Starting phenix.real_space_refine on Sat Dec 28 04:35:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsi_18633/12_2024/8qsi_18633.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsi_18633/12_2024/8qsi_18633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsi_18633/12_2024/8qsi_18633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsi_18633/12_2024/8qsi_18633.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsi_18633/12_2024/8qsi_18633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsi_18633/12_2024/8qsi_18633.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 31332 2.51 5 N 8640 2.21 5 O 10620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 326 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 50784 Number of models: 1 Model: "" Number of chains: 36 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: 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3144 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 19, 'TRANS': 381} 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: 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} Chain: "PX" 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: 22.18, per 1000 atoms: 0.44 Number of scatterers: 50784 At special positions: 0 Unit cell: (158.085, 158.085, 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 10620 8.00 N 8640 7.00 C 31332 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: 10.22 Conformation dependent library (CDL) restraints added in 5.0 seconds 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11928 Finding SS restraints... Secondary structure from input PDB file: 305 helices and 73 sheets defined 53.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'PM' and resid 5 through 9 removed outlier: 3.586A pdb=" N VALPM 9 " --> pdb=" O ILEPM 6 " (cutoff:3.500A) 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 115 through 118 Processing helix chain 'PM' and resid 119 through 129 removed outlier: 3.859A pdb=" N GLUPM 127 " --> pdb=" O ARGPM 123 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYRPM 128 " --> pdb=" O METPM 124 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VALPM 129 " --> pdb=" O ALAPM 125 " (cutoff:3.500A) Processing helix chain 'PM' and resid 130 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: 3.837A pdb=" N GLUPN 127 " --> pdb=" O ARGPN 123 " (cutoff:3.500A) removed outlier: 4.078A 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 115 through 118 Processing helix chain 'PO' and resid 119 through 129 removed outlier: 3.814A pdb=" N GLUPO 127 " --> pdb=" O ARGPO 123 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYRPO 128 " --> pdb=" O METPO 124 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VALPO 129 " --> pdb=" O ALAPO 125 " (cutoff:3.500A) Processing helix chain 'PO' and resid 130 through 133 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 115 through 118 Processing helix chain 'PP' and resid 119 through 128 removed outlier: 3.864A pdb=" N GLUPP 127 " --> pdb=" O ARGPP 123 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYRPP 128 " --> pdb=" O METPP 124 " (cutoff:3.500A) Processing helix chain 'PP' and resid 129 through 133 Processing helix chain 'PQ' and resid 5 through 9 removed outlier: 3.588A pdb=" N VALPQ 9 " --> pdb=" O ILEPQ 6 " (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 115 through 118 Processing helix chain 'PQ' and resid 119 through 127 removed outlier: 3.895A pdb=" N GLUPQ 127 " --> pdb=" O ARGPQ 123 " (cutoff:3.500A) Processing helix chain 'PQ' and resid 128 through 133 removed outlier: 6.265A pdb=" N GLUPQ 131 " --> pdb=" O TYRPQ 128 " (cutoff:3.500A) Processing helix chain 'PR' and resid 5 through 9 removed outlier: 3.625A 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 115 through 118 Processing helix chain 'PR' and resid 119 through 128 removed outlier: 3.883A pdb=" N GLUPR 127 " --> pdb=" O ARGPR 123 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYRPR 128 " --> pdb=" O METPR 124 " (cutoff:3.500A) Processing helix chain 'PR' and resid 129 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 115 through 118 Processing helix chain 'PS' and resid 119 through 128 removed outlier: 3.831A pdb=" N GLUPS 127 " --> pdb=" O ARGPS 123 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYRPS 128 " --> pdb=" O METPS 124 " (cutoff:3.500A) Processing helix chain 'PS' and resid 129 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 115 through 118 Processing helix chain 'PT' and resid 119 through 128 removed outlier: 3.831A pdb=" N GLUPT 127 " --> pdb=" O ARGPT 123 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYRPT 128 " --> pdb=" O METPT 124 " (cutoff:3.500A) Processing helix chain 'PT' and resid 129 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 115 through 118 Processing helix chain 'PU' and resid 119 through 128 removed outlier: 3.853A pdb=" N GLUPU 127 " --> pdb=" O ARGPU 123 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYRPU 128 " --> pdb=" O METPU 124 " (cutoff:3.500A) Processing helix chain 'PU' and resid 129 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 115 through 118 Processing helix chain 'PV' and resid 119 through 128 removed outlier: 3.829A pdb=" N GLUPV 127 " --> pdb=" O ARGPV 123 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYRPV 128 " --> pdb=" O METPV 124 " (cutoff:3.500A) Processing helix chain 'PV' and resid 129 through 133 Processing helix chain 'PW' and resid 5 through 9 removed outlier: 3.651A pdb=" N VALPW 9 " --> pdb=" O ILEPW 6 " (cutoff:3.500A) 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 115 through 118 Processing helix chain 'PW' and resid 119 through 128 removed outlier: 3.866A pdb=" N GLUPW 127 " --> pdb=" O ARGPW 123 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYRPW 128 " --> pdb=" O METPW 124 " (cutoff:3.500A) Processing helix chain 'PW' and resid 129 through 133 Processing helix chain 'PX' and resid 5 through 9 removed outlier: 3.629A pdb=" N VALPX 9 " --> pdb=" O ILEPX 6 " (cutoff:3.500A) 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 115 through 118 Processing helix chain 'PX' and resid 119 through 128 removed outlier: 3.862A pdb=" N GLUPX 127 " --> pdb=" O ARGPX 123 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYRPX 128 " --> pdb=" O METPX 124 " (cutoff:3.500A) Processing helix chain 'PX' and resid 129 through 133 Processing helix chain 'PA' and resid 56 through 69 Processing helix chain 'PA' and resid 70 through 86 removed outlier: 4.093A 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: 3.880A pdb=" N ARGPA 261 " --> pdb=" O ASNPA 257 " (cutoff:3.500A) Processing helix chain 'PA' and resid 294 through 310 Processing helix chain 'PA' and resid 313 through 318 Processing helix chain 'PA' and resid 326 through 356 removed outlier: 3.718A pdb=" N ARGPA 333 " --> pdb=" O PROPA 329 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLNPA 351 " --> pdb=" O SERPA 347 " (cutoff:3.500A) Processing helix chain 'PA' and resid 356 through 365 removed outlier: 3.672A 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 407 Processing helix chain 'PA' and resid 414 through 419 Processing helix chain 'PA' and resid 423 through 430 Processing helix chain 'PB' and resid 56 through 69 Processing helix chain 'PB' and resid 70 through 86 removed outlier: 4.097A pdb=" N ALAPB 74 " --> pdb=" O GLYPB 70 " (cutoff:3.500A) Processing helix chain 'PB' and resid 95 through 100 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: 3.948A 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 removed outlier: 3.544A pdb=" N ARGPB 333 " --> pdb=" O PROPB 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLNPB 351 " --> pdb=" O SERPB 347 " (cutoff:3.500A) Processing helix chain 'PB' and resid 356 through 365 removed outlier: 3.831A 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 407 Processing helix chain 'PB' and resid 414 through 419 Processing helix chain 'PB' and resid 423 through 430 Processing helix chain 'PC' and resid 56 through 69 Processing helix chain 'PC' and resid 70 through 86 removed outlier: 4.080A 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: 3.843A pdb=" N ARGPC 261 " --> pdb=" O ASNPC 257 " (cutoff:3.500A) Processing helix chain 'PC' and resid 294 through 310 Processing helix chain 'PC' and resid 313 through 318 Processing helix chain 'PC' and resid 326 through 356 removed outlier: 3.616A pdb=" N ARGPC 333 " --> pdb=" O PROPC 329 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLNPC 351 " --> pdb=" O SERPC 347 " (cutoff:3.500A) Processing helix chain 'PC' and resid 356 through 365 removed outlier: 3.779A pdb=" N SERPC 365 " --> pdb=" O VALPC 361 " (cutoff:3.500A) 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 419 Processing helix chain 'PC' and resid 423 through 430 Processing helix chain 'PD' and resid 56 through 69 Processing helix chain 'PD' and resid 70 through 86 removed outlier: 4.090A pdb=" N ALAPD 74 " --> pdb=" O GLYPD 70 " (cutoff:3.500A) Processing helix chain 'PD' and resid 95 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: 3.956A pdb=" N ARGPD 261 " --> pdb=" O ASNPD 257 " (cutoff:3.500A) Processing helix chain 'PD' and resid 294 through 310 Processing helix chain 'PD' and resid 313 through 318 Processing helix chain 'PD' and resid 326 through 356 removed outlier: 3.739A pdb=" N ARGPD 333 " --> pdb=" O PROPD 329 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLNPD 351 " --> pdb=" O SERPD 347 " (cutoff:3.500A) Processing helix chain 'PD' and resid 356 through 365 removed outlier: 3.803A 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 407 Processing helix chain 'PD' and resid 414 through 419 Processing helix chain 'PD' and resid 423 through 430 Processing helix chain 'PE' and resid 56 through 69 Processing helix chain 'PE' and resid 70 through 86 removed outlier: 4.152A pdb=" N ALAPE 74 " --> pdb=" O GLYPE 70 " (cutoff:3.500A) Processing helix chain 'PE' and resid 95 through 100 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 267 removed outlier: 3.768A 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 removed outlier: 3.744A pdb=" N ARGPE 333 " --> pdb=" O PROPE 329 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLNPE 351 " --> pdb=" O SERPE 347 " (cutoff:3.500A) Processing helix chain 'PE' and resid 356 through 364 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 407 Processing helix chain 'PE' and resid 414 through 419 Processing helix chain 'PE' and resid 423 through 430 Processing helix chain 'PF' and resid 56 through 69 Processing helix chain 'PF' and resid 70 through 86 removed outlier: 4.134A pdb=" N ALAPF 74 " --> pdb=" O GLYPF 70 " (cutoff:3.500A) Processing helix chain 'PF' and resid 95 through 100 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 267 removed outlier: 3.918A pdb=" N ARGPF 261 " --> pdb=" O ASNPF 257 " (cutoff:3.500A) Processing helix chain 'PF' and resid 294 through 310 Processing helix chain 'PF' and resid 313 through 318 Processing helix chain 'PF' and resid 326 through 356 removed outlier: 3.558A pdb=" N ARGPF 333 " --> pdb=" O PROPF 329 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLNPF 351 " --> pdb=" O SERPF 347 " (cutoff:3.500A) Processing helix chain 'PF' and resid 356 through 365 removed outlier: 3.868A 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 408 Processing helix chain 'PF' and resid 414 through 419 Processing helix chain 'PF' and resid 423 through 430 Processing helix chain 'PG' and resid 56 through 69 Processing helix chain 'PG' and resid 70 through 86 removed outlier: 4.140A 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: 3.862A pdb=" N ARGPG 261 " --> pdb=" O ASNPG 257 " (cutoff:3.500A) Processing helix chain 'PG' and resid 294 through 310 Processing helix chain 'PG' and resid 313 through 318 Processing helix chain 'PG' and resid 326 through 356 removed outlier: 3.730A pdb=" N ARGPG 333 " --> pdb=" O PROPG 329 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLNPG 351 " --> pdb=" O SERPG 347 " (cutoff:3.500A) Processing helix chain 'PG' and resid 356 through 365 removed outlier: 3.839A 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 407 Processing helix chain 'PG' and resid 414 through 419 Processing helix chain 'PG' and resid 423 through 430 Processing helix chain 'PH' and resid 56 through 69 Processing helix chain 'PH' and resid 70 through 86 removed outlier: 4.173A pdb=" N ALAPH 74 " --> pdb=" O GLYPH 70 " (cutoff:3.500A) Processing helix chain 'PH' and resid 95 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: 3.875A pdb=" N ARGPH 261 " --> pdb=" O ASNPH 257 " (cutoff:3.500A) Processing helix chain 'PH' and resid 294 through 310 Processing helix chain 'PH' and resid 313 through 318 Processing helix chain 'PH' and resid 326 through 356 removed outlier: 3.582A pdb=" N ARGPH 333 " --> pdb=" O PROPH 329 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLNPH 351 " --> pdb=" O SERPH 347 " (cutoff:3.500A) Processing helix chain 'PH' and resid 356 through 364 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 419 Processing helix chain 'PH' and resid 423 through 430 Processing helix chain 'PI' and resid 56 through 69 Processing helix chain 'PI' and resid 70 through 86 removed outlier: 4.136A 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 267 removed outlier: 3.916A pdb=" N ARGPI 261 " --> pdb=" O ASNPI 257 " (cutoff:3.500A) Processing helix chain 'PI' and resid 294 through 310 Processing helix chain 'PI' and resid 313 through 318 Processing helix chain 'PI' and resid 326 through 356 removed outlier: 3.648A pdb=" N ARGPI 333 " --> pdb=" O PROPI 329 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLNPI 351 " --> pdb=" O SERPI 347 " (cutoff:3.500A) Processing helix chain 'PI' and resid 356 through 365 removed outlier: 3.824A 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 419 Processing helix chain 'PI' and resid 423 through 430 Processing helix chain 'PJ' and resid 56 through 69 Processing helix chain 'PJ' and resid 70 through 86 removed outlier: 4.085A pdb=" N ALAPJ 74 " --> pdb=" O GLYPJ 70 " (cutoff:3.500A) Processing helix chain 'PJ' and resid 95 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 267 removed outlier: 3.915A pdb=" N ARGPJ 261 " --> pdb=" O ASNPJ 257 " (cutoff:3.500A) Processing helix chain 'PJ' and resid 294 through 310 Processing helix chain 'PJ' and resid 313 through 318 Processing helix chain 'PJ' and resid 326 through 356 removed outlier: 3.644A pdb=" N ARGPJ 333 " --> pdb=" O PROPJ 329 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLNPJ 351 " --> pdb=" O SERPJ 347 " (cutoff:3.500A) Processing helix chain 'PJ' and resid 356 through 364 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 419 Processing helix chain 'PJ' and resid 423 through 430 Processing helix chain 'PK' and resid 56 through 69 Processing helix chain 'PK' and resid 70 through 86 removed outlier: 4.117A 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: 3.936A 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 removed outlier: 3.706A pdb=" N ARGPK 333 " --> pdb=" O PROPK 329 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLNPK 351 " --> pdb=" O SERPK 347 " (cutoff:3.500A) Processing helix chain 'PK' and resid 356 through 365 removed outlier: 3.750A pdb=" N SERPK 365 " --> pdb=" O VALPK 361 " (cutoff:3.500A) 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 407 Processing helix chain 'PK' and resid 414 through 419 Processing helix chain 'PK' and resid 423 through 430 Processing helix chain 'PL' and resid 56 through 69 Processing helix chain 'PL' and resid 70 through 86 removed outlier: 4.068A 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: 3.849A pdb=" N ARGPL 261 " --> pdb=" O ASNPL 257 " (cutoff:3.500A) Processing helix chain 'PL' and resid 294 through 310 Processing helix chain 'PL' and resid 313 through 318 Processing helix chain 'PL' and resid 326 through 356 removed outlier: 3.634A pdb=" N ARGPL 333 " --> pdb=" O PROPL 329 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLNPL 351 " --> pdb=" O SERPL 347 " (cutoff:3.500A) Processing helix chain 'PL' and resid 356 through 365 removed outlier: 3.855A pdb=" N SERPL 365 " --> pdb=" O VALPL 361 " (cutoff:3.500A) 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 419 Processing helix chain 'PL' and resid 423 through 430 Processing sheet with id=AA1, first strand: chain 'PM' and resid 63 through 64 Processing sheet with id=AA2, first strand: chain 'PM' and resid 94 through 99 removed outlier: 5.920A pdb=" N GLNPM 95 " --> pdb=" O TYRPM 106 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SERPM 103 " --> pdb=" O GLUPN 97 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLUPN 97 " --> pdb=" O SERPM 103 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SERPM 105 " --> pdb=" O GLNPN 95 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLNPN 95 " --> pdb=" O TYRPN 106 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLYPN 102 " --> pdb=" O GLYPN 99 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SERPN 103 " --> pdb=" O GLUPO 97 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLUPO 97 " --> pdb=" O SERPN 103 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SERPN 105 " --> pdb=" O GLNPO 95 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLNPO 95 " --> pdb=" O TYRPO 106 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SERPO 103 " --> pdb=" O GLUPP 97 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLUPP 97 " --> pdb=" O SERPO 103 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SERPO 105 " --> pdb=" O GLNPP 95 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLNPP 95 " --> pdb=" O TYRPP 106 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SERPP 103 " --> pdb=" O GLUPQ 97 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLUPQ 97 " --> pdb=" O SERPP 103 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SERPP 105 " --> pdb=" O GLNPQ 95 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLUPQ 93 " --> pdb=" O SERPP 107 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLNPQ 95 " --> pdb=" O TYRPQ 106 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SERPQ 103 " --> pdb=" O GLUPR 97 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLUPR 97 " --> pdb=" O SERPQ 103 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SERPQ 105 " --> pdb=" O GLNPR 95 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLNPR 95 " --> pdb=" O TYRPR 106 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SERPR 103 " --> pdb=" O GLUPS 97 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLUPS 97 " --> pdb=" O SERPR 103 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SERPR 105 " --> pdb=" O GLNPS 95 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLNPS 95 " --> pdb=" O TYRPS 106 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SERPS 103 " --> pdb=" O GLUPT 97 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLUPT 97 " --> pdb=" O SERPS 103 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SERPS 105 " --> pdb=" O GLNPT 95 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLNPT 95 " --> pdb=" O TYRPT 106 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SERPT 103 " --> pdb=" O GLUPU 97 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLUPU 97 " --> pdb=" O SERPT 103 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SERPT 105 " --> pdb=" O GLNPU 95 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLUPU 93 " --> pdb=" O SERPT 107 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLNPU 95 " --> pdb=" O TYRPU 106 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SERPU 103 " --> pdb=" O GLUPV 97 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLUPV 97 " --> pdb=" O SERPU 103 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SERPU 105 " --> pdb=" O GLNPV 95 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLNPV 95 " --> pdb=" O TYRPV 106 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SERPV 103 " --> pdb=" O GLUPW 97 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLUPW 97 " --> pdb=" O SERPV 103 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SERPV 105 " --> pdb=" O GLNPW 95 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLNPW 95 " --> pdb=" O TYRPW 106 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SERPW 103 " --> pdb=" O GLUPX 97 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLUPX 97 " --> pdb=" O SERPW 103 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N SERPW 105 " --> pdb=" O GLNPX 95 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLNPX 95 " --> pdb=" O TYRPX 106 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SERPX 103 " --> pdb=" O GLUPM 97 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLUPM 97 " --> pdb=" O SERPX 103 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SERPX 105 " --> pdb=" O GLNPM 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'PM' and resid 137 through 139 Processing sheet with id=AA4, first strand: chain 'PN' and resid 63 through 64 Processing sheet with id=AA5, first strand: chain 'PN' and resid 137 through 139 Processing sheet with id=AA6, first strand: chain 'PO' and resid 63 through 64 Processing sheet with id=AA7, first strand: chain 'PO' and resid 137 through 139 Processing sheet with id=AA8, first strand: chain 'PP' and resid 63 through 64 Processing sheet with id=AA9, first strand: chain 'PP' and resid 137 through 139 Processing sheet with id=AB1, first strand: chain 'PQ' and resid 63 through 64 Processing sheet with id=AB2, first strand: chain 'PQ' and resid 137 through 139 Processing sheet with id=AB3, first strand: chain 'PR' and resid 63 through 64 Processing sheet with id=AB4, first strand: chain 'PR' and resid 137 through 139 Processing sheet with id=AB5, first strand: chain 'PS' and resid 63 through 64 Processing sheet with id=AB6, first strand: chain 'PS' and resid 137 through 139 Processing sheet with id=AB7, first strand: chain 'PT' and resid 63 through 64 Processing sheet with id=AB8, first strand: chain 'PT' and resid 137 through 139 removed outlier: 6.403A pdb=" N TYRPA 277 " --> pdb=" O VALPL 244 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VALPL 246 " --> pdb=" O TYRPA 277 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THRPA 279 " --> pdb=" O VALPL 246 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'PU' and resid 63 through 64 Processing sheet with id=AC1, first strand: chain 'PU' and resid 137 through 139 removed outlier: 6.444A pdb=" N ARGPA 242 " --> pdb=" O TYRPB 277 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THRPB 279 " --> pdb=" O ARGPA 242 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VALPA 244 " --> pdb=" O THRPB 279 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'PV' and resid 63 through 64 Processing sheet with id=AC3, first strand: chain 'PV' and resid 137 through 139 Processing sheet with id=AC4, first strand: chain 'PW' and resid 63 through 64 Processing sheet with id=AC5, first strand: chain 'PW' and resid 137 through 139 Processing sheet with id=AC6, first strand: chain 'PX' and resid 63 through 64 Processing sheet with id=AC7, first strand: chain 'PX' and resid 137 through 139 Processing sheet with id=AC8, first strand: chain 'PA' and resid 89 through 94 removed outlier: 4.658A pdb=" N ASPPA 372 " --> pdb=" O GLUPA 94 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'PA' and resid 101 through 102 Processing sheet with id=AD1, first strand: chain 'PA' and resid 150 through 156 removed outlier: 6.919A pdb=" N GLNPA 143 " --> pdb=" O LYSPA 151 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALAPA 153 " --> pdb=" O GLUPA 141 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLUPA 141 " --> pdb=" O ALAPA 153 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VALPA 139 " --> pdb=" O PROPA 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'PA' and resid 161 through 165 Processing sheet with id=AD3, first strand: chain 'PB' and resid 89 through 93 Processing sheet with id=AD4, first strand: chain 'PB' and resid 101 through 102 Processing sheet with id=AD5, first strand: chain 'PB' and resid 150 through 156 removed outlier: 4.814A pdb=" N VALPB 139 " --> pdb=" O ALAPB 156 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'PB' and resid 161 through 165 Processing sheet with id=AD7, first strand: chain 'PC' and resid 89 through 94 removed outlier: 4.630A pdb=" N ASPPC 372 " --> pdb=" O GLUPC 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'PC' and resid 101 through 102 Processing sheet with id=AD9, first strand: chain 'PC' and resid 150 through 156 removed outlier: 3.506A pdb=" N GLUPC 152 " --> pdb=" O GLNPC 143 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VALPC 139 " --> pdb=" O ALAPC 156 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'PC' and resid 161 through 165 Processing sheet with id=AE2, first strand: chain 'PD' and resid 89 through 94 removed outlier: 4.690A pdb=" N ASPPD 372 " --> pdb=" O GLUPD 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'PD' and resid 101 through 102 Processing sheet with id=AE4, first strand: chain 'PD' and resid 150 through 156 removed outlier: 3.590A pdb=" N GLUPD 152 " --> pdb=" O GLNPD 143 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VALPD 139 " --> pdb=" O ALAPD 156 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'PD' and resid 161 through 165 Processing sheet with id=AE6, first strand: chain 'PE' and resid 89 through 93 Processing sheet with id=AE7, first strand: chain 'PE' and resid 101 through 102 Processing sheet with id=AE8, first strand: chain 'PE' and resid 150 through 155 removed outlier: 6.937A pdb=" N GLNPE 143 " --> pdb=" O LYSPE 151 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALAPE 153 " --> pdb=" O GLUPE 141 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLUPE 141 " --> pdb=" O ALAPE 153 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VALPE 139 " --> pdb=" O PROPE 155 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'PE' and resid 161 through 165 removed outlier: 3.502A pdb=" N ALAPE 173 " --> pdb=" O GLUPE 164 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'PF' and resid 89 through 93 Processing sheet with id=AF2, first strand: chain 'PF' and resid 101 through 102 Processing sheet with id=AF3, first strand: chain 'PF' and resid 150 through 156 removed outlier: 3.512A pdb=" N GLUPF 152 " --> pdb=" O GLNPF 143 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VALPF 139 " --> pdb=" O ALAPF 156 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'PF' and resid 161 through 165 Processing sheet with id=AF5, first strand: chain 'PG' and resid 89 through 93 Processing sheet with id=AF6, first strand: chain 'PG' and resid 101 through 102 Processing sheet with id=AF7, first strand: chain 'PG' and resid 150 through 155 removed outlier: 6.920A pdb=" N GLNPG 143 " --> pdb=" O LYSPG 151 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALAPG 153 " --> pdb=" O GLUPG 141 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLUPG 141 " --> pdb=" O ALAPG 153 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VALPG 139 " --> pdb=" O PROPG 155 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'PG' and resid 161 through 165 Processing sheet with id=AF9, first strand: chain 'PH' and resid 89 through 94 removed outlier: 4.648A pdb=" N ASPPH 372 " --> pdb=" O GLUPH 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'PH' and resid 101 through 102 Processing sheet with id=AG2, first strand: chain 'PH' and resid 150 through 155 Processing sheet with id=AG3, first strand: chain 'PH' and resid 161 through 165 Processing sheet with id=AG4, first strand: chain 'PI' and resid 89 through 93 Processing sheet with id=AG5, first strand: chain 'PI' and resid 101 through 102 Processing sheet with id=AG6, first strand: chain 'PI' and resid 150 through 156 removed outlier: 6.969A pdb=" N GLNPI 143 " --> pdb=" O LYSPI 151 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALAPI 153 " --> pdb=" O GLUPI 141 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLUPI 141 " --> pdb=" O ALAPI 153 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VALPI 139 " --> pdb=" O PROPI 155 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'PI' and resid 161 through 165 Processing sheet with id=AG8, first strand: chain 'PJ' and resid 89 through 94 removed outlier: 4.659A pdb=" N ASPPJ 372 " --> pdb=" O GLUPJ 94 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'PJ' and resid 101 through 102 Processing sheet with id=AH1, first strand: chain 'PJ' and resid 150 through 155 removed outlier: 6.932A pdb=" N GLNPJ 143 " --> pdb=" O LYSPJ 151 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALAPJ 153 " --> pdb=" O GLUPJ 141 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLUPJ 141 " --> pdb=" O ALAPJ 153 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VALPJ 139 " --> pdb=" O PROPJ 155 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'PJ' and resid 161 through 165 Processing sheet with id=AH3, first strand: chain 'PK' and resid 89 through 93 Processing sheet with id=AH4, first strand: chain 'PK' and resid 101 through 102 Processing sheet with id=AH5, first strand: chain 'PK' and resid 150 through 156 removed outlier: 3.549A pdb=" N GLUPK 152 " --> pdb=" O GLNPK 143 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VALPK 139 " --> pdb=" O ALAPK 156 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'PK' and resid 161 through 165 Processing sheet with id=AH7, first strand: chain 'PL' and resid 89 through 93 Processing sheet with id=AH8, first strand: chain 'PL' and resid 101 through 102 Processing sheet with id=AH9, first strand: chain 'PL' and resid 150 through 156 removed outlier: 3.503A pdb=" N GLUPL 152 " --> pdb=" O GLNPL 143 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VALPL 139 " --> pdb=" O ALAPL 156 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'PL' and resid 161 through 165 removed outlier: 3.518A pdb=" N ALAPL 173 " --> pdb=" O GLUPL 164 " (cutoff:3.500A) 2781 hydrogen bonds defined for protein. 7803 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: 18.15 Time building geometry restraints manager: 11.71 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: 12135 1.33 - 1.46: 12378 1.46 - 1.58: 26871 1.58 - 1.70: 0 1.70 - 1.82: 312 Bond restraints: 51696 Sorted by residual: bond pdb=" ND1 HIPPB 291 " pdb=" P HIPPB 291 " ideal model delta sigma weight residual 1.928 1.715 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" ND1 HIPPH 291 " pdb=" P HIPPH 291 " ideal model delta sigma weight residual 1.928 1.716 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" ND1 HIPPJ 291 " pdb=" P HIPPJ 291 " ideal model delta sigma weight residual 1.928 1.716 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" ND1 HIPPL 291 " pdb=" P HIPPL 291 " ideal model delta sigma weight residual 1.928 1.716 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" ND1 HIPPD 291 " pdb=" P HIPPD 291 " ideal model delta sigma weight residual 1.928 1.716 0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 51691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 59508 2.00 - 3.99: 9296 3.99 - 5.99: 1212 5.99 - 7.98: 168 7.98 - 9.98: 4 Bond angle restraints: 70188 Sorted by residual: angle pdb=" CA ASPPB 166 " pdb=" CB ASPPB 166 " pdb=" CG ASPPB 166 " ideal model delta sigma weight residual 112.60 118.27 -5.67 1.00e+00 1.00e+00 3.21e+01 angle pdb=" CA ASPPA 166 " pdb=" CB ASPPA 166 " pdb=" CG ASPPA 166 " ideal model delta sigma weight residual 112.60 118.18 -5.58 1.00e+00 1.00e+00 3.12e+01 angle pdb=" CA ASPPK 166 " pdb=" CB ASPPK 166 " pdb=" CG ASPPK 166 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" CA ASPPJ 166 " pdb=" CB ASPPJ 166 " pdb=" CG ASPPJ 166 " ideal model delta sigma weight residual 112.60 118.13 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CA ASPPF 166 " pdb=" CB ASPPF 166 " pdb=" CG ASPPF 166 " ideal model delta sigma weight residual 112.60 118.07 -5.47 1.00e+00 1.00e+00 2.99e+01 ... (remaining 70183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 28247 17.80 - 35.60: 2229 35.60 - 53.40: 345 53.40 - 71.20: 107 71.20 - 88.99: 104 Dihedral angle restraints: 31032 sinusoidal: 12456 harmonic: 18576 Sorted by residual: dihedral pdb=" CA TYRPE 137 " pdb=" C TYRPE 137 " pdb=" N ALAPE 138 " pdb=" CA ALAPE 138 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA TYRPG 137 " pdb=" C TYRPG 137 " pdb=" N ALAPG 138 " pdb=" CA ALAPG 138 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA TYRPI 137 " pdb=" C TYRPI 137 " pdb=" N ALAPI 138 " pdb=" CA ALAPI 138 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 31029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4695 0.087 - 0.175: 2166 0.175 - 0.262: 619 0.262 - 0.349: 54 0.349 - 0.437: 50 Chirality restraints: 7584 Sorted by residual: chirality pdb=" CA ARGPV 66 " pdb=" N ARGPV 66 " pdb=" C ARGPV 66 " pdb=" CB ARGPV 66 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA ARGPX 66 " pdb=" N ARGPX 66 " pdb=" C ARGPX 66 " pdb=" CB ARGPX 66 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA ARGPU 66 " pdb=" N ARGPU 66 " pdb=" C ARGPU 66 " pdb=" CB ARGPU 66 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 ... (remaining 7581 not shown) Planarity restraints: 9456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIPPL 291 " -0.075 2.00e-02 2.50e+03 7.47e-02 9.77e+01 pdb=" CG HIPPL 291 " 0.024 2.00e-02 2.50e+03 pdb=" ND1 HIPPL 291 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 HIPPL 291 " 0.104 2.00e-02 2.50e+03 pdb=" CE1 HIPPL 291 " -0.100 2.00e-02 2.50e+03 pdb=" NE2 HIPPL 291 " 0.014 2.00e-02 2.50e+03 pdb=" P HIPPL 291 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIPPF 291 " 0.070 2.00e-02 2.50e+03 6.53e-02 7.46e+01 pdb=" CG HIPPF 291 " -0.026 2.00e-02 2.50e+03 pdb=" ND1 HIPPF 291 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 HIPPF 291 " -0.094 2.00e-02 2.50e+03 pdb=" CE1 HIPPF 291 " 0.085 2.00e-02 2.50e+03 pdb=" NE2 HIPPF 291 " -0.004 2.00e-02 2.50e+03 pdb=" P HIPPF 291 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIPPC 291 " 0.066 2.00e-02 2.50e+03 6.48e-02 7.36e+01 pdb=" CG HIPPC 291 " -0.022 2.00e-02 2.50e+03 pdb=" ND1 HIPPC 291 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 HIPPC 291 " -0.091 2.00e-02 2.50e+03 pdb=" CE1 HIPPC 291 " 0.087 2.00e-02 2.50e+03 pdb=" NE2 HIPPC 291 " -0.010 2.00e-02 2.50e+03 pdb=" P HIPPC 291 " -0.079 2.00e-02 2.50e+03 ... (remaining 9453 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 73 2.52 - 3.12: 36911 3.12 - 3.71: 79235 3.71 - 4.31: 116019 4.31 - 4.90: 190866 Nonbonded interactions: 423104 Sorted by model distance: nonbonded pdb=" OE2 GLUPO 131 " pdb="MG MGPO 201 " model vdw 1.925 2.170 nonbonded pdb=" OE2 GLUPW 131 " pdb="MG MGPW 201 " model vdw 1.931 2.170 nonbonded pdb=" OE2 GLUPU 131 " pdb="MG MGPU 201 " model vdw 1.933 2.170 nonbonded pdb=" OE2 GLUPX 131 " pdb="MG MGPX 201 " model vdw 1.933 2.170 nonbonded pdb=" OE2 GLUPR 131 " pdb="MG MGPR 201 " model vdw 1.934 2.170 ... (remaining 423099 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: 1.890 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: 0.060 Extract box with map and model: 1.610 Check model and map are aligned: 0.310 Set scattering table: 0.370 Process input model: 87.340 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 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 0.213 51696 Z= 0.664 Angle : 1.474 9.979 70188 Z= 0.946 Chirality : 0.104 0.437 7584 Planarity : 0.009 0.075 9456 Dihedral : 14.452 88.994 19104 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.39 % Allowed : 5.28 % Favored : 94.33 % Cbeta Deviations : 0.47 % 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: -0.88 (0.10), residues: 6312 helix: -0.41 (0.08), residues: 3156 sheet: -0.08 (0.22), residues: 540 loop : -0.72 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.015 TRPPE 195 HIS 0.017 0.004 HISPJ 175 PHE 0.051 0.009 PHEPB 278 TYR 0.097 0.014 TYRPD 137 ARG 0.019 0.002 ARGPX 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1539 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 1518 time to evaluate : 4.521 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: PM 11 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8906 (ttmt) REVERT: PM 20 GLN cc_start: 0.9302 (tp40) cc_final: 0.8922 (tp-100) REVERT: PN 20 GLN cc_start: 0.9342 (tp40) cc_final: 0.9074 (tp-100) REVERT: PP 3 ASP cc_start: 0.8468 (t0) cc_final: 0.8240 (m-30) REVERT: PP 11 LYS cc_start: 0.9157 (ttmt) cc_final: 0.8613 (ttmt) REVERT: PP 40 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8910 (m) REVERT: PP 90 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8325 (mm-30) REVERT: PR 11 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8767 (ttpt) REVERT: PT 20 GLN cc_start: 0.9268 (tp40) cc_final: 0.8478 (tp40) REVERT: PT 64 MET cc_start: 0.9007 (mtm) cc_final: 0.8797 (mtm) REVERT: PU 100 GLU cc_start: 0.6789 (tt0) cc_final: 0.6583 (tt0) REVERT: PU 108 THR cc_start: 0.7701 (p) cc_final: 0.7445 (m) REVERT: PV 11 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8702 (ttmt) REVERT: PV 20 GLN cc_start: 0.9337 (tp40) cc_final: 0.9027 (tp40) REVERT: PW 20 GLN cc_start: 0.9209 (tp40) cc_final: 0.8495 (tp40) REVERT: PA 59 ASP cc_start: 0.8939 (m-30) cc_final: 0.8699 (m-30) REVERT: PA 65 ASP cc_start: 0.8827 (t70) cc_final: 0.8536 (t70) REVERT: PA 177 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.7935 (ttt180) REVERT: PA 184 TYR cc_start: 0.8788 (m-80) cc_final: 0.8378 (m-80) REVERT: PA 249 GLU cc_start: 0.9009 (tt0) cc_final: 0.8777 (tp30) REVERT: PA 329 PRO cc_start: 0.9515 (Cg_exo) cc_final: 0.9269 (Cg_endo) REVERT: PA 331 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8754 (mt-10) REVERT: PA 372 ASP cc_start: 0.8806 (m-30) cc_final: 0.8552 (t0) REVERT: PA 383 ASP cc_start: 0.8411 (t0) cc_final: 0.7804 (t0) REVERT: PA 389 ASP cc_start: 0.8864 (m-30) cc_final: 0.8566 (m-30) REVERT: PA 426 ASP cc_start: 0.9079 (m-30) cc_final: 0.8834 (t0) REVERT: PA 429 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8642 (tppt) REVERT: PB 36 GLN cc_start: 0.8829 (pt0) cc_final: 0.8326 (pt0) REVERT: PB 59 ASP cc_start: 0.8861 (m-30) cc_final: 0.8634 (m-30) REVERT: PB 65 ASP cc_start: 0.8814 (t70) cc_final: 0.8570 (t70) REVERT: PB 108 MET cc_start: 0.8905 (mtp) cc_final: 0.8601 (mtm) REVERT: PB 170 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8233 (pptt) REVERT: PB 328 LYS cc_start: 0.9209 (mttt) cc_final: 0.8982 (mmtm) REVERT: PB 372 ASP cc_start: 0.8741 (m-30) cc_final: 0.8371 (t0) REVERT: PB 397 TYR cc_start: 0.9408 (m-80) cc_final: 0.9202 (m-80) REVERT: PB 426 ASP cc_start: 0.9106 (m-30) cc_final: 0.8766 (t0) REVERT: PC 36 GLN cc_start: 0.8731 (pt0) cc_final: 0.8442 (pt0) REVERT: PC 65 ASP cc_start: 0.8740 (t70) cc_final: 0.8410 (m-30) REVERT: PC 108 MET cc_start: 0.8963 (mtp) cc_final: 0.8632 (mtp) REVERT: PC 249 GLU cc_start: 0.8973 (tt0) cc_final: 0.8754 (tp30) REVERT: PC 331 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8736 (mp0) REVERT: PC 389 ASP cc_start: 0.8999 (m-30) cc_final: 0.8776 (m-30) REVERT: PC 426 ASP cc_start: 0.9058 (m-30) cc_final: 0.8852 (t0) REVERT: PC 429 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8815 (ttmm) REVERT: PD 59 ASP cc_start: 0.8985 (m-30) cc_final: 0.8712 (m-30) REVERT: PD 65 ASP cc_start: 0.8869 (t70) cc_final: 0.8568 (t70) REVERT: PD 87 GLU cc_start: 0.8635 (tp30) cc_final: 0.8413 (tm-30) REVERT: PD 177 ARG cc_start: 0.8243 (ttt-90) cc_final: 0.7948 (ttt180) REVERT: PD 184 TYR cc_start: 0.8722 (m-80) cc_final: 0.8415 (m-80) REVERT: PD 329 PRO cc_start: 0.9561 (Cg_exo) cc_final: 0.9331 (Cg_endo) REVERT: PD 331 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8757 (mt-10) REVERT: PD 372 ASP cc_start: 0.8804 (m-30) cc_final: 0.8604 (t0) REVERT: PD 389 ASP cc_start: 0.8868 (m-30) cc_final: 0.8620 (m-30) REVERT: PD 426 ASP cc_start: 0.9125 (m-30) cc_final: 0.8805 (t0) REVERT: PE 59 ASP cc_start: 0.8836 (m-30) cc_final: 0.8630 (m-30) REVERT: PE 108 MET cc_start: 0.8882 (mtp) cc_final: 0.8529 (mtm) REVERT: PE 328 LYS cc_start: 0.9197 (mttt) cc_final: 0.8827 (mptt) REVERT: PE 331 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8706 (mt-10) REVERT: PE 372 ASP cc_start: 0.8693 (m-30) cc_final: 0.8459 (t0) REVERT: PE 415 ASP cc_start: 0.9179 (m-30) cc_final: 0.8931 (p0) REVERT: PE 421 TYR cc_start: 0.9005 (m-80) cc_final: 0.8660 (m-80) REVERT: PE 426 ASP cc_start: 0.9137 (m-30) cc_final: 0.8772 (t0) REVERT: PE 429 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8867 (ttmm) REVERT: PF 58 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8623 (mp0) REVERT: PF 65 ASP cc_start: 0.8748 (t70) cc_final: 0.8482 (m-30) REVERT: PF 108 MET cc_start: 0.8998 (mtp) cc_final: 0.8789 (mtm) REVERT: PF 177 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.8223 (ttt90) REVERT: PF 184 TYR cc_start: 0.8571 (m-80) cc_final: 0.8359 (m-80) REVERT: PF 413 GLU cc_start: 0.8982 (tp30) cc_final: 0.8676 (pm20) REVERT: PF 416 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8857 (tm-30) REVERT: PF 426 ASP cc_start: 0.9052 (m-30) cc_final: 0.8809 (t0) REVERT: PF 429 LYS cc_start: 0.9102 (ttmt) cc_final: 0.8876 (ttmm) REVERT: PG 59 ASP cc_start: 0.8924 (m-30) cc_final: 0.8685 (m-30) REVERT: PG 87 GLU cc_start: 0.8742 (tp30) cc_final: 0.8468 (tm-30) REVERT: PG 108 MET cc_start: 0.8952 (mtp) cc_final: 0.8675 (mtm) REVERT: PG 177 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.7911 (ttt180) REVERT: PG 184 TYR cc_start: 0.8747 (m-80) cc_final: 0.8200 (m-80) REVERT: PG 249 GLU cc_start: 0.8950 (tt0) cc_final: 0.8738 (tp30) REVERT: PG 331 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8714 (mt-10) REVERT: PG 372 ASP cc_start: 0.8799 (m-30) cc_final: 0.8582 (t0) REVERT: PG 389 ASP cc_start: 0.8924 (m-30) cc_final: 0.8633 (m-30) REVERT: PG 416 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8740 (tm-30) REVERT: PG 426 ASP cc_start: 0.9088 (m-30) cc_final: 0.8872 (t0) REVERT: PG 429 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8788 (ttmm) REVERT: PH 59 ASP cc_start: 0.8933 (m-30) cc_final: 0.8652 (m-30) REVERT: PH 269 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8650 (ttm170) REVERT: PH 328 LYS cc_start: 0.9263 (mttt) cc_final: 0.8995 (mmtm) REVERT: PH 397 TYR cc_start: 0.9343 (m-80) cc_final: 0.9135 (m-80) REVERT: PH 426 ASP cc_start: 0.9055 (m-30) cc_final: 0.8719 (t0) REVERT: PI 58 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8764 (mp0) REVERT: PI 108 MET cc_start: 0.8936 (mtp) cc_final: 0.8604 (mtp) REVERT: PI 301 MET cc_start: 0.8813 (ttp) cc_final: 0.8425 (ttt) REVERT: PI 331 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8792 (mp0) REVERT: PI 389 ASP cc_start: 0.8879 (m-30) cc_final: 0.8676 (m-30) REVERT: PI 426 ASP cc_start: 0.9072 (m-30) cc_final: 0.8827 (t0) REVERT: PI 429 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8915 (ttmm) REVERT: PJ 65 ASP cc_start: 0.8834 (t70) cc_final: 0.8607 (t70) REVERT: PJ 177 ARG cc_start: 0.8242 (ttt-90) cc_final: 0.7962 (ttt180) REVERT: PJ 184 TYR cc_start: 0.8681 (m-80) cc_final: 0.8318 (m-80) REVERT: PJ 249 GLU cc_start: 0.8990 (tt0) cc_final: 0.8779 (tp30) REVERT: PJ 329 PRO cc_start: 0.9567 (Cg_exo) cc_final: 0.9306 (Cg_endo) REVERT: PJ 331 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8795 (mt-10) REVERT: PJ 372 ASP cc_start: 0.8787 (m-30) cc_final: 0.8536 (t0) REVERT: PJ 389 ASP cc_start: 0.8887 (m-30) cc_final: 0.8630 (m-30) REVERT: PJ 426 ASP cc_start: 0.9056 (m-30) cc_final: 0.8825 (t0) REVERT: PJ 429 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8881 (ttmm) REVERT: PK 36 GLN cc_start: 0.8810 (pt0) cc_final: 0.8368 (pt0) REVERT: PK 59 ASP cc_start: 0.8918 (m-30) cc_final: 0.8640 (m-30) REVERT: PK 65 ASP cc_start: 0.8876 (t70) cc_final: 0.8635 (t70) REVERT: PK 108 MET cc_start: 0.8978 (mtp) cc_final: 0.8694 (mtm) REVERT: PK 177 ARG cc_start: 0.8397 (ttt-90) cc_final: 0.8035 (ttt90) REVERT: PK 328 LYS cc_start: 0.9190 (mttt) cc_final: 0.8831 (mmtm) REVERT: PK 331 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8682 (mt-10) REVERT: PK 426 ASP cc_start: 0.9028 (m-30) cc_final: 0.8687 (t0) REVERT: PK 429 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8617 (tppp) REVERT: PL 58 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8644 (mp0) REVERT: PL 108 MET cc_start: 0.8972 (mtp) cc_final: 0.8742 (mtm) REVERT: PL 177 ARG cc_start: 0.8423 (ttt-90) cc_final: 0.8144 (ttt90) REVERT: PL 184 TYR cc_start: 0.8598 (m-80) cc_final: 0.8222 (m-80) REVERT: PL 331 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8736 (mt-10) REVERT: PL 389 ASP cc_start: 0.8937 (m-30) cc_final: 0.8728 (m-30) REVERT: PL 416 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8878 (tm-30) REVERT: PL 429 LYS cc_start: 0.9187 (ttmt) cc_final: 0.8963 (ttmm) outliers start: 21 outliers final: 15 residues processed: 1527 average time/residue: 1.4299 time to fit residues: 2681.6733 Evaluate side-chains 989 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 972 time to evaluate : 4.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PP residue 40 THR Chi-restraints excluded: chain PP residue 90 GLU Chi-restraints excluded: chain PA residue 379 ASP Chi-restraints excluded: chain PD residue 193 ASP Chi-restraints excluded: chain PD residue 379 ASP Chi-restraints excluded: chain PE residue 67 ARG Chi-restraints excluded: chain PE residue 146 ILE Chi-restraints excluded: chain PF residue 37 THR Chi-restraints excluded: chain PF residue 193 ASP Chi-restraints excluded: chain PG residue 193 ASP Chi-restraints excluded: chain PG residue 379 ASP Chi-restraints excluded: chain PH residue 67 ARG Chi-restraints excluded: chain PI residue 146 ILE Chi-restraints excluded: chain PI residue 193 ASP Chi-restraints excluded: chain PJ residue 193 ASP Chi-restraints excluded: chain PJ residue 379 ASP Chi-restraints excluded: chain PL residue 193 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 5.9990 chunk 491 optimal weight: 6.9990 chunk 272 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 331 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 507 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 308 optimal weight: 0.9980 chunk 378 optimal weight: 0.9980 chunk 588 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PM 117 GLN PO 20 GLN PQ 20 GLN PT 133 ASN PV 117 GLN PW 133 ASN PA 175 HIS PA 299 HIS PA 318 ASN PB 36 GLN PB 172 GLN PB 175 HIS PB 299 HIS PB 318 ASN PC 175 HIS PC 299 HIS PC 318 ASN PC 392 GLN PD 36 GLN PD 175 HIS PD 299 HIS PD 392 GLN PE 175 HIS PE 299 HIS PE 318 ASN PE 392 GLN PF 175 HIS PF 299 HIS PF 318 ASN PF 392 GLN PG 36 GLN PG 299 HIS PG 318 ASN PG 392 GLN PH 175 HIS PH 299 HIS PH 318 ASN PH 392 GLN PI 175 HIS PI 299 HIS PI 392 GLN PJ 36 GLN PJ 175 HIS PJ 299 HIS PJ 318 ASN PJ 392 GLN PK 175 HIS PK 299 HIS PK 318 ASN PK 392 GLN PL 36 GLN PL 175 HIS PL 299 HIS PL 318 ASN PL 392 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 51696 Z= 0.198 Angle : 0.601 6.991 70188 Z= 0.321 Chirality : 0.041 0.202 7584 Planarity : 0.004 0.047 9456 Dihedral : 8.866 123.236 7093 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.92 % Allowed : 13.50 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.10), residues: 6312 helix: 1.39 (0.09), residues: 3144 sheet: -0.29 (0.20), residues: 564 loop : -0.57 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPPE 134 HIS 0.004 0.001 HISPD 175 PHE 0.020 0.002 PHEPG 334 TYR 0.017 0.001 TYRPJ 135 ARG 0.009 0.001 ARGPK 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1054 time to evaluate : 4.718 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: PN 66 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8695 (mtp180) REVERT: PO 132 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8498 (m-30) REVERT: PQ 90 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8076 (mm-30) REVERT: PQ 93 GLU cc_start: 0.8651 (tt0) cc_final: 0.8445 (tt0) REVERT: PR 132 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8529 (m-30) REVERT: PS 114 LYS cc_start: 0.9172 (mmtm) cc_final: 0.8949 (mmtp) REVERT: PU 132 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8499 (m-30) REVERT: PX 44 ARG cc_start: 0.8983 (mpt180) cc_final: 0.8755 (mmt90) REVERT: PX 132 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8510 (m-30) REVERT: PA 59 ASP cc_start: 0.8850 (m-30) cc_final: 0.8574 (m-30) REVERT: PA 77 MET cc_start: 0.8406 (mmm) cc_final: 0.7975 (mmm) REVERT: PA 295 TYR cc_start: 0.8639 (p90) cc_final: 0.8403 (p90) REVERT: PA 383 ASP cc_start: 0.8417 (t0) cc_final: 0.8186 (t0) REVERT: PA 386 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8610 (mp0) REVERT: PA 389 ASP cc_start: 0.8986 (m-30) cc_final: 0.8681 (m-30) REVERT: PA 405 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8445 (mt-10) REVERT: PA 416 GLU cc_start: 0.9208 (tm-30) cc_final: 0.9003 (tm-30) REVERT: PA 429 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8668 (tppt) REVERT: PB 59 ASP cc_start: 0.8903 (m-30) cc_final: 0.8592 (m-30) REVERT: PB 328 LYS cc_start: 0.8898 (mttt) cc_final: 0.8536 (mttm) REVERT: PB 331 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8572 (mp0) REVERT: PB 413 GLU cc_start: 0.9025 (tt0) cc_final: 0.8414 (tm-30) REVERT: PB 416 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8858 (tm-30) REVERT: PB 426 ASP cc_start: 0.9062 (m-30) cc_final: 0.8790 (t0) REVERT: PC 389 ASP cc_start: 0.9054 (m-30) cc_final: 0.8849 (m-30) REVERT: PC 413 GLU cc_start: 0.9317 (tp30) cc_final: 0.8796 (tm-30) REVERT: PC 416 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8977 (tm-30) REVERT: PC 426 ASP cc_start: 0.9003 (m-30) cc_final: 0.8800 (t0) REVERT: PC 429 LYS cc_start: 0.9037 (ttmt) cc_final: 0.8672 (tppp) REVERT: PD 59 ASP cc_start: 0.8849 (m-30) cc_final: 0.8582 (m-30) REVERT: PD 177 ARG cc_start: 0.8378 (ttt-90) cc_final: 0.8014 (ttt180) REVERT: PD 184 TYR cc_start: 0.8889 (m-80) cc_final: 0.8652 (m-80) REVERT: PD 379 ASP cc_start: 0.8428 (t0) cc_final: 0.8160 (t70) REVERT: PD 389 ASP cc_start: 0.8959 (m-30) cc_final: 0.8597 (m-30) REVERT: PD 426 ASP cc_start: 0.9108 (m-30) cc_final: 0.8880 (t0) REVERT: PE 59 ASP cc_start: 0.8902 (m-30) cc_final: 0.8635 (m-30) REVERT: PE 328 LYS cc_start: 0.8893 (mttt) cc_final: 0.8535 (mttm) REVERT: PE 331 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8607 (mp0) REVERT: PE 386 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8700 (mp0) REVERT: PE 413 GLU cc_start: 0.9312 (tp30) cc_final: 0.8775 (tm-30) REVERT: PE 416 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8995 (tm-30) REVERT: PE 426 ASP cc_start: 0.9055 (m-30) cc_final: 0.8777 (t0) REVERT: PE 429 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8685 (tppp) REVERT: PF 58 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8528 (mp0) REVERT: PF 413 GLU cc_start: 0.9104 (tp30) cc_final: 0.8575 (tm-30) REVERT: PF 416 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8903 (tm-30) REVERT: PF 426 ASP cc_start: 0.9020 (m-30) cc_final: 0.8780 (t0) REVERT: PF 429 LYS cc_start: 0.9099 (ttmt) cc_final: 0.8734 (tppp) REVERT: PG 59 ASP cc_start: 0.8916 (m-30) cc_final: 0.8666 (m-30) REVERT: PG 77 MET cc_start: 0.8430 (mmm) cc_final: 0.8221 (mmm) REVERT: PG 386 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8753 (mp0) REVERT: PG 389 ASP cc_start: 0.8930 (m-30) cc_final: 0.8604 (m-30) REVERT: PG 416 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8765 (tm-30) REVERT: PG 429 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8593 (tppp) REVERT: PH 59 ASP cc_start: 0.8888 (m-30) cc_final: 0.8586 (m-30) REVERT: PH 328 LYS cc_start: 0.8938 (mttt) cc_final: 0.8553 (mmtm) REVERT: PH 331 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8665 (mp0) REVERT: PH 413 GLU cc_start: 0.9102 (tt0) cc_final: 0.8655 (tm-30) REVERT: PH 426 ASP cc_start: 0.9054 (m-30) cc_final: 0.8747 (t0) REVERT: PI 59 ASP cc_start: 0.8943 (m-30) cc_final: 0.8736 (m-30) REVERT: PI 413 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.8797 (tm-30) REVERT: PI 416 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8886 (tm-30) REVERT: PI 426 ASP cc_start: 0.8974 (m-30) cc_final: 0.8766 (t0) REVERT: PI 429 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8812 (tppp) REVERT: PJ 218 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.7974 (p0) REVERT: PJ 219 GLU cc_start: 0.8619 (mp0) cc_final: 0.8321 (mp0) REVERT: PJ 379 ASP cc_start: 0.8502 (t0) cc_final: 0.8214 (t70) REVERT: PJ 389 ASP cc_start: 0.8988 (m-30) cc_final: 0.8703 (m-30) REVERT: PJ 429 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8692 (tppp) REVERT: PK 59 ASP cc_start: 0.8905 (m-30) cc_final: 0.8619 (m-30) REVERT: PK 328 LYS cc_start: 0.8834 (mttt) cc_final: 0.8452 (mttm) REVERT: PK 331 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8570 (mp0) REVERT: PK 386 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8654 (mp0) REVERT: PK 413 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.8889 (tm-30) REVERT: PK 416 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8898 (tm-30) REVERT: PK 426 ASP cc_start: 0.9045 (m-30) cc_final: 0.8740 (t0) REVERT: PK 429 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8689 (tppp) REVERT: PL 386 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8728 (mm-30) REVERT: PL 413 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.8787 (tm-30) REVERT: PL 416 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8943 (tm-30) REVERT: PL 429 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8921 (ttmm) outliers start: 103 outliers final: 21 residues processed: 1109 average time/residue: 1.3909 time to fit residues: 1908.0992 Evaluate side-chains 862 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 832 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PM residue 17 LEU Chi-restraints excluded: chain PN residue 66 ARG Chi-restraints excluded: chain PN residue 119 THR Chi-restraints excluded: chain PO residue 119 THR Chi-restraints excluded: chain PO residue 132 ASP Chi-restraints excluded: chain PP residue 17 LEU Chi-restraints excluded: chain PR residue 18 THR Chi-restraints excluded: chain PR residue 119 THR Chi-restraints excluded: chain PR residue 132 ASP Chi-restraints excluded: chain PS residue 17 LEU Chi-restraints excluded: chain PT residue 119 THR Chi-restraints excluded: chain PU residue 119 THR Chi-restraints excluded: chain PU residue 132 ASP Chi-restraints excluded: chain PW residue 119 THR Chi-restraints excluded: chain PX residue 132 ASP Chi-restraints excluded: chain PA residue 37 THR Chi-restraints excluded: chain PA residue 193 ASP Chi-restraints excluded: chain PB residue 372 ASP Chi-restraints excluded: chain PC residue 170 LYS Chi-restraints excluded: chain PD residue 37 THR Chi-restraints excluded: chain PD residue 193 ASP Chi-restraints excluded: chain PG residue 37 THR Chi-restraints excluded: chain PG residue 193 ASP Chi-restraints excluded: chain PG residue 384 ILE Chi-restraints excluded: chain PI residue 413 GLU Chi-restraints excluded: chain PJ residue 218 ASP Chi-restraints excluded: chain PJ residue 384 ILE Chi-restraints excluded: chain PK residue 413 GLU Chi-restraints excluded: chain PL residue 193 ASP Chi-restraints excluded: chain PL residue 413 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 0.4980 chunk 182 optimal weight: 8.9990 chunk 489 optimal weight: 0.9990 chunk 400 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 589 optimal weight: 7.9990 chunk 636 optimal weight: 0.4980 chunk 525 optimal weight: 0.7980 chunk 584 optimal weight: 0.0000 chunk 200 optimal weight: 0.6980 chunk 472 optimal weight: 6.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PN 20 GLN PT 20 GLN PB 172 GLN PB 392 GLN PE 36 GLN PH 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 51696 Z= 0.143 Angle : 0.538 8.866 70188 Z= 0.283 Chirality : 0.039 0.199 7584 Planarity : 0.004 0.033 9456 Dihedral : 7.695 86.858 7062 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.64 % Allowed : 14.65 % Favored : 83.71 % 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: 0.87 (0.10), residues: 6312 helix: 1.61 (0.09), residues: 3144 sheet: -0.06 (0.21), residues: 564 loop : -0.51 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPPG 134 HIS 0.003 0.001 HISPB 299 PHE 0.017 0.001 PHEPB 334 TYR 0.022 0.001 TYRPK 364 ARG 0.007 0.001 ARGPO 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 952 time to evaluate : 4.562 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: PN 24 ASP cc_start: 0.8764 (m-30) cc_final: 0.8359 (m-30) REVERT: PP 114 LYS cc_start: 0.9011 (mmtp) cc_final: 0.8685 (mmtp) REVERT: PQ 24 ASP cc_start: 0.8718 (m-30) cc_final: 0.8390 (m-30) REVERT: PR 95 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8374 (tm-30) REVERT: PR 132 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8512 (m-30) REVERT: PT 24 ASP cc_start: 0.8740 (m-30) cc_final: 0.8303 (m-30) REVERT: PU 132 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8498 (m-30) REVERT: PW 24 ASP cc_start: 0.8756 (m-30) cc_final: 0.8326 (m-30) REVERT: PX 132 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8474 (m-30) REVERT: PA 59 ASP cc_start: 0.8832 (m-30) cc_final: 0.8548 (m-30) REVERT: PA 77 MET cc_start: 0.8383 (mmm) cc_final: 0.8025 (mmm) REVERT: PA 100 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8875 (tptp) REVERT: PA 295 TYR cc_start: 0.8597 (p90) cc_final: 0.8328 (p90) REVERT: PA 301 MET cc_start: 0.8164 (ttt) cc_final: 0.7863 (ttt) REVERT: PA 383 ASP cc_start: 0.8566 (t0) cc_final: 0.8229 (t0) REVERT: PA 386 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8612 (mp0) REVERT: PA 389 ASP cc_start: 0.8983 (m-30) cc_final: 0.8746 (m-30) REVERT: PA 416 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8998 (tm-30) REVERT: PA 429 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8589 (tppt) REVERT: PB 59 ASP cc_start: 0.8897 (m-30) cc_final: 0.8563 (m-30) REVERT: PB 301 MET cc_start: 0.8352 (ttt) cc_final: 0.8111 (ttt) REVERT: PB 331 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8494 (mp0) REVERT: PB 426 ASP cc_start: 0.9066 (m-30) cc_final: 0.8767 (t0) REVERT: PC 416 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8904 (tm-30) REVERT: PC 426 ASP cc_start: 0.9011 (m-30) cc_final: 0.8809 (t0) REVERT: PC 429 LYS cc_start: 0.9058 (ttmt) cc_final: 0.8677 (tppp) REVERT: PD 59 ASP cc_start: 0.8841 (m-30) cc_final: 0.8559 (m-30) REVERT: PD 77 MET cc_start: 0.8414 (mmm) cc_final: 0.8007 (mmm) REVERT: PD 177 ARG cc_start: 0.8470 (ttt-90) cc_final: 0.8072 (ttt180) REVERT: PD 184 TYR cc_start: 0.8970 (m-80) cc_final: 0.8675 (m-80) REVERT: PD 301 MET cc_start: 0.8115 (ttt) cc_final: 0.7877 (ttt) REVERT: PD 331 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8526 (mt-10) REVERT: PD 389 ASP cc_start: 0.8980 (m-30) cc_final: 0.8613 (m-30) REVERT: PD 416 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8770 (tm-30) REVERT: PD 426 ASP cc_start: 0.9091 (m-30) cc_final: 0.8832 (t0) REVERT: PE 59 ASP cc_start: 0.8875 (m-30) cc_final: 0.8598 (m-30) REVERT: PE 301 MET cc_start: 0.8320 (ttt) cc_final: 0.8095 (ttt) REVERT: PE 328 LYS cc_start: 0.8859 (mttt) cc_final: 0.8546 (mtmm) REVERT: PE 331 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8516 (mt-10) REVERT: PE 426 ASP cc_start: 0.9057 (m-30) cc_final: 0.8761 (t0) REVERT: PE 429 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8653 (tppp) REVERT: PF 42 MET cc_start: 0.7217 (ttp) cc_final: 0.7006 (ttp) REVERT: PF 331 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8618 (mt-10) REVERT: PF 382 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8720 (tt0) REVERT: PF 386 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8701 (mm-30) REVERT: PF 413 GLU cc_start: 0.9103 (tp30) cc_final: 0.8572 (tm-30) REVERT: PF 416 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8915 (tm-30) REVERT: PF 426 ASP cc_start: 0.9006 (m-30) cc_final: 0.8717 (t0) REVERT: PF 429 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8676 (tppp) REVERT: PG 37 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8692 (p) REVERT: PG 59 ASP cc_start: 0.8887 (m-30) cc_final: 0.8642 (m-30) REVERT: PG 301 MET cc_start: 0.8091 (ttt) cc_final: 0.7841 (ttt) REVERT: PG 331 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8517 (mt-10) REVERT: PG 386 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8711 (mp0) REVERT: PG 389 ASP cc_start: 0.8927 (m-30) cc_final: 0.8588 (m-30) REVERT: PG 416 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8799 (tm-30) REVERT: PG 429 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8535 (tppp) REVERT: PH 59 ASP cc_start: 0.8865 (m-30) cc_final: 0.8549 (m-30) REVERT: PH 328 LYS cc_start: 0.8866 (mttt) cc_final: 0.8557 (mttm) REVERT: PH 331 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8605 (mp0) REVERT: PH 372 ASP cc_start: 0.8777 (t0) cc_final: 0.8486 (t0) REVERT: PH 413 GLU cc_start: 0.9114 (tt0) cc_final: 0.8548 (tm-30) REVERT: PH 426 ASP cc_start: 0.9050 (m-30) cc_final: 0.8720 (t0) REVERT: PI 59 ASP cc_start: 0.8944 (m-30) cc_final: 0.8706 (m-30) REVERT: PI 331 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8660 (mt-10) REVERT: PI 413 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.8778 (tm-30) REVERT: PI 416 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8835 (tm-30) REVERT: PI 429 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8761 (tppp) REVERT: PJ 218 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.7986 (p0) REVERT: PJ 219 GLU cc_start: 0.8578 (mp0) cc_final: 0.8262 (mp0) REVERT: PJ 301 MET cc_start: 0.8203 (ttt) cc_final: 0.7937 (ttt) REVERT: PJ 383 ASP cc_start: 0.9155 (t0) cc_final: 0.8391 (t0) REVERT: PJ 386 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8501 (mp0) REVERT: PJ 389 ASP cc_start: 0.9003 (m-30) cc_final: 0.8706 (m-30) REVERT: PJ 429 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8607 (tppp) REVERT: PK 59 ASP cc_start: 0.8884 (m-30) cc_final: 0.8553 (m-30) REVERT: PK 413 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.8935 (tm-30) REVERT: PK 416 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8902 (tm-30) REVERT: PK 426 ASP cc_start: 0.9082 (m-30) cc_final: 0.8780 (t0) REVERT: PK 429 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8686 (ttmm) REVERT: PL 32 SER cc_start: 0.8006 (OUTLIER) cc_final: 0.7766 (m) REVERT: PL 331 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8661 (mt-10) REVERT: PL 386 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8681 (mm-30) REVERT: PL 413 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8823 (tm-30) REVERT: PL 416 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8917 (tm-30) REVERT: PL 429 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8899 (ttmm) outliers start: 88 outliers final: 12 residues processed: 990 average time/residue: 1.3053 time to fit residues: 1618.9321 Evaluate side-chains 850 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 828 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PM residue 17 LEU Chi-restraints excluded: chain PP residue 17 LEU Chi-restraints excluded: chain PR residue 132 ASP Chi-restraints excluded: chain PS residue 17 LEU Chi-restraints excluded: chain PS residue 132 ASP Chi-restraints excluded: chain PU residue 132 ASP Chi-restraints excluded: chain PV residue 90 GLU Chi-restraints excluded: chain PX residue 132 ASP Chi-restraints excluded: chain PA residue 100 LYS Chi-restraints excluded: chain PD residue 193 ASP Chi-restraints excluded: chain PG residue 37 THR Chi-restraints excluded: chain PG residue 193 ASP Chi-restraints excluded: chain PG residue 384 ILE Chi-restraints excluded: chain PI residue 170 LYS Chi-restraints excluded: chain PI residue 391 ILE Chi-restraints excluded: chain PI residue 413 GLU Chi-restraints excluded: chain PJ residue 218 ASP Chi-restraints excluded: chain PJ residue 314 LEU Chi-restraints excluded: chain PJ residue 384 ILE Chi-restraints excluded: chain PK residue 413 GLU Chi-restraints excluded: chain PL residue 32 SER Chi-restraints excluded: chain PL residue 413 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 582 optimal weight: 8.9990 chunk 443 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 281 optimal weight: 10.0000 chunk 395 optimal weight: 3.9990 chunk 591 optimal weight: 0.4980 chunk 626 optimal weight: 3.9990 chunk 309 optimal weight: 0.9980 chunk 560 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PS 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 51696 Z= 0.177 Angle : 0.530 8.581 70188 Z= 0.275 Chirality : 0.039 0.143 7584 Planarity : 0.004 0.043 9456 Dihedral : 7.452 89.209 7060 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.42 % Allowed : 15.62 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.10), residues: 6312 helix: 1.76 (0.09), residues: 3144 sheet: -0.06 (0.22), residues: 564 loop : -0.53 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPPJ 134 HIS 0.003 0.001 HISPJ 175 PHE 0.017 0.001 PHEPB 334 TYR 0.020 0.001 TYRPJ 364 ARG 0.015 0.000 ARGPH 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 862 time to evaluate : 4.564 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: PN 24 ASP cc_start: 0.8791 (m-30) cc_final: 0.8373 (m-30) REVERT: PQ 20 GLN cc_start: 0.9091 (tp40) cc_final: 0.8495 (tp-100) REVERT: PQ 24 ASP cc_start: 0.8739 (m-30) cc_final: 0.8401 (m-30) REVERT: PR 95 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8376 (tm-30) REVERT: PR 132 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8493 (m-30) REVERT: PT 20 GLN cc_start: 0.9104 (tp40) cc_final: 0.8536 (tp-100) REVERT: PT 24 ASP cc_start: 0.8740 (m-30) cc_final: 0.8349 (m-30) REVERT: PU 95 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8279 (tm-30) REVERT: PU 132 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8512 (m-30) REVERT: PW 24 ASP cc_start: 0.8792 (m-30) cc_final: 0.8374 (m-30) REVERT: PX 132 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8469 (m-30) REVERT: PA 59 ASP cc_start: 0.8842 (m-30) cc_final: 0.8561 (m-30) REVERT: PA 77 MET cc_start: 0.8365 (mmm) cc_final: 0.7989 (mmm) REVERT: PA 301 MET cc_start: 0.8409 (ttt) cc_final: 0.8066 (ttt) REVERT: PA 331 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8626 (mp0) REVERT: PA 383 ASP cc_start: 0.8635 (t0) cc_final: 0.8254 (t0) REVERT: PA 386 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8663 (mp0) REVERT: PA 389 ASP cc_start: 0.9028 (m-30) cc_final: 0.8796 (m-30) REVERT: PA 416 GLU cc_start: 0.9277 (tm-30) cc_final: 0.9011 (tm-30) REVERT: PA 429 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8551 (mptp) REVERT: PB 59 ASP cc_start: 0.8901 (m-30) cc_final: 0.8578 (m-30) REVERT: PB 301 MET cc_start: 0.8573 (ttt) cc_final: 0.8323 (ttt) REVERT: PB 413 GLU cc_start: 0.9101 (tt0) cc_final: 0.8514 (tm-30) REVERT: PB 426 ASP cc_start: 0.9097 (m-30) cc_final: 0.8771 (t0) REVERT: PC 331 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8694 (mt-10) REVERT: PC 372 ASP cc_start: 0.8689 (t0) cc_final: 0.8292 (t0) REVERT: PC 416 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8900 (tm-30) REVERT: PC 426 ASP cc_start: 0.9057 (m-30) cc_final: 0.8837 (t0) REVERT: PC 429 LYS cc_start: 0.9078 (ttmt) cc_final: 0.8696 (tppp) REVERT: PD 59 ASP cc_start: 0.8846 (m-30) cc_final: 0.8564 (m-30) REVERT: PD 177 ARG cc_start: 0.8528 (ttt-90) cc_final: 0.8162 (ttt180) REVERT: PD 184 TYR cc_start: 0.8962 (m-80) cc_final: 0.8660 (m-80) REVERT: PD 301 MET cc_start: 0.8407 (ttt) cc_final: 0.8091 (ttt) REVERT: PD 331 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8528 (mt-10) REVERT: PD 389 ASP cc_start: 0.8975 (m-30) cc_final: 0.8622 (m-30) REVERT: PD 416 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8811 (tm-30) REVERT: PD 426 ASP cc_start: 0.9105 (m-30) cc_final: 0.8846 (t0) REVERT: PE 59 ASP cc_start: 0.8880 (m-30) cc_final: 0.8606 (m-30) REVERT: PE 301 MET cc_start: 0.8542 (ttt) cc_final: 0.8304 (ttt) REVERT: PE 328 LYS cc_start: 0.8877 (mttt) cc_final: 0.8495 (mtmm) REVERT: PE 331 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8545 (mt-10) REVERT: PE 413 GLU cc_start: 0.9381 (mm-30) cc_final: 0.8927 (tm-30) REVERT: PE 426 ASP cc_start: 0.9084 (m-30) cc_final: 0.8765 (t0) REVERT: PE 429 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8648 (tppp) REVERT: PF 42 MET cc_start: 0.7316 (ttp) cc_final: 0.7081 (ttp) REVERT: PF 331 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8715 (mt-10) REVERT: PF 382 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8744 (tt0) REVERT: PF 386 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8709 (mm-30) REVERT: PF 405 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8648 (pp20) REVERT: PF 413 GLU cc_start: 0.9139 (tp30) cc_final: 0.8590 (tm-30) REVERT: PF 416 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8921 (tm-30) REVERT: PF 426 ASP cc_start: 0.9027 (m-30) cc_final: 0.8715 (t0) REVERT: PF 429 LYS cc_start: 0.9058 (ttmt) cc_final: 0.8669 (tppp) REVERT: PG 59 ASP cc_start: 0.8903 (m-30) cc_final: 0.8653 (m-30) REVERT: PG 301 MET cc_start: 0.8379 (ttt) cc_final: 0.7950 (ttt) REVERT: PG 331 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8581 (mt-10) REVERT: PG 389 ASP cc_start: 0.8994 (m-30) cc_final: 0.8729 (m-30) REVERT: PG 416 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8912 (tm-30) REVERT: PG 429 LYS cc_start: 0.8973 (ttmt) cc_final: 0.8555 (tppp) REVERT: PH 59 ASP cc_start: 0.8872 (m-30) cc_final: 0.8559 (m-30) REVERT: PH 301 MET cc_start: 0.8350 (ttt) cc_final: 0.7765 (ttt) REVERT: PH 331 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8610 (mp0) REVERT: PH 372 ASP cc_start: 0.8787 (t0) cc_final: 0.8405 (t0) REVERT: PH 426 ASP cc_start: 0.9091 (m-30) cc_final: 0.8674 (t0) REVERT: PI 59 ASP cc_start: 0.8940 (m-30) cc_final: 0.8711 (m-30) REVERT: PI 416 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8825 (tm-30) REVERT: PI 429 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8763 (tppp) REVERT: PJ 218 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.7981 (p0) REVERT: PJ 219 GLU cc_start: 0.8612 (mp0) cc_final: 0.8239 (mp0) REVERT: PJ 295 TYR cc_start: 0.8802 (p90) cc_final: 0.8472 (p90) REVERT: PJ 301 MET cc_start: 0.8414 (ttt) cc_final: 0.8138 (ttt) REVERT: PJ 389 ASP cc_start: 0.9003 (m-30) cc_final: 0.8774 (m-30) REVERT: PJ 429 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8605 (tppp) REVERT: PK 59 ASP cc_start: 0.8873 (m-30) cc_final: 0.8552 (m-30) REVERT: PK 301 MET cc_start: 0.8407 (ttt) cc_final: 0.7867 (ttt) REVERT: PK 328 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8186 (mtmm) REVERT: PK 331 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8519 (mt-10) REVERT: PK 372 ASP cc_start: 0.8806 (t0) cc_final: 0.8450 (t0) REVERT: PK 413 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.8906 (tm-30) REVERT: PK 416 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8936 (tm-30) REVERT: PK 426 ASP cc_start: 0.9094 (m-30) cc_final: 0.8762 (t0) REVERT: PK 429 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8654 (tppt) REVERT: PL 331 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8715 (mt-10) REVERT: PL 386 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8723 (mm-30) REVERT: PL 413 GLU cc_start: 0.9367 (OUTLIER) cc_final: 0.8773 (tm-30) REVERT: PL 416 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8884 (tm-30) REVERT: PL 429 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8750 (tppp) outliers start: 76 outliers final: 18 residues processed: 902 average time/residue: 1.2729 time to fit residues: 1448.1449 Evaluate side-chains 812 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 786 time to evaluate : 4.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PM residue 17 LEU Chi-restraints excluded: chain PN residue 25 ILE Chi-restraints excluded: chain PN residue 138 LEU Chi-restraints excluded: chain PP residue 17 LEU Chi-restraints excluded: chain PR residue 132 ASP Chi-restraints excluded: chain PS residue 17 LEU Chi-restraints excluded: chain PS residue 132 ASP Chi-restraints excluded: chain PT residue 138 LEU Chi-restraints excluded: chain PU residue 132 ASP Chi-restraints excluded: chain PV residue 90 GLU Chi-restraints excluded: chain PV residue 132 ASP Chi-restraints excluded: chain PW residue 138 LEU Chi-restraints excluded: chain PX residue 132 ASP Chi-restraints excluded: chain PC residue 55 LEU Chi-restraints excluded: chain PE residue 37 THR Chi-restraints excluded: chain PE residue 333 ARG Chi-restraints excluded: chain PF residue 405 GLU Chi-restraints excluded: chain PG residue 37 THR Chi-restraints excluded: chain PG residue 193 ASP Chi-restraints excluded: chain PG residue 314 LEU Chi-restraints excluded: chain PG residue 384 ILE Chi-restraints excluded: chain PJ residue 218 ASP Chi-restraints excluded: chain PJ residue 384 ILE Chi-restraints excluded: chain PK residue 328 LYS Chi-restraints excluded: chain PK residue 413 GLU Chi-restraints excluded: chain PL residue 413 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 521 optimal weight: 10.0000 chunk 355 optimal weight: 6.9990 chunk 9 optimal weight: 0.0980 chunk 466 optimal weight: 0.6980 chunk 258 optimal weight: 7.9990 chunk 534 optimal weight: 5.9990 chunk 432 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 319 optimal weight: 1.9990 chunk 562 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PQ 133 ASN PV 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 51696 Z= 0.304 Angle : 0.577 8.746 70188 Z= 0.298 Chirality : 0.041 0.151 7584 Planarity : 0.004 0.047 9456 Dihedral : 7.335 88.355 7058 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.96 % Allowed : 15.72 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.11), residues: 6312 helix: 1.80 (0.09), residues: 3144 sheet: -0.24 (0.21), residues: 564 loop : -0.57 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPPA 134 HIS 0.003 0.001 HISPF 369 PHE 0.019 0.002 PHEPA 334 TYR 0.024 0.002 TYRPC 184 ARG 0.007 0.001 ARGPJ 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 814 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: PN 24 ASP cc_start: 0.8871 (m-30) cc_final: 0.8459 (m-30) REVERT: PO 95 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8558 (tm-30) REVERT: PQ 24 ASP cc_start: 0.8833 (m-30) cc_final: 0.8459 (m-30) REVERT: PR 95 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8422 (tm-30) REVERT: PR 132 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8444 (m-30) REVERT: PT 20 GLN cc_start: 0.9179 (tp40) cc_final: 0.8639 (tp-100) REVERT: PT 24 ASP cc_start: 0.8819 (m-30) cc_final: 0.8423 (m-30) REVERT: PU 95 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8388 (tm-30) REVERT: PU 132 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8543 (m-30) REVERT: PW 24 ASP cc_start: 0.8863 (m-30) cc_final: 0.8505 (m-30) REVERT: PX 132 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8515 (m-30) REVERT: PA 59 ASP cc_start: 0.8878 (m-30) cc_final: 0.8584 (m-30) REVERT: PA 301 MET cc_start: 0.8458 (ttt) cc_final: 0.8135 (ttt) REVERT: PA 372 ASP cc_start: 0.8805 (t0) cc_final: 0.8466 (t0) REVERT: PA 383 ASP cc_start: 0.8809 (t0) cc_final: 0.7992 (t0) REVERT: PA 386 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8555 (mp0) REVERT: PA 389 ASP cc_start: 0.8997 (m-30) cc_final: 0.8667 (m-30) REVERT: PA 416 GLU cc_start: 0.9286 (tm-30) cc_final: 0.9076 (tm-30) REVERT: PA 429 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8739 (tppt) REVERT: PB 59 ASP cc_start: 0.8907 (m-30) cc_final: 0.8591 (m-30) REVERT: PB 301 MET cc_start: 0.8661 (ttt) cc_final: 0.8441 (ttt) REVERT: PB 331 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8533 (mt-10) REVERT: PB 386 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8698 (mm-30) REVERT: PB 413 GLU cc_start: 0.9118 (tt0) cc_final: 0.8608 (tm-30) REVERT: PB 426 ASP cc_start: 0.9139 (m-30) cc_final: 0.8713 (t0) REVERT: PC 261 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.7953 (mpp80) REVERT: PC 413 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8852 (tm-30) REVERT: PC 416 GLU cc_start: 0.9312 (tm-30) cc_final: 0.8916 (tm-30) REVERT: PC 426 ASP cc_start: 0.9075 (m-30) cc_final: 0.8762 (t0) REVERT: PC 429 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8756 (tppp) REVERT: PD 59 ASP cc_start: 0.8906 (m-30) cc_final: 0.8628 (m-30) REVERT: PD 77 MET cc_start: 0.8405 (mmm) cc_final: 0.8017 (mmm) REVERT: PD 185 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8377 (pt0) REVERT: PD 301 MET cc_start: 0.8389 (ttt) cc_final: 0.8096 (ttt) REVERT: PD 372 ASP cc_start: 0.8788 (t0) cc_final: 0.8421 (t0) REVERT: PD 389 ASP cc_start: 0.8974 (m-30) cc_final: 0.8613 (m-30) REVERT: PD 416 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8826 (tm-30) REVERT: PD 426 ASP cc_start: 0.9131 (m-30) cc_final: 0.8844 (t0) REVERT: PE 59 ASP cc_start: 0.8920 (m-30) cc_final: 0.8644 (m-30) REVERT: PE 98 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8219 (mp0) REVERT: PE 301 MET cc_start: 0.8611 (ttt) cc_final: 0.8386 (ttt) REVERT: PE 328 LYS cc_start: 0.9015 (mttt) cc_final: 0.8675 (mmmm) REVERT: PE 331 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8637 (mp0) REVERT: PE 413 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9026 (tm-30) REVERT: PE 426 ASP cc_start: 0.9134 (m-30) cc_final: 0.8710 (t0) REVERT: PE 429 LYS cc_start: 0.9090 (ttmt) cc_final: 0.8778 (tppp) REVERT: PF 301 MET cc_start: 0.8599 (ttt) cc_final: 0.8074 (ttt) REVERT: PF 382 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8762 (tt0) REVERT: PF 386 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8747 (mm-30) REVERT: PF 405 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8717 (pp20) REVERT: PF 413 GLU cc_start: 0.9122 (tp30) cc_final: 0.8586 (tm-30) REVERT: PF 416 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8887 (tm-30) REVERT: PF 426 ASP cc_start: 0.9061 (m-30) cc_final: 0.8717 (t0) REVERT: PF 429 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8724 (tppp) REVERT: PG 59 ASP cc_start: 0.8902 (m-30) cc_final: 0.8635 (m-30) REVERT: PG 261 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8113 (mpp80) REVERT: PG 301 MET cc_start: 0.8454 (ttt) cc_final: 0.8074 (ttt) REVERT: PG 331 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8629 (mt-10) REVERT: PG 372 ASP cc_start: 0.8726 (t0) cc_final: 0.8473 (t0) REVERT: PG 389 ASP cc_start: 0.8984 (m-30) cc_final: 0.8729 (m-30) REVERT: PG 416 GLU cc_start: 0.9241 (tm-30) cc_final: 0.9019 (tm-30) REVERT: PG 429 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8626 (tppp) REVERT: PH 59 ASP cc_start: 0.8899 (m-30) cc_final: 0.8592 (m-30) REVERT: PH 301 MET cc_start: 0.8589 (ttt) cc_final: 0.8225 (ttt) REVERT: PH 331 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8639 (mp0) REVERT: PH 372 ASP cc_start: 0.8746 (t0) cc_final: 0.8360 (t0) REVERT: PH 413 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9094 (tm-30) REVERT: PH 426 ASP cc_start: 0.9132 (m-30) cc_final: 0.8685 (t0) REVERT: PI 42 MET cc_start: 0.7056 (ttp) cc_final: 0.6771 (ttp) REVERT: PI 59 ASP cc_start: 0.9051 (m-30) cc_final: 0.8810 (m-30) REVERT: PI 331 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8748 (mt-10) REVERT: PI 386 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8743 (mm-30) REVERT: PI 413 GLU cc_start: 0.9340 (mm-30) cc_final: 0.8849 (tm-30) REVERT: PI 416 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8793 (tm-30) REVERT: PI 429 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8804 (tppp) REVERT: PJ 218 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.7940 (p0) REVERT: PJ 219 GLU cc_start: 0.8690 (mp0) cc_final: 0.8308 (mp0) REVERT: PJ 295 TYR cc_start: 0.8830 (p90) cc_final: 0.8595 (p90) REVERT: PJ 301 MET cc_start: 0.8415 (ttt) cc_final: 0.8133 (ttt) REVERT: PJ 389 ASP cc_start: 0.8978 (m-30) cc_final: 0.8740 (m-30) REVERT: PJ 429 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8833 (ttmm) REVERT: PK 59 ASP cc_start: 0.8910 (m-30) cc_final: 0.8587 (m-30) REVERT: PK 301 MET cc_start: 0.8597 (ttt) cc_final: 0.8264 (ttt) REVERT: PK 328 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8370 (mtmm) REVERT: PK 331 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8587 (mt-10) REVERT: PK 372 ASP cc_start: 0.8784 (t0) cc_final: 0.8409 (t0) REVERT: PK 413 GLU cc_start: 0.9421 (OUTLIER) cc_final: 0.8865 (tm-30) REVERT: PK 416 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8960 (tm-30) REVERT: PK 426 ASP cc_start: 0.9131 (m-30) cc_final: 0.8712 (t0) REVERT: PK 429 LYS cc_start: 0.9130 (ttmt) cc_final: 0.8831 (tppt) REVERT: PL 64 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8905 (tptp) REVERT: PL 261 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8009 (mpp80) REVERT: PL 301 MET cc_start: 0.8585 (ttt) cc_final: 0.8082 (ttt) REVERT: PL 372 ASP cc_start: 0.8840 (t0) cc_final: 0.8491 (t0) REVERT: PL 386 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8749 (mm-30) REVERT: PL 413 GLU cc_start: 0.9367 (OUTLIER) cc_final: 0.8801 (tm-30) REVERT: PL 416 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8899 (tm-30) REVERT: PL 429 LYS cc_start: 0.9218 (ttmt) cc_final: 0.8840 (tppp) outliers start: 105 outliers final: 32 residues processed: 874 average time/residue: 1.2649 time to fit residues: 1394.1315 Evaluate side-chains 806 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 761 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PM residue 17 LEU Chi-restraints excluded: chain PN residue 138 LEU Chi-restraints excluded: chain PP residue 17 LEU Chi-restraints excluded: chain PQ residue 138 LEU Chi-restraints excluded: chain PR residue 132 ASP Chi-restraints excluded: chain PS residue 17 LEU Chi-restraints excluded: chain PT residue 138 LEU Chi-restraints excluded: chain PU residue 132 ASP Chi-restraints excluded: chain PV residue 90 GLU Chi-restraints excluded: chain PV residue 138 LEU Chi-restraints excluded: chain PX residue 132 ASP Chi-restraints excluded: chain PA residue 147 THR Chi-restraints excluded: chain PA residue 286 GLU Chi-restraints excluded: chain PA residue 384 ILE Chi-restraints excluded: chain PC residue 55 LEU Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PD residue 37 THR Chi-restraints excluded: chain PD residue 76 LEU Chi-restraints excluded: chain PD residue 185 GLN Chi-restraints excluded: chain PD residue 314 LEU Chi-restraints excluded: chain PE residue 37 THR Chi-restraints excluded: chain PE residue 250 ASP Chi-restraints excluded: chain PE residue 333 ARG Chi-restraints excluded: chain PF residue 405 GLU Chi-restraints excluded: chain PG residue 37 THR Chi-restraints excluded: chain PG residue 73 VAL Chi-restraints excluded: chain PG residue 76 LEU Chi-restraints excluded: chain PG residue 250 ASP Chi-restraints excluded: chain PG residue 261 ARG Chi-restraints excluded: chain PG residue 314 LEU Chi-restraints excluded: chain PH residue 250 ASP Chi-restraints excluded: chain PH residue 303 MET Chi-restraints excluded: chain PJ residue 37 THR Chi-restraints excluded: chain PJ residue 218 ASP Chi-restraints excluded: chain PJ residue 286 GLU Chi-restraints excluded: chain PK residue 37 THR Chi-restraints excluded: chain PK residue 250 ASP Chi-restraints excluded: chain PK residue 303 MET Chi-restraints excluded: chain PK residue 328 LYS Chi-restraints excluded: chain PK residue 413 GLU Chi-restraints excluded: chain PL residue 55 LEU Chi-restraints excluded: chain PL residue 64 LYS Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PL residue 413 GLU Chi-restraints excluded: chain PL residue 423 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 210 optimal weight: 1.9990 chunk 564 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 367 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 626 optimal weight: 2.9990 chunk 520 optimal weight: 4.9990 chunk 290 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 329 optimal weight: 30.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 51696 Z= 0.201 Angle : 0.533 8.948 70188 Z= 0.276 Chirality : 0.039 0.142 7584 Planarity : 0.004 0.031 9456 Dihedral : 7.143 88.241 7056 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.57 % Allowed : 16.39 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.10), residues: 6312 helix: 1.88 (0.09), residues: 3120 sheet: -0.13 (0.22), residues: 564 loop : -0.64 (0.11), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPPJ 134 HIS 0.003 0.001 HISPK 175 PHE 0.018 0.001 PHEPH 334 TYR 0.026 0.002 TYRPG 184 ARG 0.006 0.000 ARGPN 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 814 time to evaluate : 4.544 Fit side-chains revert: symmetry clash REVERT: PN 24 ASP cc_start: 0.8836 (m-30) cc_final: 0.8404 (m-30) REVERT: PO 95 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8507 (tm-30) REVERT: PQ 24 ASP cc_start: 0.8806 (m-30) cc_final: 0.8427 (m-30) REVERT: PR 95 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8352 (tm-30) REVERT: PR 132 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8451 (m-30) REVERT: PT 20 GLN cc_start: 0.9148 (tp40) cc_final: 0.8606 (tp-100) REVERT: PT 24 ASP cc_start: 0.8783 (m-30) cc_final: 0.8380 (m-30) REVERT: PU 95 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8360 (tm-30) REVERT: PU 132 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8518 (m-30) REVERT: PW 24 ASP cc_start: 0.8838 (m-30) cc_final: 0.8491 (m-30) REVERT: PX 132 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8468 (m-30) REVERT: PA 59 ASP cc_start: 0.8864 (m-30) cc_final: 0.8564 (m-30) REVERT: PA 77 MET cc_start: 0.8371 (mmm) cc_final: 0.7957 (mmm) REVERT: PA 100 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8843 (tptp) REVERT: PA 301 MET cc_start: 0.8378 (ttt) cc_final: 0.8099 (ttt) REVERT: PA 331 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8629 (mt-10) REVERT: PA 372 ASP cc_start: 0.8860 (t0) cc_final: 0.8534 (t0) REVERT: PA 389 ASP cc_start: 0.9026 (m-30) cc_final: 0.8725 (m-30) REVERT: PA 416 GLU cc_start: 0.9287 (tm-30) cc_final: 0.9011 (tm-30) REVERT: PA 429 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8648 (mptp) REVERT: PB 59 ASP cc_start: 0.8924 (m-30) cc_final: 0.8598 (m-30) REVERT: PB 331 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8527 (mt-10) REVERT: PB 386 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8675 (mm-30) REVERT: PB 413 GLU cc_start: 0.9117 (tt0) cc_final: 0.8600 (tm-30) REVERT: PB 426 ASP cc_start: 0.9143 (m-30) cc_final: 0.8721 (t0) REVERT: PC 331 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8688 (mt-10) REVERT: PC 386 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8679 (mm-30) REVERT: PC 413 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8857 (tm-30) REVERT: PC 416 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8790 (tm-30) REVERT: PC 426 ASP cc_start: 0.9080 (m-30) cc_final: 0.8765 (t0) REVERT: PC 429 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8756 (tppp) REVERT: PD 59 ASP cc_start: 0.8887 (m-30) cc_final: 0.8613 (m-30) REVERT: PD 77 MET cc_start: 0.8332 (mmm) cc_final: 0.7912 (mmm) REVERT: PD 185 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8391 (pt0) REVERT: PD 301 MET cc_start: 0.8367 (ttt) cc_final: 0.8106 (ttt) REVERT: PD 331 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8593 (mp0) REVERT: PD 372 ASP cc_start: 0.8812 (t0) cc_final: 0.8442 (t0) REVERT: PD 389 ASP cc_start: 0.8948 (m-30) cc_final: 0.8581 (m-30) REVERT: PD 416 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8821 (tm-30) REVERT: PD 426 ASP cc_start: 0.9139 (m-30) cc_final: 0.8850 (t0) REVERT: PE 59 ASP cc_start: 0.8912 (m-30) cc_final: 0.8601 (m-30) REVERT: PE 98 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8141 (mp0) REVERT: PE 328 LYS cc_start: 0.8957 (mttt) cc_final: 0.8559 (mtmm) REVERT: PE 331 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8574 (mt-10) REVERT: PE 364 TYR cc_start: 0.8960 (m-80) cc_final: 0.8739 (m-80) REVERT: PE 401 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8741 (tm-30) REVERT: PE 413 GLU cc_start: 0.9434 (mm-30) cc_final: 0.8970 (tm-30) REVERT: PE 426 ASP cc_start: 0.9140 (m-30) cc_final: 0.8718 (t0) REVERT: PE 429 LYS cc_start: 0.9085 (ttmt) cc_final: 0.8750 (tppp) REVERT: PF 301 MET cc_start: 0.8561 (ttt) cc_final: 0.8032 (ttt) REVERT: PF 331 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8729 (mt-10) REVERT: PF 382 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8773 (tt0) REVERT: PF 386 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8727 (mm-30) REVERT: PF 405 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8692 (pp20) REVERT: PF 413 GLU cc_start: 0.9154 (tp30) cc_final: 0.8655 (tm-30) REVERT: PF 416 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8802 (tm-30) REVERT: PF 426 ASP cc_start: 0.9065 (m-30) cc_final: 0.8716 (t0) REVERT: PF 429 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8709 (tppp) REVERT: PG 59 ASP cc_start: 0.8852 (m-30) cc_final: 0.8580 (m-30) REVERT: PG 77 MET cc_start: 0.8358 (mmm) cc_final: 0.7752 (mmm) REVERT: PG 301 MET cc_start: 0.8394 (ttt) cc_final: 0.8065 (ttt) REVERT: PG 331 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8594 (mt-10) REVERT: PG 372 ASP cc_start: 0.8793 (t0) cc_final: 0.8469 (t0) REVERT: PG 389 ASP cc_start: 0.9002 (m-30) cc_final: 0.8750 (m-30) REVERT: PG 416 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8932 (tm-30) REVERT: PG 429 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8653 (tppp) REVERT: PH 59 ASP cc_start: 0.8892 (m-30) cc_final: 0.8569 (m-30) REVERT: PH 301 MET cc_start: 0.8625 (ttt) cc_final: 0.8242 (ttt) REVERT: PH 331 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8613 (mt-10) REVERT: PH 372 ASP cc_start: 0.8792 (t0) cc_final: 0.8423 (t0) REVERT: PH 413 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9065 (tm-30) REVERT: PH 426 ASP cc_start: 0.9148 (m-30) cc_final: 0.8709 (t0) REVERT: PI 59 ASP cc_start: 0.9018 (m-30) cc_final: 0.8737 (m-30) REVERT: PI 331 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8726 (mt-10) REVERT: PI 379 ASP cc_start: 0.8636 (t70) cc_final: 0.8347 (p0) REVERT: PI 386 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8724 (mm-30) REVERT: PI 413 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8853 (tm-30) REVERT: PI 416 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8828 (tm-30) REVERT: PI 429 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8765 (tppp) REVERT: PJ 58 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8676 (mm-30) REVERT: PJ 87 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: PJ 218 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.7948 (p0) REVERT: PJ 219 GLU cc_start: 0.8687 (mp0) cc_final: 0.8306 (mp0) REVERT: PJ 295 TYR cc_start: 0.8796 (p90) cc_final: 0.8452 (p90) REVERT: PJ 301 MET cc_start: 0.8389 (ttt) cc_final: 0.8124 (ttt) REVERT: PJ 389 ASP cc_start: 0.8997 (m-30) cc_final: 0.8760 (m-30) REVERT: PJ 429 LYS cc_start: 0.9099 (ttmt) cc_final: 0.8646 (tppp) REVERT: PK 59 ASP cc_start: 0.8907 (m-30) cc_final: 0.8578 (m-30) REVERT: PK 301 MET cc_start: 0.8631 (ttt) cc_final: 0.8282 (ttt) REVERT: PK 328 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8247 (mtmm) REVERT: PK 331 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8546 (mt-10) REVERT: PK 372 ASP cc_start: 0.8802 (t0) cc_final: 0.8425 (t0) REVERT: PK 413 GLU cc_start: 0.9430 (OUTLIER) cc_final: 0.8869 (tm-30) REVERT: PK 416 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8957 (tm-30) REVERT: PK 426 ASP cc_start: 0.9122 (m-30) cc_final: 0.8701 (t0) REVERT: PK 429 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8828 (tppt) REVERT: PL 55 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8302 (pp) REVERT: PL 64 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8862 (tptp) REVERT: PL 164 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8466 (mt-10) REVERT: PL 301 MET cc_start: 0.8580 (ttt) cc_final: 0.8040 (ttt) REVERT: PL 331 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8713 (mt-10) REVERT: PL 386 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8721 (mm-30) REVERT: PL 413 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.9178 (mm-30) REVERT: PL 416 GLU cc_start: 0.9301 (tm-30) cc_final: 0.8936 (tm-30) REVERT: PL 429 LYS cc_start: 0.9210 (ttmt) cc_final: 0.8877 (tppp) outliers start: 84 outliers final: 32 residues processed: 873 average time/residue: 1.2379 time to fit residues: 1366.7097 Evaluate side-chains 811 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 765 time to evaluate : 4.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PM residue 17 LEU Chi-restraints excluded: chain PN residue 138 LEU Chi-restraints excluded: chain PP residue 17 LEU Chi-restraints excluded: chain PQ residue 138 LEU Chi-restraints excluded: chain PR residue 132 ASP Chi-restraints excluded: chain PS residue 17 LEU Chi-restraints excluded: chain PT residue 138 LEU Chi-restraints excluded: chain PU residue 132 ASP Chi-restraints excluded: chain PV residue 90 GLU Chi-restraints excluded: chain PV residue 138 LEU Chi-restraints excluded: chain PW residue 138 LEU Chi-restraints excluded: chain PX residue 132 ASP Chi-restraints excluded: chain PA residue 37 THR Chi-restraints excluded: chain PA residue 73 VAL Chi-restraints excluded: chain PA residue 100 LYS Chi-restraints excluded: chain PB residue 303 MET Chi-restraints excluded: chain PC residue 55 LEU Chi-restraints excluded: chain PC residue 56 THR Chi-restraints excluded: chain PC residue 73 VAL Chi-restraints excluded: chain PD residue 73 VAL Chi-restraints excluded: chain PD residue 185 GLN Chi-restraints excluded: chain PE residue 37 THR Chi-restraints excluded: chain PE residue 303 MET Chi-restraints excluded: chain PE residue 333 ARG Chi-restraints excluded: chain PF residue 56 THR Chi-restraints excluded: chain PF residue 73 VAL Chi-restraints excluded: chain PF residue 357 MET Chi-restraints excluded: chain PF residue 405 GLU Chi-restraints excluded: chain PG residue 37 THR Chi-restraints excluded: chain PG residue 73 VAL Chi-restraints excluded: chain PG residue 286 GLU Chi-restraints excluded: chain PH residue 303 MET Chi-restraints excluded: chain PI residue 73 VAL Chi-restraints excluded: chain PJ residue 37 THR Chi-restraints excluded: chain PJ residue 56 THR Chi-restraints excluded: chain PJ residue 87 GLU Chi-restraints excluded: chain PJ residue 218 ASP Chi-restraints excluded: chain PK residue 37 THR Chi-restraints excluded: chain PK residue 303 MET Chi-restraints excluded: chain PK residue 328 LYS Chi-restraints excluded: chain PK residue 413 GLU Chi-restraints excluded: chain PL residue 55 LEU Chi-restraints excluded: chain PL residue 64 LYS Chi-restraints excluded: chain PL residue 73 VAL Chi-restraints excluded: chain PL residue 164 GLU Chi-restraints excluded: chain PL residue 413 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 604 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 357 optimal weight: 0.4980 chunk 457 optimal weight: 7.9990 chunk 354 optimal weight: 0.1980 chunk 527 optimal weight: 2.9990 chunk 350 optimal weight: 0.7980 chunk 624 optimal weight: 6.9990 chunk 390 optimal weight: 0.8980 chunk 380 optimal weight: 0.8980 chunk 288 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 51696 Z= 0.140 Angle : 0.510 9.034 70188 Z= 0.263 Chirality : 0.038 0.137 7584 Planarity : 0.003 0.032 9456 Dihedral : 6.982 87.893 7056 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.40 % Allowed : 17.10 % Favored : 81.51 % 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: 1.12 (0.11), residues: 6312 helix: 1.92 (0.09), residues: 3144 sheet: 0.32 (0.23), residues: 516 loop : -0.62 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRPPJ 134 HIS 0.003 0.001 HISPK 175 PHE 0.013 0.001 PHEPK 334 TYR 0.026 0.002 TYRPG 184 ARG 0.007 0.000 ARGPS 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 867 time to evaluate : 4.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: PN 20 GLN cc_start: 0.9048 (tp40) cc_final: 0.8437 (tp-100) REVERT: PN 24 ASP cc_start: 0.8772 (m-30) cc_final: 0.8329 (m-30) REVERT: PO 95 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8454 (tm-30) REVERT: PQ 24 ASP cc_start: 0.8747 (m-30) cc_final: 0.8373 (m-30) REVERT: PR 95 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8337 (tm-30) REVERT: PT 20 GLN cc_start: 0.9079 (tp40) cc_final: 0.8571 (tp-100) REVERT: PT 24 ASP cc_start: 0.8706 (m-30) cc_final: 0.8305 (m-30) REVERT: PU 95 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8341 (tm-30) REVERT: PU 132 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8451 (m-30) REVERT: PW 24 ASP cc_start: 0.8788 (m-30) cc_final: 0.8359 (m-30) REVERT: PX 132 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: PA 59 ASP cc_start: 0.8836 (m-30) cc_final: 0.8532 (m-30) REVERT: PA 77 MET cc_start: 0.8348 (mmm) cc_final: 0.8021 (mmm) REVERT: PA 301 MET cc_start: 0.8380 (ttt) cc_final: 0.8103 (ttt) REVERT: PA 372 ASP cc_start: 0.8851 (t0) cc_final: 0.8526 (t0) REVERT: PA 389 ASP cc_start: 0.9054 (m-30) cc_final: 0.8802 (m-30) REVERT: PA 416 GLU cc_start: 0.9270 (tm-30) cc_final: 0.9008 (tm-30) REVERT: PA 429 LYS cc_start: 0.9069 (ttmt) cc_final: 0.8612 (mmtm) REVERT: PB 59 ASP cc_start: 0.8876 (m-30) cc_final: 0.8568 (m-30) REVERT: PB 331 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8496 (mt-10) REVERT: PB 386 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8648 (mm-30) REVERT: PB 413 GLU cc_start: 0.9121 (tt0) cc_final: 0.8524 (tm-30) REVERT: PB 426 ASP cc_start: 0.9125 (m-30) cc_final: 0.8709 (t0) REVERT: PC 331 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8653 (mt-10) REVERT: PC 386 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8676 (mm-30) REVERT: PC 413 GLU cc_start: 0.9261 (mm-30) cc_final: 0.8849 (tm-30) REVERT: PC 416 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8836 (tm-30) REVERT: PC 426 ASP cc_start: 0.9068 (m-30) cc_final: 0.8748 (t0) REVERT: PC 429 LYS cc_start: 0.9112 (ttmt) cc_final: 0.8758 (tppp) REVERT: PD 59 ASP cc_start: 0.8858 (m-30) cc_final: 0.8575 (m-30) REVERT: PD 77 MET cc_start: 0.8286 (mmm) cc_final: 0.7869 (mmm) REVERT: PD 177 ARG cc_start: 0.8588 (ttt-90) cc_final: 0.8319 (ttt180) REVERT: PD 295 TYR cc_start: 0.8778 (p90) cc_final: 0.8378 (p90) REVERT: PD 301 MET cc_start: 0.8396 (ttt) cc_final: 0.8116 (ttt) REVERT: PD 372 ASP cc_start: 0.8839 (t0) cc_final: 0.8490 (t0) REVERT: PD 389 ASP cc_start: 0.8954 (m-30) cc_final: 0.8710 (m-30) REVERT: PD 416 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8819 (tm-30) REVERT: PD 426 ASP cc_start: 0.9134 (m-30) cc_final: 0.8811 (t0) REVERT: PE 59 ASP cc_start: 0.8883 (m-30) cc_final: 0.8581 (m-30) REVERT: PE 97 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8648 (p0) REVERT: PE 328 LYS cc_start: 0.8854 (mttt) cc_final: 0.8621 (mtmm) REVERT: PE 331 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8603 (mt-10) REVERT: PE 364 TYR cc_start: 0.8942 (m-80) cc_final: 0.8698 (m-80) REVERT: PE 401 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8704 (tm-30) REVERT: PE 413 GLU cc_start: 0.9427 (mm-30) cc_final: 0.8979 (tm-30) REVERT: PE 426 ASP cc_start: 0.9138 (m-30) cc_final: 0.8732 (t0) REVERT: PE 429 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8743 (tppp) REVERT: PF 301 MET cc_start: 0.8517 (ttt) cc_final: 0.8028 (ttt) REVERT: PF 331 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8689 (mt-10) REVERT: PF 386 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8752 (mm-30) REVERT: PF 405 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8625 (pp20) REVERT: PF 416 GLU cc_start: 0.9272 (tm-30) cc_final: 0.8795 (tm-30) REVERT: PF 426 ASP cc_start: 0.9064 (m-30) cc_final: 0.8718 (t0) REVERT: PF 429 LYS cc_start: 0.9063 (ttmt) cc_final: 0.8674 (tppp) REVERT: PG 59 ASP cc_start: 0.8829 (m-30) cc_final: 0.8560 (m-30) REVERT: PG 295 TYR cc_start: 0.8727 (p90) cc_final: 0.8418 (p90) REVERT: PG 301 MET cc_start: 0.8335 (ttt) cc_final: 0.8020 (ttt) REVERT: PG 331 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8524 (mt-10) REVERT: PG 372 ASP cc_start: 0.8819 (t0) cc_final: 0.8491 (t0) REVERT: PG 389 ASP cc_start: 0.8995 (m-30) cc_final: 0.8729 (m-30) REVERT: PG 416 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8994 (tm-30) REVERT: PG 429 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8626 (tppp) REVERT: PH 59 ASP cc_start: 0.8870 (m-30) cc_final: 0.8559 (m-30) REVERT: PH 301 MET cc_start: 0.8599 (ttt) cc_final: 0.8226 (ttt) REVERT: PH 331 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8690 (mt-10) REVERT: PH 372 ASP cc_start: 0.8839 (t0) cc_final: 0.8486 (t0) REVERT: PH 413 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9031 (tm-30) REVERT: PH 426 ASP cc_start: 0.9150 (m-30) cc_final: 0.8703 (t0) REVERT: PI 59 ASP cc_start: 0.8970 (m-30) cc_final: 0.8704 (m-30) REVERT: PI 331 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8713 (mt-10) REVERT: PI 386 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8648 (mm-30) REVERT: PI 413 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8837 (tm-30) REVERT: PI 416 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8772 (tm-30) REVERT: PI 429 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8753 (tppp) REVERT: PJ 218 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.7950 (p0) REVERT: PJ 219 GLU cc_start: 0.8661 (mp0) cc_final: 0.8291 (mp0) REVERT: PJ 295 TYR cc_start: 0.8762 (p90) cc_final: 0.8397 (p90) REVERT: PJ 301 MET cc_start: 0.8395 (ttt) cc_final: 0.8126 (ttt) REVERT: PJ 331 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8554 (mt-10) REVERT: PJ 389 ASP cc_start: 0.8992 (m-30) cc_final: 0.8746 (m-30) REVERT: PJ 429 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8627 (tppp) REVERT: PK 59 ASP cc_start: 0.8883 (m-30) cc_final: 0.8559 (m-30) REVERT: PK 301 MET cc_start: 0.8613 (ttt) cc_final: 0.8276 (ttt) REVERT: PK 331 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8702 (mt-10) REVERT: PK 372 ASP cc_start: 0.8849 (t0) cc_final: 0.8486 (t0) REVERT: PK 416 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8947 (tm-30) REVERT: PK 426 ASP cc_start: 0.9145 (m-30) cc_final: 0.8727 (t0) REVERT: PK 429 LYS cc_start: 0.9084 (ttmt) cc_final: 0.8788 (tppt) REVERT: PL 55 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8254 (pp) REVERT: PL 64 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8892 (tttp) REVERT: PL 164 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8427 (mt-10) REVERT: PL 301 MET cc_start: 0.8550 (ttt) cc_final: 0.8031 (ttt) REVERT: PL 331 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8637 (mt-10) REVERT: PL 386 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8755 (mm-30) REVERT: PL 413 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.8775 (tm-30) REVERT: PL 416 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8839 (tm-30) REVERT: PL 429 LYS cc_start: 0.9169 (ttmt) cc_final: 0.8861 (tppp) outliers start: 75 outliers final: 30 residues processed: 917 average time/residue: 1.2339 time to fit residues: 1447.7346 Evaluate side-chains 826 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 787 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PM residue 17 LEU Chi-restraints excluded: chain PM residue 115 ASP Chi-restraints excluded: chain PN residue 138 LEU Chi-restraints excluded: chain PP residue 17 LEU Chi-restraints excluded: chain PP residue 138 LEU Chi-restraints excluded: chain PQ residue 138 LEU Chi-restraints excluded: chain PS residue 17 LEU Chi-restraints excluded: chain PS residue 132 ASP Chi-restraints excluded: chain PT residue 138 LEU Chi-restraints excluded: chain PU residue 132 ASP Chi-restraints excluded: chain PV residue 90 GLU Chi-restraints excluded: chain PV residue 138 LEU Chi-restraints excluded: chain PW residue 138 LEU Chi-restraints excluded: chain PX residue 132 ASP Chi-restraints excluded: chain PA residue 73 VAL Chi-restraints excluded: chain PA residue 286 GLU Chi-restraints excluded: chain PC residue 55 LEU Chi-restraints excluded: chain PC residue 73 VAL Chi-restraints excluded: chain PD residue 37 THR Chi-restraints excluded: chain PD residue 73 VAL Chi-restraints excluded: chain PE residue 37 THR Chi-restraints excluded: chain PE residue 97 ASP Chi-restraints excluded: chain PF residue 56 THR Chi-restraints excluded: chain PF residue 73 VAL Chi-restraints excluded: chain PF residue 357 MET Chi-restraints excluded: chain PF residue 405 GLU Chi-restraints excluded: chain PG residue 73 VAL Chi-restraints excluded: chain PI residue 73 VAL Chi-restraints excluded: chain PI residue 357 MET Chi-restraints excluded: chain PJ residue 56 THR Chi-restraints excluded: chain PJ residue 218 ASP Chi-restraints excluded: chain PJ residue 286 GLU Chi-restraints excluded: chain PK residue 303 MET Chi-restraints excluded: chain PL residue 55 LEU Chi-restraints excluded: chain PL residue 64 LYS Chi-restraints excluded: chain PL residue 164 GLU Chi-restraints excluded: chain PL residue 357 MET Chi-restraints excluded: chain PL residue 413 GLU Chi-restraints excluded: chain PL residue 423 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 386 optimal weight: 3.9990 chunk 249 optimal weight: 20.0000 chunk 373 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 397 optimal weight: 0.8980 chunk 425 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 490 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 51696 Z= 0.252 Angle : 0.561 9.610 70188 Z= 0.288 Chirality : 0.040 0.143 7584 Planarity : 0.004 0.055 9456 Dihedral : 7.007 88.968 7056 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.29 % Allowed : 17.65 % Favored : 81.06 % 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: 1.11 (0.11), residues: 6312 helix: 1.91 (0.09), residues: 3144 sheet: -0.05 (0.22), residues: 564 loop : -0.52 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRPPC 134 HIS 0.004 0.001 HISPJ 175 PHE 0.019 0.002 PHEPJ 334 TYR 0.028 0.002 TYRPG 184 ARG 0.007 0.000 ARGPS 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 806 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: PN 20 GLN cc_start: 0.9150 (tp40) cc_final: 0.8531 (tp-100) REVERT: PN 24 ASP cc_start: 0.8836 (m-30) cc_final: 0.8399 (m-30) REVERT: PO 95 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8553 (tm-30) REVERT: PQ 24 ASP cc_start: 0.8823 (m-30) cc_final: 0.8462 (m-30) REVERT: PR 95 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8379 (tm-30) REVERT: PT 20 GLN cc_start: 0.9099 (tp40) cc_final: 0.8568 (tp-100) REVERT: PT 24 ASP cc_start: 0.8795 (m-30) cc_final: 0.8389 (m-30) REVERT: PU 95 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8423 (tm-30) REVERT: PU 132 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8501 (m-30) REVERT: PW 20 GLN cc_start: 0.9141 (tp40) cc_final: 0.8484 (tp-100) REVERT: PW 24 ASP cc_start: 0.8851 (m-30) cc_final: 0.8499 (m-30) REVERT: PX 95 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8277 (tm-30) REVERT: PX 132 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8410 (m-30) REVERT: PA 59 ASP cc_start: 0.8899 (m-30) cc_final: 0.8612 (m-30) REVERT: PA 77 MET cc_start: 0.8405 (mmm) cc_final: 0.8190 (mmm) REVERT: PA 372 ASP cc_start: 0.8880 (t0) cc_final: 0.8551 (t0) REVERT: PA 389 ASP cc_start: 0.9037 (m-30) cc_final: 0.8782 (m-30) REVERT: PA 413 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8775 (tm-30) REVERT: PA 416 GLU cc_start: 0.9235 (tm-30) cc_final: 0.9035 (tm-30) REVERT: PA 429 LYS cc_start: 0.9109 (ttmt) cc_final: 0.8645 (mmtm) REVERT: PB 59 ASP cc_start: 0.8858 (m-30) cc_final: 0.8555 (m-30) REVERT: PB 98 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8336 (mp0) REVERT: PB 331 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8573 (mt-10) REVERT: PB 386 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8661 (mm-30) REVERT: PB 413 GLU cc_start: 0.9118 (tt0) cc_final: 0.8606 (tm-30) REVERT: PB 426 ASP cc_start: 0.9149 (m-30) cc_final: 0.8707 (t0) REVERT: PC 64 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8883 (tptp) REVERT: PC 261 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.7947 (mpp80) REVERT: PC 331 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8695 (mt-10) REVERT: PC 386 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8693 (mm-30) REVERT: PC 413 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8882 (tm-30) REVERT: PC 416 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8838 (tm-30) REVERT: PC 426 ASP cc_start: 0.9094 (m-30) cc_final: 0.8751 (t0) REVERT: PC 429 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8787 (tppp) REVERT: PD 59 ASP cc_start: 0.8908 (m-30) cc_final: 0.8617 (m-30) REVERT: PD 77 MET cc_start: 0.8425 (mmm) cc_final: 0.8175 (mmm) REVERT: PD 301 MET cc_start: 0.8421 (ttt) cc_final: 0.8152 (ttt) REVERT: PD 331 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8575 (mt-10) REVERT: PD 372 ASP cc_start: 0.8862 (t0) cc_final: 0.8509 (t0) REVERT: PD 389 ASP cc_start: 0.8928 (m-30) cc_final: 0.8566 (m-30) REVERT: PD 416 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8813 (tm-30) REVERT: PD 426 ASP cc_start: 0.9153 (m-30) cc_final: 0.8798 (t0) REVERT: PE 59 ASP cc_start: 0.8929 (m-30) cc_final: 0.8620 (m-30) REVERT: PE 328 LYS cc_start: 0.8944 (mttt) cc_final: 0.8637 (mtmm) REVERT: PE 331 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8621 (mt-10) REVERT: PE 364 TYR cc_start: 0.8942 (m-80) cc_final: 0.8628 (m-80) REVERT: PE 401 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8738 (tm-30) REVERT: PE 413 GLU cc_start: 0.9440 (mm-30) cc_final: 0.8980 (tm-30) REVERT: PE 416 GLU cc_start: 0.9281 (tm-30) cc_final: 0.8948 (tm-30) REVERT: PE 426 ASP cc_start: 0.9147 (m-30) cc_final: 0.8703 (t0) REVERT: PE 429 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8784 (tppp) REVERT: PF 64 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8865 (tptp) REVERT: PF 301 MET cc_start: 0.8511 (ttt) cc_final: 0.8030 (ttt) REVERT: PF 331 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8743 (mt-10) REVERT: PF 386 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8753 (mm-30) REVERT: PF 405 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8698 (pp20) REVERT: PF 413 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8874 (tm-30) REVERT: PF 416 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8871 (tm-30) REVERT: PF 426 ASP cc_start: 0.9095 (m-30) cc_final: 0.8714 (t0) REVERT: PF 429 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8776 (tppp) REVERT: PG 59 ASP cc_start: 0.8897 (m-30) cc_final: 0.8630 (m-30) REVERT: PG 77 MET cc_start: 0.8368 (mmm) cc_final: 0.7760 (mmm) REVERT: PG 210 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8811 (mp) REVERT: PG 261 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8112 (mpp80) REVERT: PG 301 MET cc_start: 0.8402 (ttt) cc_final: 0.8093 (ttt) REVERT: PG 331 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8569 (mt-10) REVERT: PG 372 ASP cc_start: 0.8800 (t0) cc_final: 0.8475 (t0) REVERT: PG 389 ASP cc_start: 0.9012 (m-30) cc_final: 0.8748 (m-30) REVERT: PG 429 LYS cc_start: 0.9090 (ttmt) cc_final: 0.8659 (tppp) REVERT: PH 59 ASP cc_start: 0.8916 (m-30) cc_final: 0.8599 (m-30) REVERT: PH 301 MET cc_start: 0.8624 (ttt) cc_final: 0.8263 (ttt) REVERT: PH 331 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8732 (mt-10) REVERT: PH 372 ASP cc_start: 0.8824 (t0) cc_final: 0.8485 (t0) REVERT: PH 413 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9032 (tm-30) REVERT: PH 426 ASP cc_start: 0.9163 (m-30) cc_final: 0.8706 (t0) REVERT: PI 331 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8747 (mt-10) REVERT: PI 372 ASP cc_start: 0.8788 (t0) cc_final: 0.8447 (t0) REVERT: PI 386 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8629 (mm-30) REVERT: PI 413 GLU cc_start: 0.9366 (mm-30) cc_final: 0.8892 (tm-30) REVERT: PI 416 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8778 (tm-30) REVERT: PI 429 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8811 (tppp) REVERT: PJ 218 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.7940 (p0) REVERT: PJ 219 GLU cc_start: 0.8699 (mp0) cc_final: 0.8311 (mp0) REVERT: PJ 295 TYR cc_start: 0.8805 (p90) cc_final: 0.8495 (p90) REVERT: PJ 301 MET cc_start: 0.8417 (ttt) cc_final: 0.8152 (ttt) REVERT: PJ 331 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8605 (mt-10) REVERT: PJ 389 ASP cc_start: 0.9003 (m-30) cc_final: 0.8774 (m-30) REVERT: PJ 429 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8665 (tppp) REVERT: PK 59 ASP cc_start: 0.8923 (m-30) cc_final: 0.8600 (m-30) REVERT: PK 301 MET cc_start: 0.8624 (ttt) cc_final: 0.8303 (ttt) REVERT: PK 331 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8726 (mt-10) REVERT: PK 372 ASP cc_start: 0.8850 (t0) cc_final: 0.8489 (t0) REVERT: PK 413 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9085 (tm-30) REVERT: PK 416 GLU cc_start: 0.9284 (tm-30) cc_final: 0.8956 (tm-30) REVERT: PK 426 ASP cc_start: 0.9153 (m-30) cc_final: 0.8729 (t0) REVERT: PK 429 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8809 (tppt) REVERT: PL 64 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8865 (tptp) REVERT: PL 164 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: PL 261 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.7949 (mpp80) REVERT: PL 301 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8089 (ttt) REVERT: PL 331 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8727 (mt-10) REVERT: PL 372 ASP cc_start: 0.8864 (t0) cc_final: 0.8530 (t0) REVERT: PL 386 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8743 (mm-30) REVERT: PL 413 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.8802 (tm-30) REVERT: PL 416 GLU cc_start: 0.9299 (tm-30) cc_final: 0.8864 (tm-30) REVERT: PL 429 LYS cc_start: 0.9177 (ttmt) cc_final: 0.8861 (tppp) outliers start: 69 outliers final: 27 residues processed: 860 average time/residue: 1.2280 time to fit residues: 1354.0140 Evaluate side-chains 817 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 776 time to evaluate : 4.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PM residue 17 LEU Chi-restraints excluded: chain PN residue 138 LEU Chi-restraints excluded: chain PP residue 17 LEU Chi-restraints excluded: chain PQ residue 138 LEU Chi-restraints excluded: chain PS residue 17 LEU Chi-restraints excluded: chain PT residue 138 LEU Chi-restraints excluded: chain PU residue 132 ASP Chi-restraints excluded: chain PV residue 138 LEU Chi-restraints excluded: chain PX residue 132 ASP Chi-restraints excluded: chain PA residue 286 GLU Chi-restraints excluded: chain PC residue 55 LEU Chi-restraints excluded: chain PC residue 56 THR Chi-restraints excluded: chain PC residue 64 LYS Chi-restraints excluded: chain PC residue 73 VAL Chi-restraints excluded: chain PC residue 261 ARG Chi-restraints excluded: chain PD residue 37 THR Chi-restraints excluded: chain PD residue 73 VAL Chi-restraints excluded: chain PE residue 37 THR Chi-restraints excluded: chain PF residue 56 THR Chi-restraints excluded: chain PF residue 64 LYS Chi-restraints excluded: chain PF residue 73 VAL Chi-restraints excluded: chain PF residue 405 GLU Chi-restraints excluded: chain PG residue 73 VAL Chi-restraints excluded: chain PG residue 210 ILE Chi-restraints excluded: chain PG residue 261 ARG Chi-restraints excluded: chain PG residue 286 GLU Chi-restraints excluded: chain PH residue 303 MET Chi-restraints excluded: chain PI residue 73 VAL Chi-restraints excluded: chain PJ residue 56 THR Chi-restraints excluded: chain PJ residue 73 VAL Chi-restraints excluded: chain PJ residue 218 ASP Chi-restraints excluded: chain PJ residue 286 GLU Chi-restraints excluded: chain PK residue 303 MET Chi-restraints excluded: chain PL residue 56 THR Chi-restraints excluded: chain PL residue 64 LYS Chi-restraints excluded: chain PL residue 73 VAL Chi-restraints excluded: chain PL residue 164 GLU Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PL residue 301 MET Chi-restraints excluded: chain PL residue 413 GLU Chi-restraints excluded: chain PL residue 423 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 568 optimal weight: 3.9990 chunk 598 optimal weight: 2.9990 chunk 545 optimal weight: 0.9980 chunk 582 optimal weight: 10.0000 chunk 350 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 457 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 525 optimal weight: 0.0870 chunk 550 optimal weight: 3.9990 chunk 579 optimal weight: 9.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PO 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 51696 Z= 0.257 Angle : 0.566 9.624 70188 Z= 0.291 Chirality : 0.040 0.143 7584 Planarity : 0.004 0.047 9456 Dihedral : 7.010 88.738 7056 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.08 % Allowed : 18.16 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.11), residues: 6312 helix: 1.88 (0.09), residues: 3132 sheet: -0.07 (0.22), residues: 564 loop : -0.55 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRPPC 134 HIS 0.004 0.001 HISPJ 175 PHE 0.021 0.002 PHEPI 334 TYR 0.029 0.002 TYRPG 184 ARG 0.006 0.000 ARGPS 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 797 time to evaluate : 4.558 Fit side-chains revert: symmetry clash REVERT: PN 24 ASP cc_start: 0.8849 (m-30) cc_final: 0.8406 (m-30) REVERT: PO 95 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8532 (tm-30) REVERT: PQ 24 ASP cc_start: 0.8834 (m-30) cc_final: 0.8463 (m-30) REVERT: PR 95 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8385 (tm-30) REVERT: PT 20 GLN cc_start: 0.9118 (tp40) cc_final: 0.8613 (tp-100) REVERT: PT 24 ASP cc_start: 0.8812 (m-30) cc_final: 0.8395 (m-30) REVERT: PU 95 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8431 (tm-30) REVERT: PU 132 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: PW 20 GLN cc_start: 0.9143 (tp40) cc_final: 0.8498 (tp-100) REVERT: PW 24 ASP cc_start: 0.8821 (m-30) cc_final: 0.8463 (m-30) REVERT: PX 95 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8291 (tm-30) REVERT: PX 132 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8467 (m-30) REVERT: PA 59 ASP cc_start: 0.8905 (m-30) cc_final: 0.8616 (m-30) REVERT: PA 77 MET cc_start: 0.8404 (mmm) cc_final: 0.8017 (mmm) REVERT: PA 372 ASP cc_start: 0.8915 (t0) cc_final: 0.8604 (t0) REVERT: PA 389 ASP cc_start: 0.9039 (m-30) cc_final: 0.8721 (m-30) REVERT: PA 429 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8659 (mmtm) REVERT: PB 59 ASP cc_start: 0.8877 (m-30) cc_final: 0.8572 (m-30) REVERT: PB 98 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8332 (mp0) REVERT: PB 331 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8569 (mt-10) REVERT: PB 386 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8668 (mm-30) REVERT: PB 413 GLU cc_start: 0.9119 (tt0) cc_final: 0.8609 (tm-30) REVERT: PB 426 ASP cc_start: 0.9189 (m-30) cc_final: 0.8718 (t0) REVERT: PC 331 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8697 (mt-10) REVERT: PC 372 ASP cc_start: 0.8813 (t0) cc_final: 0.8471 (t0) REVERT: PC 386 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8700 (mm-30) REVERT: PC 413 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8904 (tm-30) REVERT: PC 416 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8849 (tm-30) REVERT: PC 426 ASP cc_start: 0.9108 (m-30) cc_final: 0.8758 (t0) REVERT: PC 429 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8870 (tppp) REVERT: PD 59 ASP cc_start: 0.8916 (m-30) cc_final: 0.8656 (m-30) REVERT: PD 269 ARG cc_start: 0.9099 (tmm-80) cc_final: 0.8840 (ttm-80) REVERT: PD 295 TYR cc_start: 0.8813 (p90) cc_final: 0.8479 (p90) REVERT: PD 331 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8578 (mt-10) REVERT: PD 372 ASP cc_start: 0.8875 (t0) cc_final: 0.8510 (t0) REVERT: PD 389 ASP cc_start: 0.8938 (m-30) cc_final: 0.8593 (m-30) REVERT: PD 416 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8915 (tm-30) REVERT: PD 426 ASP cc_start: 0.9165 (m-30) cc_final: 0.8810 (t0) REVERT: PE 59 ASP cc_start: 0.8878 (m-30) cc_final: 0.8576 (m-30) REVERT: PE 98 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8233 (mp0) REVERT: PE 328 LYS cc_start: 0.8974 (mttt) cc_final: 0.8557 (mtmm) REVERT: PE 331 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8597 (mt-10) REVERT: PE 364 TYR cc_start: 0.8933 (m-80) cc_final: 0.8637 (m-80) REVERT: PE 401 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8720 (tm-30) REVERT: PE 426 ASP cc_start: 0.9159 (m-30) cc_final: 0.8709 (t0) REVERT: PF 301 MET cc_start: 0.8473 (ttt) cc_final: 0.7968 (ttt) REVERT: PF 331 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8729 (mt-10) REVERT: PF 386 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8737 (mm-30) REVERT: PF 405 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8713 (pp20) REVERT: PF 413 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8878 (tm-30) REVERT: PF 416 GLU cc_start: 0.9286 (tm-30) cc_final: 0.8880 (tm-30) REVERT: PF 426 ASP cc_start: 0.9108 (m-30) cc_final: 0.8724 (t0) REVERT: PF 429 LYS cc_start: 0.9148 (ttmt) cc_final: 0.8814 (tppp) REVERT: PG 59 ASP cc_start: 0.8910 (m-30) cc_final: 0.8648 (m-30) REVERT: PG 77 MET cc_start: 0.8382 (mmm) cc_final: 0.7860 (mmm) REVERT: PG 210 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8803 (mp) REVERT: PG 261 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8111 (mpp80) REVERT: PG 269 ARG cc_start: 0.9095 (tmm-80) cc_final: 0.8841 (ttm-80) REVERT: PG 301 MET cc_start: 0.8372 (ttt) cc_final: 0.8059 (ttt) REVERT: PG 331 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8571 (mt-10) REVERT: PG 372 ASP cc_start: 0.8810 (t0) cc_final: 0.8486 (t0) REVERT: PG 389 ASP cc_start: 0.9019 (m-30) cc_final: 0.8770 (m-30) REVERT: PG 415 ASP cc_start: 0.9131 (m-30) cc_final: 0.8902 (p0) REVERT: PG 429 LYS cc_start: 0.9097 (ttmt) cc_final: 0.8673 (tppp) REVERT: PH 59 ASP cc_start: 0.8937 (m-30) cc_final: 0.8622 (m-30) REVERT: PH 301 MET cc_start: 0.8621 (ttt) cc_final: 0.8281 (ttt) REVERT: PH 331 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8749 (mt-10) REVERT: PH 372 ASP cc_start: 0.8823 (t0) cc_final: 0.8490 (t0) REVERT: PH 413 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9027 (tm-30) REVERT: PH 426 ASP cc_start: 0.9145 (m-30) cc_final: 0.8684 (t0) REVERT: PI 106 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9076 (mm-30) REVERT: PI 184 TYR cc_start: 0.8767 (m-10) cc_final: 0.8500 (m-10) REVERT: PI 331 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8731 (mt-10) REVERT: PI 372 ASP cc_start: 0.8811 (t0) cc_final: 0.8487 (t0) REVERT: PI 386 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8632 (mm-30) REVERT: PI 413 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8886 (tm-30) REVERT: PI 416 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8769 (tm-30) REVERT: PI 429 LYS cc_start: 0.9240 (ttmt) cc_final: 0.8932 (tppp) REVERT: PJ 218 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.7968 (p0) REVERT: PJ 219 GLU cc_start: 0.8708 (mp0) cc_final: 0.8308 (mp0) REVERT: PJ 301 MET cc_start: 0.8427 (ttt) cc_final: 0.8192 (ttt) REVERT: PJ 331 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8607 (mt-10) REVERT: PJ 389 ASP cc_start: 0.8994 (m-30) cc_final: 0.8770 (m-30) REVERT: PJ 413 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8803 (tm-30) REVERT: PJ 429 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8676 (tppp) REVERT: PK 59 ASP cc_start: 0.8959 (m-30) cc_final: 0.8631 (m-30) REVERT: PK 301 MET cc_start: 0.8629 (ttt) cc_final: 0.8297 (ttt) REVERT: PK 331 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8580 (mt-10) REVERT: PK 372 ASP cc_start: 0.8862 (t0) cc_final: 0.8507 (t0) REVERT: PK 413 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9022 (tm-30) REVERT: PK 416 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8941 (tm-30) REVERT: PK 426 ASP cc_start: 0.9154 (m-30) cc_final: 0.8723 (t0) REVERT: PK 429 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8831 (tppt) REVERT: PL 64 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8867 (tptp) REVERT: PL 164 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8427 (mt-10) REVERT: PL 261 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.7957 (mpp80) REVERT: PL 301 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8160 (ttt) REVERT: PL 331 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8698 (mt-10) REVERT: PL 372 ASP cc_start: 0.8815 (t0) cc_final: 0.8470 (t0) REVERT: PL 386 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8732 (mm-30) REVERT: PL 413 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.8805 (tm-30) REVERT: PL 416 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8839 (tm-30) REVERT: PL 429 LYS cc_start: 0.9211 (ttmt) cc_final: 0.8906 (tppp) outliers start: 58 outliers final: 29 residues processed: 838 average time/residue: 1.2143 time to fit residues: 1292.7571 Evaluate side-chains 814 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 774 time to evaluate : 4.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PM residue 17 LEU Chi-restraints excluded: chain PN residue 138 LEU Chi-restraints excluded: chain PP residue 17 LEU Chi-restraints excluded: chain PQ residue 138 LEU Chi-restraints excluded: chain PS residue 17 LEU Chi-restraints excluded: chain PT residue 138 LEU Chi-restraints excluded: chain PU residue 132 ASP Chi-restraints excluded: chain PW residue 138 LEU Chi-restraints excluded: chain PX residue 132 ASP Chi-restraints excluded: chain PA residue 286 GLU Chi-restraints excluded: chain PC residue 55 LEU Chi-restraints excluded: chain PC residue 56 THR Chi-restraints excluded: chain PC residue 73 VAL Chi-restraints excluded: chain PD residue 37 THR Chi-restraints excluded: chain PE residue 37 THR Chi-restraints excluded: chain PE residue 333 ARG Chi-restraints excluded: chain PF residue 55 LEU Chi-restraints excluded: chain PF residue 56 THR Chi-restraints excluded: chain PF residue 73 VAL Chi-restraints excluded: chain PF residue 405 GLU Chi-restraints excluded: chain PG residue 37 THR Chi-restraints excluded: chain PG residue 73 VAL Chi-restraints excluded: chain PG residue 210 ILE Chi-restraints excluded: chain PG residue 261 ARG Chi-restraints excluded: chain PG residue 286 GLU Chi-restraints excluded: chain PH residue 303 MET Chi-restraints excluded: chain PI residue 73 VAL Chi-restraints excluded: chain PJ residue 56 THR Chi-restraints excluded: chain PJ residue 73 VAL Chi-restraints excluded: chain PJ residue 218 ASP Chi-restraints excluded: chain PJ residue 286 GLU Chi-restraints excluded: chain PK residue 303 MET Chi-restraints excluded: chain PL residue 56 THR Chi-restraints excluded: chain PL residue 64 LYS Chi-restraints excluded: chain PL residue 73 VAL Chi-restraints excluded: chain PL residue 164 GLU Chi-restraints excluded: chain PL residue 261 ARG Chi-restraints excluded: chain PL residue 301 MET Chi-restraints excluded: chain PL residue 413 GLU Chi-restraints excluded: chain PL residue 423 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 382 optimal weight: 0.4980 chunk 615 optimal weight: 0.9990 chunk 375 optimal weight: 0.0270 chunk 291 optimal weight: 3.9990 chunk 427 optimal weight: 7.9990 chunk 645 optimal weight: 0.5980 chunk 594 optimal weight: 0.1980 chunk 514 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 397 optimal weight: 0.8980 chunk 315 optimal weight: 3.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: PR 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 51696 Z= 0.138 Angle : 0.529 9.120 70188 Z= 0.272 Chirality : 0.038 0.137 7584 Planarity : 0.003 0.039 9456 Dihedral : 6.911 87.930 7056 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.86 % Allowed : 18.46 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.11), residues: 6312 helix: 1.85 (0.09), residues: 3156 sheet: 0.14 (0.22), residues: 540 loop : -0.53 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPPJ 134 HIS 0.004 0.001 HISPB 299 PHE 0.017 0.001 PHEPI 334 TYR 0.027 0.002 TYRPG 184 ARG 0.006 0.000 ARGPS 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12624 Ramachandran restraints generated. 6312 Oldfield, 0 Emsley, 6312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 851 time to evaluate : 4.533 Fit side-chains revert: symmetry clash REVERT: PN 20 GLN cc_start: 0.9067 (tp40) cc_final: 0.8435 (tp-100) REVERT: PN 24 ASP cc_start: 0.8765 (m-30) cc_final: 0.8351 (m-30) REVERT: PO 95 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8458 (tm-30) REVERT: PQ 20 GLN cc_start: 0.9119 (tp40) cc_final: 0.8462 (tp-100) REVERT: PQ 24 ASP cc_start: 0.8734 (m-30) cc_final: 0.8368 (m-30) REVERT: PR 95 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8356 (tm-30) REVERT: PT 20 GLN cc_start: 0.9044 (tp40) cc_final: 0.8516 (tp-100) REVERT: PT 24 ASP cc_start: 0.8711 (m-30) cc_final: 0.8270 (m-30) REVERT: PU 95 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8363 (tm-30) REVERT: PU 132 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: PV 40 THR cc_start: 0.8508 (m) cc_final: 0.8082 (m) REVERT: PW 20 GLN cc_start: 0.9101 (tp40) cc_final: 0.8499 (tp-100) REVERT: PW 24 ASP cc_start: 0.8778 (m-30) cc_final: 0.8443 (m-30) REVERT: PW 66 ARG cc_start: 0.9117 (mtt90) cc_final: 0.8885 (mtt180) REVERT: PX 132 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8453 (m-30) REVERT: PA 59 ASP cc_start: 0.8846 (m-30) cc_final: 0.8543 (m-30) REVERT: PA 77 MET cc_start: 0.8280 (mmm) cc_final: 0.7841 (mmm) REVERT: PA 331 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8629 (mt-10) REVERT: PA 372 ASP cc_start: 0.8880 (t0) cc_final: 0.8562 (t0) REVERT: PA 389 ASP cc_start: 0.9029 (m-30) cc_final: 0.8763 (m-30) REVERT: PA 415 ASP cc_start: 0.9082 (m-30) cc_final: 0.8877 (p0) REVERT: PA 429 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8617 (mmtm) REVERT: PB 59 ASP cc_start: 0.8832 (m-30) cc_final: 0.8525 (m-30) REVERT: PB 98 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8278 (mp0) REVERT: PB 331 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8553 (mt-10) REVERT: PB 386 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8627 (mm-30) REVERT: PB 426 ASP cc_start: 0.9186 (m-30) cc_final: 0.8719 (t0) REVERT: PC 55 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8106 (pp) REVERT: PC 331 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8648 (mt-10) REVERT: PC 372 ASP cc_start: 0.8797 (t0) cc_final: 0.8448 (t0) REVERT: PC 386 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8700 (mm-30) REVERT: PC 413 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8919 (tm-30) REVERT: PC 416 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8800 (tm-30) REVERT: PC 426 ASP cc_start: 0.9098 (m-30) cc_final: 0.8743 (t0) REVERT: PC 429 LYS cc_start: 0.9148 (ttmt) cc_final: 0.8838 (tppp) REVERT: PD 59 ASP cc_start: 0.8873 (m-30) cc_final: 0.8603 (m-30) REVERT: PD 77 MET cc_start: 0.8277 (mmm) cc_final: 0.7730 (mmm) REVERT: PD 177 ARG cc_start: 0.8614 (ttt-90) cc_final: 0.8350 (ttt180) REVERT: PD 269 ARG cc_start: 0.9058 (tmm-80) cc_final: 0.8823 (ttm-80) REVERT: PD 331 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8508 (mt-10) REVERT: PD 372 ASP cc_start: 0.8890 (t0) cc_final: 0.8557 (t0) REVERT: PD 389 ASP cc_start: 0.8926 (m-30) cc_final: 0.8682 (m-30) REVERT: PD 416 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8924 (tm-30) REVERT: PD 426 ASP cc_start: 0.9160 (m-30) cc_final: 0.8791 (t0) REVERT: PE 59 ASP cc_start: 0.8900 (m-30) cc_final: 0.8591 (m-30) REVERT: PE 98 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8212 (mp0) REVERT: PE 331 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8688 (mt-10) REVERT: PE 364 TYR cc_start: 0.8948 (m-80) cc_final: 0.8741 (m-80) REVERT: PE 401 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8700 (tm-30) REVERT: PE 426 ASP cc_start: 0.9151 (m-30) cc_final: 0.8718 (t0) REVERT: PF 331 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8719 (mt-10) REVERT: PF 386 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8702 (mm-30) REVERT: PF 405 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8654 (pp20) REVERT: PF 413 GLU cc_start: 0.9333 (mm-30) cc_final: 0.8865 (tm-30) REVERT: PF 416 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8773 (tm-30) REVERT: PF 426 ASP cc_start: 0.9097 (m-30) cc_final: 0.8719 (t0) REVERT: PF 429 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8771 (tppp) REVERT: PG 59 ASP cc_start: 0.8865 (m-30) cc_final: 0.8599 (m-30) REVERT: PG 77 MET cc_start: 0.8247 (mmm) cc_final: 0.7680 (mmm) REVERT: PG 269 ARG cc_start: 0.9052 (tmm-80) cc_final: 0.8825 (ttm-80) REVERT: PG 295 TYR cc_start: 0.8738 (p90) cc_final: 0.8364 (p90) REVERT: PG 301 MET cc_start: 0.8314 (ttt) cc_final: 0.8058 (ttt) REVERT: PG 331 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8513 (mt-10) REVERT: PG 372 ASP cc_start: 0.8783 (t0) cc_final: 0.8484 (t0) REVERT: PG 389 ASP cc_start: 0.9028 (m-30) cc_final: 0.8776 (m-30) REVERT: PG 415 ASP cc_start: 0.9230 (m-30) cc_final: 0.8979 (p0) REVERT: PG 429 LYS cc_start: 0.9060 (ttmt) cc_final: 0.8620 (tppp) REVERT: PH 59 ASP cc_start: 0.8893 (m-30) cc_final: 0.8577 (m-30) REVERT: PH 301 MET cc_start: 0.8588 (ttt) cc_final: 0.8210 (ttt) REVERT: PH 331 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8688 (mt-10) REVERT: PH 372 ASP cc_start: 0.8812 (t0) cc_final: 0.8505 (t0) REVERT: PH 413 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9015 (tm-30) REVERT: PH 426 ASP cc_start: 0.9148 (m-30) cc_final: 0.8682 (t0) REVERT: PI 184 TYR cc_start: 0.8689 (m-10) cc_final: 0.8438 (m-10) REVERT: PI 331 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8676 (mt-10) REVERT: PI 386 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8611 (mm-30) REVERT: PI 413 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8870 (tm-30) REVERT: PI 416 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8826 (tm-30) REVERT: PI 429 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8871 (tppp) REVERT: PJ 218 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.7948 (p0) REVERT: PJ 219 GLU cc_start: 0.8679 (mp0) cc_final: 0.8301 (mp0) REVERT: PJ 301 MET cc_start: 0.8363 (ttt) cc_final: 0.8114 (ttt) REVERT: PJ 331 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8533 (mt-10) REVERT: PJ 389 ASP cc_start: 0.8999 (m-30) cc_final: 0.8766 (m-30) REVERT: PJ 429 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8633 (tppp) REVERT: PK 59 ASP cc_start: 0.8892 (m-30) cc_final: 0.8565 (m-30) REVERT: PK 98 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8147 (mp0) REVERT: PK 301 MET cc_start: 0.8589 (ttt) cc_final: 0.8300 (ttt) REVERT: PK 331 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8696 (mt-10) REVERT: PK 372 ASP cc_start: 0.8879 (t0) cc_final: 0.8548 (t0) REVERT: PK 413 GLU cc_start: 0.9374 (mm-30) cc_final: 0.8961 (tm-30) REVERT: PK 416 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8924 (tm-30) REVERT: PK 426 ASP cc_start: 0.9163 (m-30) cc_final: 0.8725 (t0) REVERT: PK 429 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8800 (tppt) REVERT: PL 55 LEU cc_start: 0.8702 (mm) cc_final: 0.8294 (pp) REVERT: PL 64 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8825 (tttp) REVERT: PL 301 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8159 (ttt) REVERT: PL 331 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8668 (mt-10) REVERT: PL 372 ASP cc_start: 0.8764 (t0) cc_final: 0.8442 (OUTLIER) REVERT: PL 386 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8727 (mm-30) REVERT: PL 416 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8842 (tm-30) REVERT: PL 429 LYS cc_start: 0.9168 (ttmt) cc_final: 0.8874 (tppp) outliers start: 46 outliers final: 28 residues processed: 882 average time/residue: 1.1981 time to fit residues: 1346.9160 Evaluate side-chains 798 residues out of total 5364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 764 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain PM residue 17 LEU Chi-restraints excluded: chain PN residue 138 LEU Chi-restraints excluded: chain PP residue 17 LEU Chi-restraints excluded: chain PQ residue 138 LEU Chi-restraints excluded: chain PS residue 17 LEU Chi-restraints excluded: chain PT residue 138 LEU Chi-restraints excluded: chain PU residue 132 ASP Chi-restraints excluded: chain PX residue 132 ASP Chi-restraints excluded: chain PA residue 286 GLU Chi-restraints excluded: chain PC residue 55 LEU Chi-restraints excluded: chain PC residue 56 THR Chi-restraints excluded: chain PC residue 73 VAL Chi-restraints excluded: chain PD residue 37 THR Chi-restraints excluded: chain PE residue 37 THR Chi-restraints excluded: chain PF residue 55 LEU Chi-restraints excluded: chain PF residue 56 THR Chi-restraints excluded: chain PF residue 73 VAL Chi-restraints excluded: chain PF residue 405 GLU Chi-restraints excluded: chain PG residue 73 VAL Chi-restraints excluded: chain PG residue 286 GLU Chi-restraints excluded: chain PH residue 219 GLU Chi-restraints excluded: chain PI residue 73 VAL Chi-restraints excluded: chain PI residue 357 MET Chi-restraints excluded: chain PJ residue 56 THR Chi-restraints excluded: chain PJ residue 73 VAL Chi-restraints excluded: chain PJ residue 218 ASP Chi-restraints excluded: chain PJ residue 286 GLU Chi-restraints excluded: chain PK residue 219 GLU Chi-restraints excluded: chain PK residue 303 MET Chi-restraints excluded: chain PL residue 56 THR Chi-restraints excluded: chain PL residue 64 LYS Chi-restraints excluded: chain PL residue 73 VAL Chi-restraints excluded: chain PL residue 301 MET Chi-restraints excluded: chain PL residue 357 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 408 optimal weight: 7.9990 chunk 547 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 474 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 514 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 528 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** PM 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.095816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.073222 restraints weight = 90928.828| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.90 r_work: 0.2758 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 51696 Z= 0.156 Angle : 0.547 10.602 70188 Z= 0.279 Chirality : 0.038 0.137 7584 Planarity : 0.004 0.059 9456 Dihedral : 6.884 87.797 7056 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.88 % Allowed : 18.89 % Favored : 80.24 % 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: 1.12 (0.11), residues: 6312 helix: 1.88 (0.09), residues: 3156 sheet: 0.15 (0.22), residues: 540 loop : -0.52 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRPPE 134 HIS 0.004 0.001 HISPK 175 PHE 0.018 0.001 PHEPI 334 TYR 0.028 0.002 TYRPH 364 ARG 0.009 0.000 ARGPG 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19949.88 seconds wall clock time: 343 minutes 34.26 seconds (20614.26 seconds total)