Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 11:57:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy8_27070/10_2023/8cy8_27070_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy8_27070/10_2023/8cy8_27070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy8_27070/10_2023/8cy8_27070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy8_27070/10_2023/8cy8_27070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy8_27070/10_2023/8cy8_27070_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cy8_27070/10_2023/8cy8_27070_updated.pdb" } resolution = 2.94 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= 0.095 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: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 18264 2.51 5 N 4884 2.21 5 O 5460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 28800 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "B" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "C" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "D" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "E" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "F" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "G" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "H" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "I" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "J" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "K" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "L" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2393 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.78, per 1000 atoms: 0.51 Number of scatterers: 28800 At special positions: 0 Unit cell: (153.34, 150.88, 138.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 5460 8.00 N 4884 7.00 C 18264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.27 Conformation dependent library (CDL) restraints added in 4.5 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 228 helices and 12 sheets defined 58.1% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'A' and resid 8 through 10 No H-bonds generated for 'chain 'A' and resid 8 through 10' Processing helix chain 'A' and resid 14 through 17 No H-bonds generated for 'chain 'A' and resid 14 through 17' Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.614A pdb=" N ALA A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 229 removed outlier: 3.759A pdb=" N PHE A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 removed outlier: 4.006A pdb=" N LYS A 234 " --> pdb=" O HIS A 231 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 237 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 254 through 267 Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 270 through 284 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 314 through 325 removed outlier: 3.691A pdb=" N ALA A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 10 No H-bonds generated for 'chain 'B' and resid 8 through 10' Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.525A pdb=" N LYS B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 17' Processing helix chain 'B' and resid 28 through 40 removed outlier: 3.785A pdb=" N ALA B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 40 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 74 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 231 through 242 removed outlier: 4.053A pdb=" N LYS B 234 " --> pdb=" O HIS B 231 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 235 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 236 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 242 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'B' and resid 254 through 267 Proline residue: B 265 - end of helix Processing helix chain 'B' and resid 270 through 284 Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 314 through 325 removed outlier: 3.760A pdb=" N ALA B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 10 No H-bonds generated for 'chain 'C' and resid 8 through 10' Processing helix chain 'C' and resid 13 through 17 removed outlier: 3.708A pdb=" N LYS C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 13 through 17' Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.724A pdb=" N ALA C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 40 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 87 through 94 removed outlier: 3.502A pdb=" N ASN C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 162 through 173 Processing helix chain 'C' and resid 185 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 231 through 242 removed outlier: 4.079A pdb=" N LYS C 234 " --> pdb=" O HIS C 231 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 235 " --> pdb=" O GLU C 232 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 237 " --> pdb=" O LYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 254 through 267 Proline residue: C 265 - end of helix Processing helix chain 'C' and resid 270 through 284 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 314 through 324 removed outlier: 3.664A pdb=" N ALA C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 10 No H-bonds generated for 'chain 'D' and resid 8 through 10' Processing helix chain 'D' and resid 13 through 18 removed outlier: 3.842A pdb=" N LYS D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER D 18 " --> pdb=" O ASN D 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 13 through 18' Processing helix chain 'D' and resid 28 through 40 removed outlier: 3.760A pdb=" N ALA D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN D 40 " --> pdb=" O ASN D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 74 Processing helix chain 'D' and resid 87 through 94 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 111 through 114 No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 162 through 173 Processing helix chain 'D' and resid 185 through 198 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.996A pdb=" N LYS D 234 " --> pdb=" O HIS D 231 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 235 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 237 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN D 242 " --> pdb=" O LEU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 254 through 267 Proline residue: D 265 - end of helix Processing helix chain 'D' and resid 270 through 284 Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 314 through 325 removed outlier: 3.708A pdb=" N ALA D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 10 No H-bonds generated for 'chain 'E' and resid 8 through 10' Processing helix chain 'E' and resid 13 through 17 Processing helix chain 'E' and resid 28 through 40 removed outlier: 3.746A pdb=" N ALA E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 74 Processing helix chain 'E' and resid 87 through 94 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 111 through 114 No H-bonds generated for 'chain 'E' and resid 111 through 114' Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 162 through 173 removed outlier: 3.510A pdb=" N ILE E 173 " --> pdb=" O TYR E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 198 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 231 through 242 removed outlier: 3.988A pdb=" N LYS E 234 " --> pdb=" O HIS E 231 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU E 235 " --> pdb=" O GLU E 232 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN E 242 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'E' and resid 254 through 267 Proline residue: E 265 - end of helix Processing helix chain 'E' and resid 270 through 285 Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 314 through 324 removed outlier: 3.685A pdb=" N ALA E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 10 No H-bonds generated for 'chain 'F' and resid 8 through 10' Processing helix chain 'F' and resid 13 through 17 removed outlier: 3.623A pdb=" N LYS F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 13 through 17' Processing helix chain 'F' and resid 28 through 40 removed outlier: 3.850A pdb=" N ALA F 32 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN F 40 " --> pdb=" O ASN F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 74 Processing helix chain 'F' and resid 84 through 94 removed outlier: 4.747A pdb=" N ALA F 88 " --> pdb=" O ASP F 84 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 111 through 114 No H-bonds generated for 'chain 'F' and resid 111 through 114' Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 162 through 173 Processing helix chain 'F' and resid 185 through 198 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 229 Processing helix chain 'F' and resid 231 through 242 removed outlier: 4.004A pdb=" N LYS F 234 " --> pdb=" O HIS F 231 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 235 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL F 237 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 251 Processing helix chain 'F' and resid 254 through 267 Proline residue: F 265 - end of helix Processing helix chain 'F' and resid 270 through 285 Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 314 through 324 removed outlier: 3.710A pdb=" N ALA F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 10 No H-bonds generated for 'chain 'G' and resid 8 through 10' Processing helix chain 'G' and resid 13 through 18 removed outlier: 3.848A pdb=" N LYS G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER G 18 " --> pdb=" O ASN G 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 13 through 18' Processing helix chain 'G' and resid 28 through 40 removed outlier: 3.810A pdb=" N ALA G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP G 39 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 74 Processing helix chain 'G' and resid 87 through 94 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 111 through 114 No H-bonds generated for 'chain 'G' and resid 111 through 114' Processing helix chain 'G' and resid 135 through 140 Processing helix chain 'G' and resid 162 through 173 Processing helix chain 'G' and resid 185 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 229 Processing helix chain 'G' and resid 231 through 242 removed outlier: 4.052A pdb=" N LYS G 234 " --> pdb=" O HIS G 231 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 235 " --> pdb=" O GLU G 232 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE G 236 " --> pdb=" O MET G 233 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL G 237 " --> pdb=" O LYS G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 251 Processing helix chain 'G' and resid 254 through 267 Proline residue: G 265 - end of helix Processing helix chain 'G' and resid 270 through 284 Processing helix chain 'G' and resid 287 through 297 Processing helix chain 'G' and resid 301 through 311 Processing helix chain 'G' and resid 314 through 324 removed outlier: 3.686A pdb=" N ALA G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 10 No H-bonds generated for 'chain 'H' and resid 8 through 10' Processing helix chain 'H' and resid 13 through 17 removed outlier: 3.769A pdb=" N LYS H 17 " --> pdb=" O LEU H 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 13 through 17' Processing helix chain 'H' and resid 28 through 40 removed outlier: 3.750A pdb=" N ALA H 32 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN H 40 " --> pdb=" O ASN H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 74 Processing helix chain 'H' and resid 84 through 94 removed outlier: 4.721A pdb=" N ALA H 88 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 98 No H-bonds generated for 'chain 'H' and resid 96 through 98' Processing helix chain 'H' and resid 111 through 114 No H-bonds generated for 'chain 'H' and resid 111 through 114' Processing helix chain 'H' and resid 135 through 140 Processing helix chain 'H' and resid 162 through 173 Processing helix chain 'H' and resid 185 through 198 Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 222 through 229 Processing helix chain 'H' and resid 231 through 242 removed outlier: 3.979A pdb=" N LYS H 234 " --> pdb=" O HIS H 231 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU H 235 " --> pdb=" O GLU H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 251 Processing helix chain 'H' and resid 254 through 267 Proline residue: H 265 - end of helix Processing helix chain 'H' and resid 270 through 284 Processing helix chain 'H' and resid 287 through 297 Processing helix chain 'H' and resid 301 through 311 Processing helix chain 'H' and resid 314 through 324 removed outlier: 3.734A pdb=" N ALA H 324 " --> pdb=" O ARG H 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 10 No H-bonds generated for 'chain 'I' and resid 8 through 10' Processing helix chain 'I' and resid 13 through 17 removed outlier: 3.509A pdb=" N LYS I 17 " --> pdb=" O LEU I 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 13 through 17' Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.671A pdb=" N ALA I 32 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 74 Processing helix chain 'I' and resid 87 through 94 Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 111 through 114 No H-bonds generated for 'chain 'I' and resid 111 through 114' Processing helix chain 'I' and resid 135 through 140 Processing helix chain 'I' and resid 162 through 173 Processing helix chain 'I' and resid 185 through 198 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 222 through 229 Processing helix chain 'I' and resid 231 through 242 removed outlier: 3.954A pdb=" N LYS I 234 " --> pdb=" O HIS I 231 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU I 235 " --> pdb=" O GLU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 251 Processing helix chain 'I' and resid 254 through 267 Proline residue: I 265 - end of helix Processing helix chain 'I' and resid 270 through 284 Processing helix chain 'I' and resid 287 through 297 Processing helix chain 'I' and resid 301 through 311 Processing helix chain 'I' and resid 314 through 324 removed outlier: 3.682A pdb=" N ALA I 324 " --> pdb=" O ARG I 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 10 No H-bonds generated for 'chain 'J' and resid 8 through 10' Processing helix chain 'J' and resid 13 through 17 Processing helix chain 'J' and resid 28 through 40 removed outlier: 3.772A pdb=" N ALA J 32 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP J 39 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 74 Processing helix chain 'J' and resid 87 through 94 Processing helix chain 'J' and resid 96 through 98 No H-bonds generated for 'chain 'J' and resid 96 through 98' Processing helix chain 'J' and resid 111 through 114 No H-bonds generated for 'chain 'J' and resid 111 through 114' Processing helix chain 'J' and resid 135 through 140 Processing helix chain 'J' and resid 162 through 173 Processing helix chain 'J' and resid 185 through 198 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 222 through 229 Processing helix chain 'J' and resid 231 through 242 removed outlier: 4.034A pdb=" N LYS J 234 " --> pdb=" O HIS J 231 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 235 " --> pdb=" O GLU J 232 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 236 " --> pdb=" O MET J 233 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 237 " --> pdb=" O LYS J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 245 through 251 Processing helix chain 'J' and resid 254 through 267 Proline residue: J 265 - end of helix Processing helix chain 'J' and resid 270 through 285 Processing helix chain 'J' and resid 287 through 297 Processing helix chain 'J' and resid 301 through 311 Processing helix chain 'J' and resid 314 through 324 removed outlier: 3.696A pdb=" N ALA J 324 " --> pdb=" O ARG J 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 10 No H-bonds generated for 'chain 'K' and resid 8 through 10' Processing helix chain 'K' and resid 13 through 17 removed outlier: 3.773A pdb=" N LYS K 17 " --> pdb=" O LEU K 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 13 through 17' Processing helix chain 'K' and resid 28 through 40 removed outlier: 3.770A pdb=" N ALA K 32 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP K 39 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN K 40 " --> pdb=" O ASN K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 74 Processing helix chain 'K' and resid 84 through 94 removed outlier: 4.765A pdb=" N ALA K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 98 No H-bonds generated for 'chain 'K' and resid 96 through 98' Processing helix chain 'K' and resid 111 through 114 No H-bonds generated for 'chain 'K' and resid 111 through 114' Processing helix chain 'K' and resid 135 through 140 Processing helix chain 'K' and resid 162 through 173 removed outlier: 3.505A pdb=" N ILE K 173 " --> pdb=" O TYR K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 198 removed outlier: 3.544A pdb=" N GLU K 196 " --> pdb=" O ASP K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 222 through 229 Processing helix chain 'K' and resid 231 through 242 removed outlier: 4.071A pdb=" N LYS K 234 " --> pdb=" O HIS K 231 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU K 235 " --> pdb=" O GLU K 232 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL K 237 " --> pdb=" O LYS K 234 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP K 238 " --> pdb=" O LEU K 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 251 Processing helix chain 'K' and resid 254 through 267 Proline residue: K 265 - end of helix Processing helix chain 'K' and resid 270 through 284 Processing helix chain 'K' and resid 287 through 297 Processing helix chain 'K' and resid 301 through 311 Processing helix chain 'K' and resid 314 through 324 removed outlier: 3.684A pdb=" N ALA K 324 " --> pdb=" O ARG K 320 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 10 No H-bonds generated for 'chain 'L' and resid 8 through 10' Processing helix chain 'L' and resid 13 through 18 removed outlier: 3.853A pdb=" N LYS L 17 " --> pdb=" O LEU L 13 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER L 18 " --> pdb=" O ASN L 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 13 through 18' Processing helix chain 'L' and resid 28 through 40 removed outlier: 3.701A pdb=" N ALA L 32 " --> pdb=" O SER L 28 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP L 39 " --> pdb=" O MET L 35 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN L 40 " --> pdb=" O ASN L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 74 Processing helix chain 'L' and resid 84 through 94 removed outlier: 4.723A pdb=" N ALA L 88 " --> pdb=" O ASP L 84 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASP L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 111 through 114 No H-bonds generated for 'chain 'L' and resid 111 through 114' Processing helix chain 'L' and resid 135 through 140 Processing helix chain 'L' and resid 162 through 172 Processing helix chain 'L' and resid 185 through 198 Processing helix chain 'L' and resid 202 through 217 Processing helix chain 'L' and resid 222 through 229 Processing helix chain 'L' and resid 231 through 242 removed outlier: 4.041A pdb=" N LYS L 234 " --> pdb=" O HIS L 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU L 235 " --> pdb=" O GLU L 232 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL L 237 " --> pdb=" O LYS L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 251 Processing helix chain 'L' and resid 254 through 267 Proline residue: L 265 - end of helix Processing helix chain 'L' and resid 270 through 284 Processing helix chain 'L' and resid 287 through 297 Processing helix chain 'L' and resid 301 through 311 Processing helix chain 'L' and resid 314 through 324 removed outlier: 3.678A pdb=" N ALA L 324 " --> pdb=" O ARG L 320 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 43 through 47 removed outlier: 6.800A pdb=" N VAL A 77 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE A 24 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N MET A 79 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 104 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE A 80 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA A 106 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP A 125 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N PHE A 107 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 127 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE A 154 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 43 through 47 removed outlier: 6.769A pdb=" N VAL B 77 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE B 24 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N MET B 79 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 104 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE B 80 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA B 106 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP B 125 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE B 107 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE B 127 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE B 154 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 43 through 47 removed outlier: 6.759A pdb=" N VAL C 77 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE C 24 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET C 79 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA C 104 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE C 80 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA C 106 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP C 125 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE C 107 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE C 127 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE C 154 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 43 through 47 removed outlier: 6.746A pdb=" N VAL D 77 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE D 24 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET D 79 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA D 104 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE D 80 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA D 106 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP D 125 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE D 107 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE D 127 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE D 154 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.622A pdb=" N VAL E 77 " --> pdb=" O ALA E 22 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE E 24 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET E 79 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA E 104 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE E 80 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA E 106 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP E 125 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE E 107 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE E 127 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE E 154 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 43 through 47 removed outlier: 6.713A pdb=" N VAL F 77 " --> pdb=" O ALA F 22 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE F 24 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET F 79 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA F 104 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE F 80 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA F 106 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP F 125 " --> pdb=" O ILE F 105 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE F 107 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE F 127 " --> pdb=" O PHE F 107 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE F 154 " --> pdb=" O THR F 183 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 43 through 47 removed outlier: 6.754A pdb=" N VAL G 77 " --> pdb=" O ALA G 22 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE G 24 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET G 79 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA G 104 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE G 80 " --> pdb=" O ALA G 104 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA G 106 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP G 125 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE G 107 " --> pdb=" O ASP G 125 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE G 127 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE G 154 " --> pdb=" O THR G 183 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 43 through 47 removed outlier: 6.748A pdb=" N VAL H 77 " --> pdb=" O ALA H 22 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE H 24 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET H 79 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA H 104 " --> pdb=" O ILE H 78 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE H 80 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA H 106 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP H 125 " --> pdb=" O ILE H 105 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE H 107 " --> pdb=" O ASP H 125 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE H 127 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE H 154 " --> pdb=" O THR H 183 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 43 through 47 removed outlier: 6.678A pdb=" N VAL I 77 " --> pdb=" O ALA I 22 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE I 24 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET I 79 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA I 104 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE I 80 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA I 106 " --> pdb=" O ILE I 80 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASP I 125 " --> pdb=" O ILE I 105 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE I 107 " --> pdb=" O ASP I 125 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE I 127 " --> pdb=" O PHE I 107 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE I 154 " --> pdb=" O THR I 183 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 43 through 47 removed outlier: 6.763A pdb=" N VAL J 77 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE J 24 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET J 79 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA J 104 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE J 80 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA J 106 " --> pdb=" O ILE J 80 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP J 125 " --> pdb=" O ILE J 105 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE J 107 " --> pdb=" O ASP J 125 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE J 127 " --> pdb=" O PHE J 107 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE J 154 " --> pdb=" O THR J 183 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 43 through 47 removed outlier: 6.745A pdb=" N VAL K 77 " --> pdb=" O ALA K 22 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE K 24 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET K 79 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA K 104 " --> pdb=" O ILE K 78 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE K 80 " --> pdb=" O ALA K 104 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA K 106 " --> pdb=" O ILE K 80 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASP K 125 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE K 107 " --> pdb=" O ASP K 125 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE K 127 " --> pdb=" O PHE K 107 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE K 154 " --> pdb=" O THR K 183 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 43 through 47 removed outlier: 6.737A pdb=" N VAL L 77 " --> pdb=" O ALA L 22 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE L 24 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET L 79 " --> pdb=" O ILE L 24 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA L 104 " --> pdb=" O ILE L 78 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE L 80 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA L 106 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP L 125 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N PHE L 107 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE L 127 " --> pdb=" O PHE L 107 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE L 154 " --> pdb=" O THR L 183 " (cutoff:3.500A) 1284 hydrogen bonds defined for protein. 3645 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: 9.17 Time building geometry restraints manager: 13.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4992 1.30 - 1.43: 6974 1.43 - 1.55: 16942 1.55 - 1.68: 0 1.68 - 1.81: 336 Bond restraints: 29244 Sorted by residual: bond pdb=" CG GLN E 197 " pdb=" CD GLN E 197 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.74e+00 bond pdb=" CB ASP D 125 " pdb=" CG ASP D 125 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.72e+00 bond pdb=" CG GLN C 197 " pdb=" CD GLN C 197 " ideal model delta sigma weight residual 1.516 1.468 0.048 2.50e-02 1.60e+03 3.62e+00 bond pdb=" CB ASP I 125 " pdb=" CG ASP I 125 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.56e+00 bond pdb=" CB ASP L 125 " pdb=" CG ASP L 125 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.55e+00 ... (remaining 29239 not shown) Histogram of bond angle deviations from ideal: 94.46 - 102.37: 149 102.37 - 110.27: 6730 110.27 - 118.17: 15577 118.17 - 126.07: 16652 126.07 - 133.98: 252 Bond angle restraints: 39360 Sorted by residual: angle pdb=" CG MET A 35 " pdb=" SD MET A 35 " pdb=" CE MET A 35 " ideal model delta sigma weight residual 100.90 94.46 6.44 2.20e+00 2.07e-01 8.56e+00 angle pdb=" CB MET C 35 " pdb=" CG MET C 35 " pdb=" SD MET C 35 " ideal model delta sigma weight residual 112.70 120.89 -8.19 3.00e+00 1.11e-01 7.46e+00 angle pdb=" CB MET I 79 " pdb=" CG MET I 79 " pdb=" SD MET I 79 " ideal model delta sigma weight residual 112.70 120.51 -7.81 3.00e+00 1.11e-01 6.78e+00 angle pdb=" CB MET D 79 " pdb=" CG MET D 79 " pdb=" SD MET D 79 " ideal model delta sigma weight residual 112.70 120.42 -7.72 3.00e+00 1.11e-01 6.62e+00 angle pdb=" CG MET F 35 " pdb=" SD MET F 35 " pdb=" CE MET F 35 " ideal model delta sigma weight residual 100.90 95.26 5.64 2.20e+00 2.07e-01 6.57e+00 ... (remaining 39355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16341 17.99 - 35.98: 1068 35.98 - 53.97: 176 53.97 - 71.96: 46 71.96 - 89.95: 21 Dihedral angle restraints: 17652 sinusoidal: 7008 harmonic: 10644 Sorted by residual: dihedral pdb=" CB GLU E 295 " pdb=" CG GLU E 295 " pdb=" CD GLU E 295 " pdb=" OE1 GLU E 295 " ideal model delta sinusoidal sigma weight residual 0.00 89.95 -89.95 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU A 295 " pdb=" CG GLU A 295 " pdb=" CD GLU A 295 " pdb=" OE1 GLU A 295 " ideal model delta sinusoidal sigma weight residual 0.00 88.96 -88.96 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU D 295 " pdb=" CG GLU D 295 " pdb=" CD GLU D 295 " pdb=" OE1 GLU D 295 " ideal model delta sinusoidal sigma weight residual 0.00 -87.38 87.38 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 17649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1798 0.033 - 0.065: 1509 0.065 - 0.098: 748 0.098 - 0.130: 343 0.130 - 0.163: 54 Chirality restraints: 4452 Sorted by residual: chirality pdb=" CA GLU D 94 " pdb=" N GLU D 94 " pdb=" C GLU D 94 " pdb=" CB GLU D 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA GLU J 94 " pdb=" N GLU J 94 " pdb=" C GLU J 94 " pdb=" CB GLU J 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 4449 not shown) Planarity restraints: 5076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F 31 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C HIS F 31 " 0.033 2.00e-02 2.50e+03 pdb=" O HIS F 31 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA F 32 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA J 130 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO J 131 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 131 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 131 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 264 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 265 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.023 5.00e-02 4.00e+02 ... (remaining 5073 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1180 2.72 - 3.26: 28407 3.26 - 3.81: 43798 3.81 - 4.35: 56424 4.35 - 4.90: 97555 Nonbonded interactions: 227364 Sorted by model distance: nonbonded pdb=" O ALA C 32 " pdb=" ND2 ASN C 36 " model vdw 2.171 2.520 nonbonded pdb=" N GLY D 123 " pdb=" OE1 GLU D 158 " model vdw 2.204 2.520 nonbonded pdb=" OE1 GLU C 190 " pdb=" OH TYR D 220 " model vdw 2.209 2.440 nonbonded pdb=" N GLY J 123 " pdb=" OE1 GLU J 158 " model vdw 2.217 2.520 nonbonded pdb=" N GLY F 123 " pdb=" OE1 GLU F 158 " model vdw 2.219 2.520 ... (remaining 227359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 330) selection = (chain 'B' and resid 3 through 330) selection = chain 'C' selection = (chain 'D' and resid 3 through 330) selection = (chain 'E' and resid 3 through 330) selection = (chain 'F' and resid 3 through 330) selection = (chain 'G' and resid 3 through 330) selection = (chain 'H' and resid 3 through 330) selection = (chain 'I' and resid 3 through 330) selection = (chain 'J' and resid 3 through 330) selection = (chain 'K' and resid 3 through 330) selection = (chain 'L' and resid 3 through 330) } 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: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 20.670 Check model and map are aligned: 0.540 Set scattering table: 0.280 Process input model: 73.890 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.011 0.061 29244 Z= 0.692 Angle : 0.785 8.737 39360 Z= 0.423 Chirality : 0.056 0.163 4452 Planarity : 0.006 0.045 5076 Dihedral : 12.769 89.946 10836 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 1.60 (0.14), residues: 3672 helix: 1.32 (0.11), residues: 2208 sheet: 1.60 (0.24), residues: 492 loop : 0.39 (0.22), residues: 972 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 3.160 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 1.5068 time to fit residues: 894.7385 Evaluate side-chains 434 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 3.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 10.0000 chunk 281 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 291 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 0.0470 chunk 337 optimal weight: 0.7980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 242 GLN C 36 ASN C 242 GLN F 242 GLN G 242 GLN H 242 GLN I 242 GLN J 242 GLN L 36 ASN L 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29244 Z= 0.152 Angle : 0.435 7.842 39360 Z= 0.230 Chirality : 0.042 0.132 4452 Planarity : 0.004 0.039 5076 Dihedral : 4.505 78.503 4008 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.93 % Allowed : 7.84 % Favored : 91.24 % 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: 1.78 (0.14), residues: 3672 helix: 1.61 (0.11), residues: 2148 sheet: 1.65 (0.24), residues: 492 loop : 0.17 (0.21), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 471 time to evaluate : 3.317 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 475 average time/residue: 1.5045 time to fit residues: 828.2414 Evaluate side-chains 417 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 416 time to evaluate : 3.072 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 4.4717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 281 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 93 optimal weight: 0.0970 chunk 338 optimal weight: 3.9990 chunk 365 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 335 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 242 GLN C 36 ASN F 242 GLN G 242 GLN H 31 HIS I 242 GLN L 36 ASN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 29244 Z= 0.265 Angle : 0.486 7.997 39360 Z= 0.258 Chirality : 0.044 0.130 4452 Planarity : 0.004 0.038 5076 Dihedral : 4.469 67.939 4008 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.59 % Allowed : 9.46 % Favored : 88.96 % 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: 1.47 (0.14), residues: 3672 helix: 1.32 (0.11), residues: 2160 sheet: 1.51 (0.23), residues: 492 loop : 0.12 (0.20), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 446 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 7 residues processed: 459 average time/residue: 1.4113 time to fit residues: 755.7183 Evaluate side-chains 446 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 439 time to evaluate : 3.176 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.6645 time to fit residues: 7.0040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.8980 chunk 254 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 227 optimal weight: 0.0270 chunk 339 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 chunk 177 optimal weight: 0.1980 chunk 321 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN F 242 GLN G 242 GLN I 242 GLN L 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29244 Z= 0.126 Angle : 0.407 9.167 39360 Z= 0.214 Chirality : 0.041 0.129 4452 Planarity : 0.003 0.035 5076 Dihedral : 4.053 51.275 4008 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.42 % Allowed : 10.12 % Favored : 88.46 % 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: 1.88 (0.14), residues: 3672 helix: 1.61 (0.11), residues: 2172 sheet: 1.73 (0.23), residues: 492 loop : 0.35 (0.21), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 466 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 6 residues processed: 486 average time/residue: 1.4301 time to fit residues: 810.3816 Evaluate side-chains 433 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 427 time to evaluate : 3.066 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.7778 time to fit residues: 6.5507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 148 optimal weight: 0.0770 chunk 306 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 242 GLN C 36 ASN C 209 GLN F 242 GLN G 242 GLN H 31 HIS H 242 GLN I 242 GLN K 242 GLN L 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 29244 Z= 0.271 Angle : 0.494 8.892 39360 Z= 0.260 Chirality : 0.044 0.145 4452 Planarity : 0.004 0.036 5076 Dihedral : 4.352 49.344 4008 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.49 % Allowed : 10.55 % Favored : 87.96 % 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: 1.58 (0.14), residues: 3672 helix: 1.40 (0.11), residues: 2148 sheet: 1.34 (0.23), residues: 504 loop : 0.31 (0.20), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 454 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 12 residues processed: 473 average time/residue: 1.3690 time to fit residues: 758.8297 Evaluate side-chains 436 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 424 time to evaluate : 3.141 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 7 residues processed: 5 average time/residue: 0.8166 time to fit residues: 10.1817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 3.9990 chunk 323 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 359 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN C 36 ASN F 242 GLN G 242 GLN H 31 HIS H 242 GLN I 242 GLN K 242 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 29244 Z= 0.268 Angle : 0.507 9.469 39360 Z= 0.264 Chirality : 0.044 0.140 4452 Planarity : 0.004 0.037 5076 Dihedral : 4.382 47.229 4008 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.42 % Allowed : 11.51 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.14), residues: 3672 helix: 1.16 (0.11), residues: 2208 sheet: 1.21 (0.23), residues: 504 loop : 0.31 (0.21), residues: 960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 460 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 14 residues processed: 479 average time/residue: 1.4402 time to fit residues: 805.5037 Evaluate side-chains 447 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 433 time to evaluate : 3.398 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 9 residues processed: 5 average time/residue: 0.7757 time to fit residues: 9.6950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 302 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 358 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 chunk 218 optimal weight: 10.0000 chunk 165 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 161 ASN B 242 GLN C 36 ASN F 242 GLN H 31 HIS H 242 GLN I 242 GLN J 14 ASN K 242 GLN L 36 ASN L 242 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29244 Z= 0.130 Angle : 0.444 11.089 39360 Z= 0.228 Chirality : 0.041 0.143 4452 Planarity : 0.003 0.036 5076 Dihedral : 4.040 47.197 4008 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.96 % Allowed : 13.23 % Favored : 85.81 % 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: 1.87 (0.14), residues: 3672 helix: 1.64 (0.11), residues: 2148 sheet: 1.43 (0.23), residues: 504 loop : 0.46 (0.21), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 444 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 456 average time/residue: 1.4165 time to fit residues: 754.3286 Evaluate side-chains 434 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 422 time to evaluate : 3.086 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 3 average time/residue: 0.8954 time to fit residues: 7.7523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 70 optimal weight: 0.1980 chunk 69 optimal weight: 0.0470 chunk 227 optimal weight: 0.0270 chunk 244 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 281 optimal weight: 0.7980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 242 GLN C 242 GLN F 242 GLN H 31 HIS H 242 GLN I 242 GLN L 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29244 Z= 0.125 Angle : 0.441 10.255 39360 Z= 0.228 Chirality : 0.041 0.145 4452 Planarity : 0.003 0.033 5076 Dihedral : 3.889 51.059 4008 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.83 % Allowed : 13.36 % Favored : 85.81 % 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: 2.09 (0.14), residues: 3672 helix: 1.75 (0.11), residues: 2160 sheet: 1.81 (0.23), residues: 492 loop : 0.54 (0.22), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 433 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 449 average time/residue: 1.3976 time to fit residues: 736.1945 Evaluate side-chains 422 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 408 time to evaluate : 3.403 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 1.6172 time to fit residues: 8.1636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.8980 chunk 343 optimal weight: 2.9990 chunk 313 optimal weight: 10.0000 chunk 334 optimal weight: 0.5980 chunk 201 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 262 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 332 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN C 242 GLN D 161 ASN G 14 ASN H 242 GLN I 31 HIS I 242 GLN J 242 GLN K 242 GLN L 242 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29244 Z= 0.176 Angle : 0.480 9.874 39360 Z= 0.247 Chirality : 0.042 0.150 4452 Planarity : 0.003 0.033 5076 Dihedral : 4.005 47.967 4008 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.09 % Allowed : 13.72 % Favored : 85.19 % 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: 2.00 (0.14), residues: 3672 helix: 1.63 (0.11), residues: 2172 sheet: 1.76 (0.23), residues: 492 loop : 0.62 (0.22), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 419 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 440 average time/residue: 1.4159 time to fit residues: 729.4010 Evaluate side-chains 420 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 402 time to evaluate : 3.295 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.9541 time to fit residues: 8.1233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 5.9990 chunk 353 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 167 optimal weight: 0.0980 chunk 245 optimal weight: 3.9990 chunk 370 optimal weight: 4.9990 chunk 341 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 30 optimal weight: 0.0070 chunk 227 optimal weight: 0.3980 chunk 180 optimal weight: 0.9980 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 242 GLN C 140 ASN C 242 GLN F 31 HIS F 242 GLN G 242 GLN H 242 GLN I 242 GLN J 242 GLN L 242 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29244 Z= 0.131 Angle : 0.463 11.004 39360 Z= 0.236 Chirality : 0.041 0.150 4452 Planarity : 0.003 0.032 5076 Dihedral : 3.895 51.550 4008 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.89 % Allowed : 14.02 % Favored : 85.09 % 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: 2.17 (0.14), residues: 3672 helix: 1.80 (0.11), residues: 2148 sheet: 1.61 (0.24), residues: 504 loop : 0.72 (0.22), residues: 1020 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 408 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 425 average time/residue: 1.4178 time to fit residues: 705.7779 Evaluate side-chains 415 residues out of total 3024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 397 time to evaluate : 3.347 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 1.4205 time to fit residues: 9.4156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 0.9980 chunk 314 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 43 optimal weight: 0.0050 chunk 82 optimal weight: 0.5980 chunk 295 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN C 242 GLN F 242 GLN G 242 GLN H 242 GLN I 242 GLN J 242 GLN K 242 GLN L 242 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.165935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124644 restraints weight = 33365.802| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.00 r_work: 0.3249 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29244 Z= 0.150 Angle : 0.477 10.419 39360 Z= 0.242 Chirality : 0.042 0.150 4452 Planarity : 0.003 0.032 5076 Dihedral : 3.913 46.810 4008 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.06 % Allowed : 13.92 % Favored : 85.02 % 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: 2.14 (0.14), residues: 3672 helix: 1.74 (0.11), residues: 2160 sheet: 1.61 (0.24), residues: 504 loop : 0.80 (0.21), residues: 1008 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11356.91 seconds wall clock time: 202 minutes 8.55 seconds (12128.55 seconds total)