 0.9190 (m) cc_final: 0.8980 (p) REVERT: PV 66 ARG cc_start: 0.9367 (mpp-170) cc_final: 0.9129 (mtt180) outliers start: 133 outliers final: 69 residues processed: 1562 average time/residue: 1.3115 time to fit residues: 2548.9853 Evaluate side-chains 1552 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1460 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PX residue 34 SER Chi-restraints excluded: chain PX residue 66 ARG Chi-restraints excluded: chain PX residue 113 GLU Chi-restraints excluded: chain PA residue 69 SER Chi-restraints excluded: chain PA residue 164 GLU Chi-restraints excluded: chain PA residue 236 LEU Chi-restraints excluded: chain PA residue 261 ARG Chi-restraints excluded: chain PA residue 365 SER Chi-restraints excluded: chain PA residue 376 GLU Chi-restraints excluded: chain PA residue 386 GLU Chi-restraints excluded: chain PA residue 391 ILE Chi-restraints excluded: chain PA residue 423 SER Chi-restraints excluded: chain PB residue 146 ILE Chi-restraints excluded: chain PB residue 250 ASP Chi-restraints excluded: chain PB residue 386 GLU Chi-restraints excluded: chain PC residue 56 THR Chi-restraints excluded: chain PC residue 69 SER Chi-restraints excluded: chain PC residue 146 ILE Chi-restraints excluded: chain PC residue 249 GLU Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PC residue 391 ILE Chi-restraints excluded: chain PC residue 401 GLU Chi-restraints excluded: chain PD residue 34 THR Chi-restraints excluded: chain PD residue 236 LEU Chi-restraints excluded: chain PD residue 261 ARG Chi-restraints excluded: chain PD residue 365 SER Chi-restraints excluded: chain PD residue 376 GLU Chi-restraints excluded: chain PD residue 386 GLU Chi-restraints excluded: chain PD residue 423 SER Chi-restraints excluded: chain PE residue 249 GLU Chi-restraints excluded: chain PE residue 250 ASP Chi-restraints excluded: chain PE residue 261 ARG Chi-restraints excluded: chain PE residue 386 GLU Chi-restraints excluded: chain PE residue 409 LEU Chi-restraints excluded: chain PE residue 429 LYS Chi-restraints excluded: chain PF residue 60 LEU Chi-restraints excluded: chain PF residue 69 SER Chi-restraints excluded: chain PF residue 146 ILE Chi-restraints excluded: chain PF residue 249 GLU Chi-restraints excluded: chain PF residue 261 ARG Chi-restraints excluded: chain PG residue 34 THR Chi-restraints excluded: chain PG residue 69 SER Chi-restraints excluded: chain PG residue 236 LEU Chi-restraints excluded: chain PG residue 249 GLU Chi-restraints excluded: chain PG residue 261 ARG Chi-restraints excluded: chain PG residue 365 SER Chi-restraints excluded: chain PG residue 386 GLU Chi-restraints excluded: chain PG residue 391 ILE Chi-restraints excluded: chain PG residue 413 GLU Chi-restraints excluded: chain PH residue 69 SER Chi-restraints excluded: chain PH residue 146 ILE Chi-restraints excluded: chain PH residue 249 GLU Chi-restraints excluded: chain PH residue 261 ARG Chi-restraints excluded: chain PH residue 386 GLU Chi-restraints excluded: chain PH residue 429 LYS Chi-restraints excluded: chain PI residue 104 ASP Chi-restraints excluded: chain PI residue 210 ILE Chi-restraints excluded: chain PI residue 249 GLU Chi-restraints excluded: chain PI residue 261 ARG Chi-restraints excluded: chain PI residue 326 SER Chi-restraints excluded: chain PI residue 386 GLU Chi-restraints excluded: chain PI residue 429 LYS Chi-restraints excluded: chain PJ residue 236 LEU Chi-restraints excluded: chain PJ residue 365 SER Chi-restraints excluded: chain PJ residue 386 GLU Chi-restraints excluded: chain PJ residue 391 ILE Chi-restraints excluded: chain PJ residue 423 SER Chi-restraints excluded: chain PK residue 69 SER Chi-restraints excluded: chain PK residue 261 ARG Chi-restraints excluded: chain PK residue 386 GLU Chi-restraints excluded: chain PK residue 409 LEU Chi-restraints excluded: chain PL residue 56 THR Chi-restraints excluded: chain PL residue 60 LEU Chi-restraints excluded: chain PL residue 69 SER Chi-restraints excluded: chain PL residue 141 GLU Chi-restraints excluded: chain PL residue 146 ILE Chi-restraints excluded: chain PL residue 210 ILE Chi-restraints excluded: chain PL residue 249 GLU Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PN residue 18 THR Chi-restraints excluded: chain PO residue 66 ARG Chi-restraints excluded: chain PO residue 113 GLU Chi-restraints excluded: chain PP residue 66 ARG Chi-restraints excluded: chain PP residue 96 SER Chi-restraints excluded: chain PQ residue 96 SER Chi-restraints excluded: chain PR residue 66 ARG Chi-restraints excluded: chain PS residue 113 GLU Chi-restraints excluded: chain PT residue 66 ARG Chi-restraints excluded: chain PT residue 96 SER Chi-restraints excluded: chain PT residue 113 GLU Chi-restraints excluded: chain PV residue 96 SER Chi-restraints excluded: chain PV residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 375 optimal weight: 20.0000 chunk 604 optimal weight: 9.9990 chunk 368 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 419 optimal weight: 7.9990 chunk 633 optimal weight: 9.9990 chunk 583 optimal weight: 10.0000 chunk 504 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 389 optimal weight: 10.0000 chunk 309 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PX 28 GLN PX 39 ASN PX 117 GLN PC 92 HIS PC 143 GLN PD 36 GLN PD 92 HIS PF 92 HIS PF 393 GLN PI 92 HIS PJ 36 GLN PJ 92 HIS PJ 393 GLN PL 92 HIS PM 39 ASN PO 28 GLN PO 39 ASN PO 117 GLN PP 39 ASN PR 28 GLN PR 39 ASN PR 117 GLN PS 39 ASN PU 28 GLN PV 39 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 51240 Z= 0.353 Angle : 0.665 12.624 69576 Z= 0.336 Chirality : 0.042 0.173 7536 Planarity : 0.004 0.049 9348 Dihedral : 7.200 85.736 6996 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.29 % Allowed : 23.06 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.10), residues: 6252 helix: 1.96 (0.09), residues: 3168 sheet: 1.41 (0.23), residues: 396 loop : -0.39 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPPB 134 HIS 0.005 0.001 HISPH 175 PHE 0.023 0.002 PHEPF 334 TYR 0.026 0.002 TYRPV 76 ARG 0.010 0.001 ARGPH 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12504 Ramachandran restraints generated. 6252 Oldfield, 0 Emsley, 6252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1580 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1458 time to evaluate : 4.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PX 20 GLN cc_start: 0.8861 (tp40) cc_final: 0.8540 (tp40) REVERT: PX 114 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8377 (mmtp) REVERT: PA 42 MET cc_start: 0.7627 (tpp) cc_final: 0.7298 (tpp) REVERT: PA 67 ARG cc_start: 0.9258 (tpp80) cc_final: 0.8736 (tpt90) REVERT: PA 98 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8607 (mp0) REVERT: PA 164 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7524 (mt-10) REVERT: PA 261 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8102 (mmm-85) REVERT: PA 370 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8896 (mp0) REVERT: PA 408 ASP cc_start: 0.8703 (t0) cc_final: 0.8426 (t0) REVERT: PA 426 ASP cc_start: 0.8904 (m-30) cc_final: 0.8441 (m-30) REVERT: PB 149 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8460 (mm-30) REVERT: PB 215 ARG cc_start: 0.9139 (mtp180) cc_final: 0.8916 (mtm110) REVERT: PB 261 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8494 (mmm-85) REVERT: PB 301 MET cc_start: 0.8589 (ttt) cc_final: 0.8378 (ttt) REVERT: PB 389 ASP cc_start: 0.8749 (m-30) cc_final: 0.8443 (m-30) REVERT: PC 67 ARG cc_start: 0.9216 (tpp80) cc_final: 0.8564 (tpt90) REVERT: PC 149 GLU cc_start: 0.8753 (mp0) cc_final: 0.8429 (mm-30) REVERT: PC 170 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8669 (mmmm) REVERT: PC 261 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8649 (mmm-85) REVERT: PC 370 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8783 (mp0) REVERT: PC 383 ASP cc_start: 0.8857 (t0) cc_final: 0.8456 (t0) REVERT: PC 414 ASP cc_start: 0.8615 (t0) cc_final: 0.7839 (t0) REVERT: PD 67 ARG cc_start: 0.9278 (tpp80) cc_final: 0.8748 (tpt90) REVERT: PD 112 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8587 (mt-10) REVERT: PD 261 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8120 (mmm-85) REVERT: PD 370 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8802 (mp0) REVERT: PD 379 ASP cc_start: 0.8702 (t0) cc_final: 0.8481 (t0) REVERT: PD 408 ASP cc_start: 0.8631 (t0) cc_final: 0.8387 (t0) REVERT: PD 419 ASP cc_start: 0.8943 (m-30) cc_final: 0.8699 (m-30) REVERT: PD 426 ASP cc_start: 0.8915 (m-30) cc_final: 0.8425 (m-30) REVERT: PD 431 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8984 (tp30) REVERT: PE 98 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8589 (mp0) REVERT: PE 149 GLU cc_start: 0.8716 (mp0) cc_final: 0.8406 (mm-30) REVERT: PE 261 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8387 (mmm-85) REVERT: PE 301 MET cc_start: 0.8645 (ttt) cc_final: 0.8438 (ttt) REVERT: PE 383 ASP cc_start: 0.8769 (t0) cc_final: 0.8228 (t0) REVERT: PE 386 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: PE 389 ASP cc_start: 0.8641 (m-30) cc_final: 0.8401 (m-30) REVERT: PF 67 ARG cc_start: 0.9212 (tpp80) cc_final: 0.8576 (tpt90) REVERT: PF 149 GLU cc_start: 0.8621 (mp0) cc_final: 0.8370 (mm-30) REVERT: PF 170 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8642 (mmmm) REVERT: PF 261 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8464 (mmm-85) REVERT: PF 370 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8766 (mp0) REVERT: PF 383 ASP cc_start: 0.8865 (t0) cc_final: 0.8470 (t0) REVERT: PF 389 ASP cc_start: 0.8639 (m-30) cc_final: 0.8383 (m-30) REVERT: PG 42 MET cc_start: 0.7545 (tpp) cc_final: 0.6495 (tmm) REVERT: PG 67 ARG cc_start: 0.9304 (tpp80) cc_final: 0.8665 (tpt90) REVERT: PG 98 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8593 (mp0) REVERT: PG 261 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8282 (mmm-85) REVERT: PG 301 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8389 (ttt) REVERT: PG 408 ASP cc_start: 0.8706 (t0) cc_final: 0.8327 (t0) REVERT: PH 98 GLU cc_start: 0.9010 (mp0) cc_final: 0.8475 (mp0) REVERT: PH 112 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8263 (mt-10) REVERT: PH 144 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8219 (mt-10) REVERT: PH 149 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8344 (mm-30) REVERT: PH 227 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8753 (mm-30) REVERT: PH 261 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8382 (mmm-85) REVERT: PH 376 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8176 (tm-30) REVERT: PH 383 ASP cc_start: 0.8741 (t0) cc_final: 0.7927 (t0) REVERT: PH 386 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8391 (mp0) REVERT: PH 389 ASP cc_start: 0.8748 (m-30) cc_final: 0.8414 (m-30) REVERT: PH 414 ASP cc_start: 0.8426 (t0) cc_final: 0.8035 (t0) REVERT: PH 428 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8573 (mt-10) REVERT: PI 42 MET cc_start: 0.6981 (tpt) cc_final: 0.6528 (tpp) REVERT: PI 67 ARG cc_start: 0.9231 (tpp80) cc_final: 0.8594 (tpt90) REVERT: PI 98 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8700 (mp0) REVERT: PI 149 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8318 (mm-30) REVERT: PI 210 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9196 (mp) REVERT: PI 261 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8499 (mmm-85) REVERT: PI 326 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7981 (p) REVERT: PI 331 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8465 (mt-10) REVERT: PI 370 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8747 (mp0) REVERT: PI 383 ASP cc_start: 0.8899 (t0) cc_final: 0.8472 (t0) REVERT: PI 389 ASP cc_start: 0.8807 (m-30) cc_final: 0.8552 (m-30) REVERT: PI 426 ASP cc_start: 0.9036 (m-30) cc_final: 0.8745 (m-30) REVERT: PJ 149 GLU cc_start: 0.8707 (mp0) cc_final: 0.8400 (mm-30) REVERT: PJ 370 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8811 (mp0) REVERT: PJ 391 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9120 (mt) REVERT: PJ 408 ASP cc_start: 0.8712 (t0) cc_final: 0.8352 (t0) REVERT: PJ 426 ASP cc_start: 0.8922 (m-30) cc_final: 0.8467 (m-30) REVERT: PK 261 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8007 (mmm-85) REVERT: PK 301 MET cc_start: 0.8565 (ttt) cc_final: 0.8364 (ttt) REVERT: PK 392 GLN cc_start: 0.9078 (tt0) cc_final: 0.8535 (mt0) REVERT: PL 67 ARG cc_start: 0.9290 (tpp80) cc_final: 0.8586 (tpt90) REVERT: PL 112 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8558 (mt-10) REVERT: PL 144 GLU cc_start: 0.8559 (mt-10) cc_final: 0.7784 (mt-10) REVERT: PL 261 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8667 (mmm-85) REVERT: PL 315 GLU cc_start: 0.8917 (mp0) cc_final: 0.8535 (mp0) REVERT: PL 383 ASP cc_start: 0.8785 (t0) cc_final: 0.8500 (t0) REVERT: PM 13 ASP cc_start: 0.9137 (m-30) cc_final: 0.8842 (m-30) REVERT: PO 13 ASP cc_start: 0.9089 (m-30) cc_final: 0.8750 (m-30) REVERT: PO 20 GLN cc_start: 0.8842 (tp40) cc_final: 0.8506 (tp40) REVERT: PO 24 ASP cc_start: 0.8789 (m-30) cc_final: 0.8517 (m-30) REVERT: PO 66 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8312 (mtp180) REVERT: PP 66 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.8652 (mtp180) REVERT: PR 13 ASP cc_start: 0.9114 (m-30) cc_final: 0.8880 (m-30) REVERT: PR 20 GLN cc_start: 0.8860 (tp40) cc_final: 0.8564 (tp40) REVERT: PR 66 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8143 (mtp180) REVERT: PS 13 ASP cc_start: 0.9110 (m-30) cc_final: 0.8849 (m-30) REVERT: PS 66 ARG cc_start: 0.9319 (mtt90) cc_final: 0.9043 (mtt180) REVERT: PT 66 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.8908 (mtt180) REVERT: PT 100 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6053 (mm-30) REVERT: PU 20 GLN cc_start: 0.8829 (tp40) cc_final: 0.8572 (tp40) REVERT: PU 64 MET cc_start: 0.9216 (mtm) cc_final: 0.8970 (mtp) REVERT: PU 90 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8553 (mp0) REVERT: PU 107 SER cc_start: 0.9237 (m) cc_final: 0.9027 (p) REVERT: PV 66 ARG cc_start: 0.9398 (mpp-170) cc_final: 0.9065 (mtt180) REVERT: PW 100 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7386 (pm20) outliers start: 122 outliers final: 75 residues processed: 1517 average time/residue: 1.3049 time to fit residues: 2465.4273 Evaluate side-chains 1485 residues out of total 5316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1386 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PX residue 34 SER Chi-restraints excluded: chain PX residue 113 GLU Chi-restraints excluded: chain PX residue 114 LYS Chi-restraints excluded: chain PA residue 69 SER Chi-restraints excluded: chain PA residue 164 GLU Chi-restraints excluded: chain PA residue 236 LEU Chi-restraints excluded: chain PA residue 261 ARG Chi-restraints excluded: chain PA residue 365 SER Chi-restraints excluded: chain PA residue 376 GLU Chi-restraints excluded: chain PA residue 386 GLU Chi-restraints excluded: chain PA residue 391 ILE Chi-restraints excluded: chain PA residue 423 SER Chi-restraints excluded: chain PB residue 250 ASP Chi-restraints excluded: chain PB residue 261 ARG Chi-restraints excluded: chain PB residue 386 GLU Chi-restraints excluded: chain PC residue 56 THR Chi-restraints excluded: chain PC residue 69 SER Chi-restraints excluded: chain PC residue 146 ILE Chi-restraints excluded: chain PC residue 249 GLU Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PC residue 391 ILE Chi-restraints excluded: chain PC residue 401 GLU Chi-restraints excluded: chain PD residue 34 THR Chi-restraints excluded: chain PD residue 147 THR Chi-restraints excluded: chain PD residue 236 LEU Chi-restraints excluded: chain PD residue 261 ARG Chi-restraints excluded: chain PD residue 365 SER Chi-restraints excluded: chain PD residue 376 GLU Chi-restraints excluded: chain PD residue 386 GLU Chi-restraints excluded: chain PD residue 423 SER Chi-restraints excluded: chain PE residue 34 THR Chi-restraints excluded: chain PE residue 250 ASP Chi-restraints excluded: chain PE residue 261 ARG Chi-restraints excluded: chain PE residue 386 GLU Chi-restraints excluded: chain PF residue 56 THR Chi-restraints excluded: chain PF residue 60 LEU Chi-restraints excluded: chain PF residue 69 SER Chi-restraints excluded: chain PF residue 104 ASP Chi-restraints excluded: chain PF residue 146 ILE Chi-restraints excluded: chain PF residue 249 GLU Chi-restraints excluded: chain PF residue 261 ARG Chi-restraints excluded: chain PF residue 401 GLU Chi-restraints excluded: chain PG residue 34 THR Chi-restraints excluded: chain PG residue 69 SER Chi-restraints excluded: chain PG residue 236 LEU Chi-restraints excluded: chain PG residue 249 GLU Chi-restraints excluded: chain PG residue 261 ARG Chi-restraints excluded: chain PG residue 301 MET Chi-restraints excluded: chain PG residue 365 SER Chi-restraints excluded: chain PG residue 386 GLU Chi-restraints excluded: chain PG residue 413 GLU Chi-restraints excluded: chain PG residue 423 SER Chi-restraints excluded: chain PH residue 56 THR Chi-restraints excluded: chain PH residue 69 SER Chi-restraints excluded: chain PH residue 146 ILE Chi-restraints excluded: chain PH residue 249 GLU Chi-restraints excluded: chain PH residue 261 ARG Chi-restraints excluded: chain PH residue 386 GLU Chi-restraints excluded: chain PH residue 429 LYS Chi-restraints excluded: chain PI residue 69 SER Chi-restraints excluded: chain PI residue 104 ASP Chi-restraints excluded: chain PI residue 146 ILE Chi-restraints excluded: chain PI residue 210 ILE Chi-restraints excluded: chain PI residue 249 GLU Chi-restraints excluded: chain PI residue 261 ARG Chi-restraints excluded: chain PI residue 326 SER Chi-restraints excluded: chain PI residue 386 GLU Chi-restraints excluded: chain PI residue 429 LYS Chi-restraints excluded: chain PJ residue 56 THR Chi-restraints excluded: chain PJ residue 146 ILE Chi-restraints excluded: chain PJ residue 236 LEU Chi-restraints excluded: chain PJ residue 365 SER Chi-restraints excluded: chain PJ residue 386 GLU Chi-restraints excluded: chain PJ residue 391 ILE Chi-restraints excluded: chain PJ residue 423 SER Chi-restraints excluded: chain PK residue 69 SER Chi-restraints excluded: chain PK residue 261 ARG Chi-restraints excluded: chain PK residue 333 ARG Chi-restraints excluded: chain PK residue 386 GLU Chi-restraints excluded: chain PK residue 409 LEU Chi-restraints excluded: chain PL residue 56 THR Chi-restraints excluded: chain PL residue 69 SER Chi-restraints excluded: chain PL residue 141 GLU Chi-restraints excluded: chain PL residue 146 ILE Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PL residue 429 LYS Chi-restraints excluded: chain PN residue 18 THR Chi-restraints excluded: chain PO residue 66 ARG Chi-restraints excluded: chain PO residue 113 GLU Chi-restraints excluded: chain PP residue 66 ARG Chi-restraints excluded: chain PQ residue 96 SER Chi-restraints excluded: chain PR residue 66 ARG Chi-restraints excluded: chain PS residue 113 GLU Chi-restraints excluded: chain PT residue 66 ARG Chi-restraints excluded: chain PT residue 96 SER Chi-restraints excluded: chain PT residue 100 GLU Chi-restraints excluded: chain PT residue 113 GLU Chi-restraints excluded: chain PU residue 113 GLU Chi-restraints excluded: chain PV residue 113 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 400 optimal weight: 3.9990 chunk 537 optimal weight: 0.1980 chunk 154 optimal weight: 0.4980 chunk 465 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 505 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 518 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PX 28 GLN PX 39 ASN PX 117 GLN PA 393 GLN PC 92 HIS PC 393 GLN PD 36 GLN PF 92 HIS PI 92 HIS PI 392 GLN PJ 36 GLN PJ 92 HIS PJ 393 GLN PL 92 HIS PL 232 GLN PM 39 ASN PO 28 GLN PO 39 ASN PP 39 ASN PR 28 GLN PR 39 ASN PR 117 GLN PS 39 ASN PU 28 GLN PV 39 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.074322 restraints weight = 71000.766| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.68 r_work: 0.2647 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 51240 Z= 0.209 Angle : 0.625 12.957 69576 Z= 0.315 Chirality : 0.040 0.153 7536 Planarity : 0.004 0.047 9348 Dihedral : 7.101 84.169 6996 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.18 % Allowed : 23.31 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.10), residues: 6252 helix: 2.00 (0.09), residues: 3156 sheet: 1.55 (0.23), residues: 396 loop : -0.35 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPPB 134 HIS 0.004 0.001 HISPH 175 PHE 0.020 0.001 PHEPL 334 TYR 0.014 0.001 TYRPX 76 ARG 0.010 0.000 ARGPE 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34316.41 seconds wall clock time: 585 minutes 23.14 seconds (35123.14 seconds total)