Starting phenix.real_space_refine on Sun Mar 17 13:25:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk7_20355/03_2024/6pk7_20355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk7_20355/03_2024/6pk7_20355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk7_20355/03_2024/6pk7_20355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk7_20355/03_2024/6pk7_20355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk7_20355/03_2024/6pk7_20355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pk7_20355/03_2024/6pk7_20355_updated.pdb" } resolution = 3.1 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= 0.041 sd= 1.139 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 92 5.16 5 C 11312 2.51 5 N 3080 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17820 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4399 Classifications: {'peptide': 557} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "D" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4399 Classifications: {'peptide': 557} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "E" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4399 Classifications: {'peptide': 557} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "F" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4399 Classifications: {'peptide': 557} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'ADP': 1, 'CTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'ADP': 1, 'CTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'ADP': 1, 'CTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'ADP': 1, 'CTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU A 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU A 155 " occ=0.75 residue: pdb=" N CYS A 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS A 243 " occ=0.75 residue: pdb=" N GLU D 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU D 155 " occ=0.75 residue: pdb=" N CYS D 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS D 243 " occ=0.75 residue: pdb=" N GLU E 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU E 155 " occ=0.75 residue: pdb=" N CYS E 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS E 243 " occ=0.75 residue: pdb=" N GLU F 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU F 155 " occ=0.75 residue: pdb=" N CYS F 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS F 243 " occ=0.75 Time building chain proxies: 9.52, per 1000 atoms: 0.53 Number of scatterers: 17820 At special positions: 0 Unit cell: (143.85, 89.25, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 20 15.00 O 3316 8.00 N 3080 7.00 C 11312 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: 6.81 Conformation dependent library (CDL) restraints added in 3.3 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 16 sheets defined 36.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 90 through 103 removed outlier: 3.732A pdb=" N GLN A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.759A pdb=" N GLU A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 167 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 195 through 207 Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.818A pdb=" N MET A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 251 through 259 removed outlier: 4.223A pdb=" N VAL A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 removed outlier: 3.793A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 4.805A pdb=" N ASN A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 removed outlier: 3.709A pdb=" N ALA A 327 " --> pdb=" O HIS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.832A pdb=" N THR A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 removed outlier: 3.717A pdb=" N ALA A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.657A pdb=" N GLN A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 412 Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 486 through 488 No H-bonds generated for 'chain 'A' and resid 486 through 488' Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 527 through 530 removed outlier: 3.807A pdb=" N SER A 530 " --> pdb=" O PRO A 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 527 through 530' Processing helix chain 'A' and resid 538 through 545 Processing helix chain 'A' and resid 551 through 556 removed outlier: 3.847A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 556 " --> pdb=" O ASN A 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 556' Processing helix chain 'D' and resid 16 through 28 Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 74 through 77 No H-bonds generated for 'chain 'D' and resid 74 through 77' Processing helix chain 'D' and resid 90 through 103 removed outlier: 3.732A pdb=" N GLN D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.759A pdb=" N GLU D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 167 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 195 through 207 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.819A pdb=" N MET D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 240 No H-bonds generated for 'chain 'D' and resid 238 through 240' Processing helix chain 'D' and resid 251 through 259 removed outlier: 4.223A pdb=" N VAL D 255 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 269 removed outlier: 3.793A pdb=" N GLU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 293 removed outlier: 4.803A pdb=" N ASN D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 327 removed outlier: 3.709A pdb=" N ALA D 327 " --> pdb=" O HIS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 349 removed outlier: 3.831A pdb=" N THR D 348 " --> pdb=" O LYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 363 removed outlier: 3.716A pdb=" N ALA D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 389 removed outlier: 3.657A pdb=" N GLN D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 412 Processing helix chain 'D' and resid 465 through 468 No H-bonds generated for 'chain 'D' and resid 465 through 468' Processing helix chain 'D' and resid 486 through 488 No H-bonds generated for 'chain 'D' and resid 486 through 488' Processing helix chain 'D' and resid 490 through 492 No H-bonds generated for 'chain 'D' and resid 490 through 492' Processing helix chain 'D' and resid 527 through 530 removed outlier: 3.807A pdb=" N SER D 530 " --> pdb=" O PRO D 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 527 through 530' Processing helix chain 'D' and resid 538 through 545 Processing helix chain 'D' and resid 551 through 556 removed outlier: 3.847A pdb=" N LEU D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 551 through 556' Processing helix chain 'E' and resid 16 through 28 Processing helix chain 'E' and resid 69 through 71 No H-bonds generated for 'chain 'E' and resid 69 through 71' Processing helix chain 'E' and resid 74 through 77 No H-bonds generated for 'chain 'E' and resid 74 through 77' Processing helix chain 'E' and resid 90 through 103 removed outlier: 3.732A pdb=" N GLN E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 128 Processing helix chain 'E' and resid 156 through 169 removed outlier: 3.759A pdb=" N GLU E 161 " --> pdb=" O MET E 157 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 166 " --> pdb=" O ALA E 162 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN E 167 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE E 168 " --> pdb=" O ARG E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 195 through 207 Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.819A pdb=" N MET E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 251 through 259 removed outlier: 4.224A pdb=" N VAL E 255 " --> pdb=" O TYR E 251 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 269 removed outlier: 3.793A pdb=" N GLU E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 293 removed outlier: 4.804A pdb=" N ASN E 287 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG E 291 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 327 removed outlier: 3.709A pdb=" N ALA E 327 " --> pdb=" O HIS E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 344 through 349 removed outlier: 3.831A pdb=" N THR E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 363 removed outlier: 3.717A pdb=" N ALA E 357 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS E 360 " --> pdb=" O GLU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.657A pdb=" N GLN E 383 " --> pdb=" O LEU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 465 through 468 No H-bonds generated for 'chain 'E' and resid 465 through 468' Processing helix chain 'E' and resid 486 through 488 No H-bonds generated for 'chain 'E' and resid 486 through 488' Processing helix chain 'E' and resid 490 through 492 No H-bonds generated for 'chain 'E' and resid 490 through 492' Processing helix chain 'E' and resid 527 through 530 removed outlier: 3.807A pdb=" N SER E 530 " --> pdb=" O PRO E 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 527 through 530' Processing helix chain 'E' and resid 538 through 545 Processing helix chain 'E' and resid 551 through 556 removed outlier: 3.846A pdb=" N LEU E 555 " --> pdb=" O LEU E 551 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN E 556 " --> pdb=" O ASN E 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 551 through 556' Processing helix chain 'F' and resid 16 through 28 Processing helix chain 'F' and resid 69 through 71 No H-bonds generated for 'chain 'F' and resid 69 through 71' Processing helix chain 'F' and resid 74 through 77 No H-bonds generated for 'chain 'F' and resid 74 through 77' Processing helix chain 'F' and resid 90 through 103 removed outlier: 3.732A pdb=" N GLN F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 128 Processing helix chain 'F' and resid 156 through 169 removed outlier: 3.759A pdb=" N GLU F 161 " --> pdb=" O MET F 157 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN F 167 " --> pdb=" O PHE F 163 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 195 through 207 Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.818A pdb=" N MET F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 240 No H-bonds generated for 'chain 'F' and resid 238 through 240' Processing helix chain 'F' and resid 251 through 259 removed outlier: 4.223A pdb=" N VAL F 255 " --> pdb=" O TYR F 251 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 269 removed outlier: 3.793A pdb=" N GLU F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 293 removed outlier: 4.804A pdb=" N ASN F 287 " --> pdb=" O PHE F 283 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG F 291 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 327 removed outlier: 3.708A pdb=" N ALA F 327 " --> pdb=" O HIS F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 344 through 349 removed outlier: 3.832A pdb=" N THR F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 363 removed outlier: 3.717A pdb=" N ALA F 357 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 389 removed outlier: 3.657A pdb=" N GLN F 383 " --> pdb=" O LEU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 412 Processing helix chain 'F' and resid 465 through 468 No H-bonds generated for 'chain 'F' and resid 465 through 468' Processing helix chain 'F' and resid 486 through 488 No H-bonds generated for 'chain 'F' and resid 486 through 488' Processing helix chain 'F' and resid 490 through 492 No H-bonds generated for 'chain 'F' and resid 490 through 492' Processing helix chain 'F' and resid 527 through 530 removed outlier: 3.807A pdb=" N SER F 530 " --> pdb=" O PRO F 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 527 through 530' Processing helix chain 'F' and resid 538 through 545 Processing helix chain 'F' and resid 551 through 556 removed outlier: 3.847A pdb=" N LEU F 555 " --> pdb=" O LEU F 551 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN F 556 " --> pdb=" O ASN F 552 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 551 through 556' Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 7.561A pdb=" N ILE A 88 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS A 38 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE A 142 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE A 37 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 144 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE A 39 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU A 146 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 4 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 147 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 6 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 5 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 213 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N SER A 181 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL A 215 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 335 through 338 removed outlier: 3.514A pdb=" N VAL A 521 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE A 520 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 498 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 482 through 484 removed outlier: 3.588A pdb=" N ASP A 420 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 449 through 456 removed outlier: 3.689A pdb=" N GLU A 476 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 87 through 89 removed outlier: 7.560A pdb=" N ILE D 88 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS D 38 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE D 142 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE D 37 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL D 144 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE D 39 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU D 146 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE D 4 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU D 147 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 6 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 5 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU D 213 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N SER D 181 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL D 215 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 335 through 338 removed outlier: 3.514A pdb=" N VAL D 521 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE D 520 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER D 498 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 482 through 484 removed outlier: 3.588A pdb=" N ASP D 420 " --> pdb=" O VAL D 430 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 449 through 456 removed outlier: 3.690A pdb=" N GLU D 476 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 87 through 89 removed outlier: 7.560A pdb=" N ILE E 88 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS E 38 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE E 142 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE E 37 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL E 144 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE E 39 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU E 146 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE E 4 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU E 147 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL E 6 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU E 5 " --> pdb=" O CYS E 176 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU E 213 " --> pdb=" O HIS E 179 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N SER E 181 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL E 215 " --> pdb=" O SER E 181 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 335 through 338 removed outlier: 3.514A pdb=" N VAL E 521 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE E 520 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER E 498 " --> pdb=" O GLU E 513 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 482 through 484 removed outlier: 3.589A pdb=" N ASP E 420 " --> pdb=" O VAL E 430 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 449 through 456 removed outlier: 3.690A pdb=" N GLU E 476 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 87 through 89 removed outlier: 7.561A pdb=" N ILE F 88 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS F 38 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE F 142 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE F 37 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL F 144 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE F 39 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLU F 146 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE F 4 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU F 147 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL F 6 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU F 5 " --> pdb=" O CYS F 176 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU F 213 " --> pdb=" O HIS F 179 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N SER F 181 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL F 215 " --> pdb=" O SER F 181 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 335 through 338 removed outlier: 3.514A pdb=" N VAL F 521 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N PHE F 520 " --> pdb=" O LEU F 514 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER F 498 " --> pdb=" O GLU F 513 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 482 through 484 removed outlier: 3.588A pdb=" N ASP F 420 " --> pdb=" O VAL F 430 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 449 through 456 removed outlier: 3.690A pdb=" N GLU F 476 " --> pdb=" O ARG F 453 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1404 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: 5.38 Time building geometry restraints manager: 7.36 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: 2964 1.30 - 1.43: 4519 1.43 - 1.55: 10545 1.55 - 1.68: 36 1.68 - 1.81: 140 Bond restraints: 18204 Sorted by residual: bond pdb=" CA TYR D 53 " pdb=" C TYR D 53 " ideal model delta sigma weight residual 1.524 1.433 0.091 1.27e-02 6.20e+03 5.16e+01 bond pdb=" CA TYR F 53 " pdb=" C TYR F 53 " ideal model delta sigma weight residual 1.524 1.433 0.091 1.27e-02 6.20e+03 5.15e+01 bond pdb=" CA TYR A 53 " pdb=" C TYR A 53 " ideal model delta sigma weight residual 1.524 1.433 0.091 1.27e-02 6.20e+03 5.15e+01 bond pdb=" CA TYR E 53 " pdb=" C TYR E 53 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.27e-02 6.20e+03 5.07e+01 bond pdb=" CA ALA E 315 " pdb=" C ALA E 315 " ideal model delta sigma weight residual 1.523 1.434 0.089 1.30e-02 5.92e+03 4.71e+01 ... (remaining 18199 not shown) Histogram of bond angle deviations from ideal: 92.08 - 101.81: 75 101.81 - 111.54: 7919 111.54 - 121.27: 12091 121.27 - 131.00: 4501 131.00 - 140.73: 94 Bond angle restraints: 24680 Sorted by residual: angle pdb=" N SER A 51 " pdb=" CA SER A 51 " pdb=" C SER A 51 " ideal model delta sigma weight residual 109.64 92.08 17.56 1.56e+00 4.11e-01 1.27e+02 angle pdb=" N SER F 51 " pdb=" CA SER F 51 " pdb=" C SER F 51 " ideal model delta sigma weight residual 109.64 92.13 17.51 1.56e+00 4.11e-01 1.26e+02 angle pdb=" N SER D 51 " pdb=" CA SER D 51 " pdb=" C SER D 51 " ideal model delta sigma weight residual 109.64 92.13 17.51 1.56e+00 4.11e-01 1.26e+02 angle pdb=" N SER E 51 " pdb=" CA SER E 51 " pdb=" C SER E 51 " ideal model delta sigma weight residual 109.64 92.20 17.44 1.56e+00 4.11e-01 1.25e+02 angle pdb=" N GLU E 54 " pdb=" CA GLU E 54 " pdb=" C GLU E 54 " ideal model delta sigma weight residual 110.53 99.89 10.64 1.29e+00 6.01e-01 6.80e+01 ... (remaining 24675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 10801 33.94 - 67.87: 161 67.87 - 101.81: 16 101.81 - 135.74: 2 135.74 - 169.68: 4 Dihedral angle restraints: 10984 sinusoidal: 4580 harmonic: 6404 Sorted by residual: dihedral pdb=" CA ARG D 311 " pdb=" C ARG D 311 " pdb=" N ASP D 312 " pdb=" CA ASP D 312 " ideal model delta harmonic sigma weight residual -180.00 -118.06 -61.94 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ARG E 311 " pdb=" C ARG E 311 " pdb=" N ASP E 312 " pdb=" CA ASP E 312 " ideal model delta harmonic sigma weight residual -180.00 -118.10 -61.90 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ARG F 311 " pdb=" C ARG F 311 " pdb=" N ASP F 312 " pdb=" CA ASP F 312 " ideal model delta harmonic sigma weight residual -180.00 -118.11 -61.89 0 5.00e+00 4.00e-02 1.53e+02 ... (remaining 10981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2297 0.091 - 0.182: 395 0.182 - 0.273: 36 0.273 - 0.364: 8 0.364 - 0.455: 12 Chirality restraints: 2748 Sorted by residual: chirality pdb=" CB ILE F 214 " pdb=" CA ILE F 214 " pdb=" CG1 ILE F 214 " pdb=" CG2 ILE F 214 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CB ILE A 214 " pdb=" CA ILE A 214 " pdb=" CG1 ILE A 214 " pdb=" CG2 ILE A 214 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.14e+00 chirality pdb=" CB ILE D 214 " pdb=" CA ILE D 214 " pdb=" CG1 ILE D 214 " pdb=" CG2 ILE D 214 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.14e+00 ... (remaining 2745 not shown) Planarity restraints: 3168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 53 " -0.053 2.00e-02 2.50e+03 2.74e-02 1.50e+01 pdb=" CG TYR F 53 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR F 53 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR F 53 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR F 53 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 53 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR F 53 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR F 53 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 53 " 0.053 2.00e-02 2.50e+03 2.74e-02 1.50e+01 pdb=" CG TYR E 53 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 53 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR E 53 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR E 53 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 53 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 53 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 53 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 53 " -0.053 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR A 53 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 53 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 53 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 53 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 53 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 53 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 53 " -0.025 2.00e-02 2.50e+03 ... (remaining 3165 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.30: 18 2.30 - 2.95: 8018 2.95 - 3.60: 25751 3.60 - 4.25: 43470 4.25 - 4.90: 69714 Nonbonded interactions: 146971 Sorted by model distance: nonbonded pdb=" OE2 GLU A 155 " pdb=" O2' CTP A 602 " model vdw 1.655 2.440 nonbonded pdb=" OE2 GLU F 155 " pdb=" O2' CTP F 602 " model vdw 1.656 2.440 nonbonded pdb=" OE2 GLU E 155 " pdb=" O2' CTP E 602 " model vdw 1.656 2.440 nonbonded pdb=" OE2 GLU D 155 " pdb=" O2' CTP D 602 " model vdw 1.656 2.440 nonbonded pdb=" OD1 ASP A 153 " pdb=" NZ LYS D 195 " model vdw 1.872 2.520 ... (remaining 146966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 0.010 Extract box with map and model: 6.920 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 47.970 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 0.091 18204 Z= 0.691 Angle : 1.252 17.556 24680 Z= 0.695 Chirality : 0.075 0.455 2748 Planarity : 0.009 0.069 3168 Dihedral : 12.859 169.679 6872 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.60 % Favored : 91.22 % Rotamer: Outliers : 0.41 % Allowed : 5.98 % Favored : 93.61 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -4.98 (0.14), residues: 2220 helix: -4.03 (0.10), residues: 812 sheet: -3.12 (0.28), residues: 316 loop : -2.68 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP D 124 HIS 0.012 0.002 HIS E 55 PHE 0.032 0.004 PHE A 482 TYR 0.053 0.005 TYR A 53 ARG 0.007 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 548 time to evaluate : 1.977 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: A 57 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 299 CYS cc_start: 0.7605 (m) cc_final: 0.7282 (m) REVERT: A 363 LYS cc_start: 0.8836 (tmmm) cc_final: 0.8495 (ttpt) REVERT: A 436 MET cc_start: 0.8353 (ttm) cc_final: 0.8152 (ttm) REVERT: D 57 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7505 (tm-30) REVERT: D 299 CYS cc_start: 0.7604 (m) cc_final: 0.7298 (m) REVERT: D 363 LYS cc_start: 0.8811 (tmmm) cc_final: 0.8468 (ttpt) REVERT: D 436 MET cc_start: 0.8360 (ttm) cc_final: 0.8130 (ttm) REVERT: E 157 MET cc_start: 0.7886 (mmt) cc_final: 0.7654 (mmt) REVERT: E 299 CYS cc_start: 0.7526 (m) cc_final: 0.7232 (m) REVERT: E 363 LYS cc_start: 0.8748 (tmmm) cc_final: 0.8433 (ttpt) REVERT: E 379 LEU cc_start: 0.8407 (tt) cc_final: 0.7912 (tt) REVERT: E 436 MET cc_start: 0.8290 (ttm) cc_final: 0.8073 (ttm) REVERT: F 157 MET cc_start: 0.7883 (mmt) cc_final: 0.7651 (mmt) REVERT: F 299 CYS cc_start: 0.7531 (m) cc_final: 0.7225 (m) REVERT: F 363 LYS cc_start: 0.8755 (tmmm) cc_final: 0.8433 (ttpt) REVERT: F 436 MET cc_start: 0.8345 (ttm) cc_final: 0.8123 (ttm) outliers start: 8 outliers final: 4 residues processed: 556 average time/residue: 0.3712 time to fit residues: 286.5251 Evaluate side-chains 281 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 277 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain F residue 322 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN A 502 GLN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D 502 GLN ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 ASN E 502 GLN ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 ASN ** F 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 ASN F 502 GLN ** F 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18204 Z= 0.223 Angle : 0.718 7.549 24680 Z= 0.361 Chirality : 0.049 0.187 2748 Planarity : 0.006 0.053 3168 Dihedral : 11.907 175.660 2516 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.89 % Allowed : 14.43 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.54 (0.16), residues: 2220 helix: -2.29 (0.15), residues: 820 sheet: -2.58 (0.25), residues: 368 loop : -2.18 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 285 HIS 0.002 0.001 HIS E 235 PHE 0.016 0.002 PHE D 50 TYR 0.022 0.002 TYR D 307 ARG 0.003 0.000 ARG F 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 366 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.8924 (mmm160) cc_final: 0.8702 (mmp-170) REVERT: A 363 LYS cc_start: 0.8740 (tmmm) cc_final: 0.8508 (ttpt) REVERT: A 408 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 503 ASP cc_start: 0.8346 (p0) cc_final: 0.7708 (p0) REVERT: A 510 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7540 (mm-30) REVERT: A 534 MET cc_start: 0.8495 (mmt) cc_final: 0.8295 (mmm) REVERT: D 102 ARG cc_start: 0.8925 (mmm160) cc_final: 0.8707 (mmp-170) REVERT: D 363 LYS cc_start: 0.8732 (tmmm) cc_final: 0.8501 (ttpt) REVERT: D 408 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8253 (tm-30) REVERT: D 436 MET cc_start: 0.8309 (ttm) cc_final: 0.8020 (ttm) REVERT: D 510 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7583 (mm-30) REVERT: E 102 ARG cc_start: 0.8915 (mmm160) cc_final: 0.8705 (mmp-170) REVERT: E 295 LEU cc_start: 0.9037 (mt) cc_final: 0.8804 (mt) REVERT: E 363 LYS cc_start: 0.8698 (tmmm) cc_final: 0.8471 (ttpt) REVERT: E 408 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8146 (tm-30) REVERT: E 436 MET cc_start: 0.8281 (ttm) cc_final: 0.8049 (ttm) REVERT: E 503 ASP cc_start: 0.8215 (p0) cc_final: 0.7522 (p0) REVERT: E 508 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7488 (mtm-85) REVERT: E 510 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7648 (mm-30) REVERT: F 102 ARG cc_start: 0.8920 (mmm160) cc_final: 0.8708 (mmp-170) REVERT: F 295 LEU cc_start: 0.9021 (mt) cc_final: 0.8798 (mt) REVERT: F 363 LYS cc_start: 0.8722 (tmmm) cc_final: 0.8498 (ttpt) REVERT: F 408 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8207 (tm-30) REVERT: F 510 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7602 (mm-30) outliers start: 56 outliers final: 29 residues processed: 405 average time/residue: 0.3011 time to fit residues: 180.1449 Evaluate side-chains 277 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 496 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS A 480 HIS ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN D 127 ASN ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN E 478 HIS ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 ASN ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 HIS ** F 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18204 Z= 0.323 Angle : 0.741 7.907 24680 Z= 0.368 Chirality : 0.050 0.227 2748 Planarity : 0.005 0.048 3168 Dihedral : 11.332 165.188 2504 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 5.52 % Allowed : 14.54 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.89 (0.17), residues: 2220 helix: -1.38 (0.17), residues: 840 sheet: -2.41 (0.25), residues: 380 loop : -2.08 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 285 HIS 0.005 0.001 HIS D 116 PHE 0.018 0.002 PHE D 50 TYR 0.018 0.002 TYR A 540 ARG 0.003 0.001 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 292 time to evaluate : 2.129 Fit side-chains REVERT: A 102 ARG cc_start: 0.8924 (mmm160) cc_final: 0.8253 (mmp-170) REVERT: A 295 LEU cc_start: 0.9138 (mt) cc_final: 0.8922 (mt) REVERT: A 408 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8427 (tm-30) REVERT: A 498 SER cc_start: 0.8277 (t) cc_final: 0.7933 (p) REVERT: D 102 ARG cc_start: 0.8909 (mmm160) cc_final: 0.8233 (mmp-170) REVERT: D 295 LEU cc_start: 0.9130 (mt) cc_final: 0.8918 (mt) REVERT: D 408 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8455 (tm-30) REVERT: D 436 MET cc_start: 0.8122 (ttm) cc_final: 0.7888 (ttm) REVERT: D 498 SER cc_start: 0.8273 (t) cc_final: 0.7925 (p) REVERT: E 102 ARG cc_start: 0.8918 (mmm160) cc_final: 0.8469 (mmp-170) REVERT: E 295 LEU cc_start: 0.9134 (mt) cc_final: 0.8931 (mt) REVERT: E 363 LYS cc_start: 0.8676 (tmmm) cc_final: 0.8368 (ttpp) REVERT: E 436 MET cc_start: 0.8131 (ttm) cc_final: 0.7887 (ttm) REVERT: E 498 SER cc_start: 0.8352 (t) cc_final: 0.8004 (p) REVERT: E 503 ASP cc_start: 0.8195 (p0) cc_final: 0.7494 (p0) REVERT: E 508 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7390 (mtm-85) REVERT: F 102 ARG cc_start: 0.8919 (mmm160) cc_final: 0.8213 (mmp-170) REVERT: F 363 LYS cc_start: 0.8685 (tmmm) cc_final: 0.8376 (ttpp) REVERT: F 408 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8402 (tm-30) REVERT: F 498 SER cc_start: 0.8349 (t) cc_final: 0.8003 (p) REVERT: F 508 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7911 (mtm-85) outliers start: 107 outliers final: 79 residues processed: 360 average time/residue: 0.3060 time to fit residues: 164.0419 Evaluate side-chains 328 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 247 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 417 LYS Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 484 VAL Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 508 ARG Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 496 ASP Chi-restraints excluded: chain F residue 508 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18204 Z= 0.355 Angle : 0.731 10.569 24680 Z= 0.362 Chirality : 0.050 0.258 2748 Planarity : 0.005 0.049 3168 Dihedral : 10.872 153.074 2504 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.40 % Favored : 93.42 % Rotamer: Outliers : 6.34 % Allowed : 14.74 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.49 (0.17), residues: 2220 helix: -0.86 (0.17), residues: 832 sheet: -2.35 (0.25), residues: 380 loop : -1.95 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 285 HIS 0.005 0.001 HIS E 116 PHE 0.021 0.002 PHE E 50 TYR 0.020 0.002 TYR A 540 ARG 0.003 0.001 ARG D 532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 253 time to evaluate : 2.030 Fit side-chains REVERT: A 75 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: A 102 ARG cc_start: 0.8727 (mmm160) cc_final: 0.8389 (mmp-170) REVERT: A 157 MET cc_start: 0.8111 (mmt) cc_final: 0.7859 (mmp) REVERT: A 402 MET cc_start: 0.8168 (ttm) cc_final: 0.7830 (ttm) REVERT: A 470 ASP cc_start: 0.7509 (t0) cc_final: 0.7271 (t0) REVERT: A 498 SER cc_start: 0.8387 (t) cc_final: 0.8026 (p) REVERT: A 510 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7791 (mm-30) REVERT: D 75 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: D 102 ARG cc_start: 0.8722 (mmm160) cc_final: 0.8388 (mmp-170) REVERT: D 157 MET cc_start: 0.8112 (mmt) cc_final: 0.7856 (mmp) REVERT: D 402 MET cc_start: 0.8160 (ttm) cc_final: 0.7830 (ttm) REVERT: D 408 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8416 (tm-30) REVERT: D 436 MET cc_start: 0.8202 (ttm) cc_final: 0.7891 (ttm) REVERT: D 470 ASP cc_start: 0.7466 (t0) cc_final: 0.7219 (t0) REVERT: D 498 SER cc_start: 0.8382 (t) cc_final: 0.8019 (p) REVERT: D 510 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7845 (mm-30) REVERT: E 75 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7480 (mt-10) REVERT: E 102 ARG cc_start: 0.8716 (mmm160) cc_final: 0.8378 (mmp-170) REVERT: E 363 LYS cc_start: 0.8731 (tmmm) cc_final: 0.8510 (ttmt) REVERT: E 402 MET cc_start: 0.8186 (ttm) cc_final: 0.7831 (ttm) REVERT: E 436 MET cc_start: 0.8038 (ttm) cc_final: 0.7823 (ttm) REVERT: E 470 ASP cc_start: 0.7466 (t0) cc_final: 0.7211 (t0) REVERT: E 498 SER cc_start: 0.8290 (t) cc_final: 0.7880 (p) REVERT: E 510 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7827 (mm-30) REVERT: F 102 ARG cc_start: 0.8719 (mmm160) cc_final: 0.8380 (mmp-170) REVERT: F 363 LYS cc_start: 0.8736 (tmmm) cc_final: 0.8510 (ttmt) REVERT: F 402 MET cc_start: 0.8173 (ttm) cc_final: 0.7805 (ttm) REVERT: F 408 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8392 (tm-30) REVERT: F 470 ASP cc_start: 0.7507 (t0) cc_final: 0.7248 (t0) REVERT: F 498 SER cc_start: 0.8372 (t) cc_final: 0.8009 (p) REVERT: F 510 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7818 (mm-30) outliers start: 123 outliers final: 92 residues processed: 337 average time/residue: 0.3165 time to fit residues: 165.1290 Evaluate side-chains 337 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 243 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 507 ASP Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 417 LYS Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 417 LYS Chi-restraints excluded: chain F residue 424 PHE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 489 ILE Chi-restraints excluded: chain F residue 537 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 146 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 108 optimal weight: 0.0060 chunk 190 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18204 Z= 0.171 Angle : 0.634 10.907 24680 Z= 0.308 Chirality : 0.046 0.189 2748 Planarity : 0.005 0.046 3168 Dihedral : 9.722 133.226 2504 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.77 % Favored : 94.05 % Rotamer: Outliers : 3.71 % Allowed : 18.04 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.89 (0.18), residues: 2220 helix: -0.26 (0.18), residues: 828 sheet: -2.04 (0.26), residues: 368 loop : -1.72 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 285 HIS 0.003 0.001 HIS D 517 PHE 0.016 0.001 PHE F 50 TYR 0.011 0.001 TYR F 307 ARG 0.002 0.000 ARG D 508 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 343 time to evaluate : 2.094 Fit side-chains REVERT: A 75 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: A 102 ARG cc_start: 0.8676 (mmm160) cc_final: 0.8432 (mmp-170) REVERT: A 402 MET cc_start: 0.7876 (ttm) cc_final: 0.7517 (ttm) REVERT: A 470 ASP cc_start: 0.7386 (t0) cc_final: 0.7143 (t0) REVERT: A 498 SER cc_start: 0.8146 (t) cc_final: 0.7739 (p) REVERT: A 510 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7746 (mm-30) REVERT: D 75 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: D 102 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8465 (mmp-170) REVERT: D 408 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8190 (tm-30) REVERT: D 436 MET cc_start: 0.8227 (ttm) cc_final: 0.7934 (ttm) REVERT: D 470 ASP cc_start: 0.7389 (t0) cc_final: 0.7086 (t0) REVERT: D 498 SER cc_start: 0.8147 (t) cc_final: 0.7726 (p) REVERT: E 102 ARG cc_start: 0.8666 (mmm160) cc_final: 0.8422 (mmp-170) REVERT: E 436 MET cc_start: 0.8229 (ttm) cc_final: 0.7857 (ttm) REVERT: E 470 ASP cc_start: 0.7417 (t0) cc_final: 0.7113 (t0) REVERT: E 498 SER cc_start: 0.8156 (t) cc_final: 0.7721 (p) REVERT: F 46 ASP cc_start: 0.7170 (t0) cc_final: 0.6921 (t0) REVERT: F 408 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8216 (tm-30) REVERT: F 470 ASP cc_start: 0.7406 (t0) cc_final: 0.7104 (t0) REVERT: F 498 SER cc_start: 0.8212 (t) cc_final: 0.7803 (p) outliers start: 72 outliers final: 57 residues processed: 377 average time/residue: 0.2699 time to fit residues: 156.8646 Evaluate side-chains 347 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 288 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 496 ASP Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 212 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 HIS ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 480 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18204 Z= 0.178 Angle : 0.622 11.384 24680 Z= 0.303 Chirality : 0.046 0.159 2748 Planarity : 0.005 0.046 3168 Dihedral : 9.252 132.215 2504 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.23 % Favored : 94.59 % Rotamer: Outliers : 4.07 % Allowed : 19.48 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.69 (0.18), residues: 2220 helix: -0.03 (0.18), residues: 832 sheet: -1.86 (0.27), residues: 348 loop : -1.72 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 285 HIS 0.003 0.001 HIS A 517 PHE 0.018 0.001 PHE D 50 TYR 0.014 0.001 TYR F 42 ARG 0.003 0.000 ARG D 508 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 313 time to evaluate : 1.874 Fit side-chains REVERT: A 75 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: A 470 ASP cc_start: 0.7334 (t0) cc_final: 0.7117 (t0) REVERT: A 498 SER cc_start: 0.8174 (t) cc_final: 0.7755 (p) REVERT: D 75 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: D 102 ARG cc_start: 0.8694 (mmm160) cc_final: 0.8384 (mmp-170) REVERT: D 408 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8204 (tm-30) REVERT: D 436 MET cc_start: 0.8205 (ttm) cc_final: 0.7792 (ttm) REVERT: D 470 ASP cc_start: 0.7373 (t0) cc_final: 0.7109 (t0) REVERT: D 498 SER cc_start: 0.8192 (t) cc_final: 0.7776 (p) REVERT: E 40 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7728 (t0) REVERT: E 436 MET cc_start: 0.8135 (ttm) cc_final: 0.7871 (ttm) REVERT: E 470 ASP cc_start: 0.7398 (t0) cc_final: 0.7142 (t0) REVERT: E 498 SER cc_start: 0.8121 (t) cc_final: 0.7718 (p) REVERT: F 40 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7740 (t0) REVERT: F 46 ASP cc_start: 0.7084 (t0) cc_final: 0.6685 (t0) REVERT: F 408 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8187 (tm-30) REVERT: F 470 ASP cc_start: 0.7394 (t0) cc_final: 0.7137 (t0) REVERT: F 498 SER cc_start: 0.8157 (t) cc_final: 0.7764 (p) outliers start: 79 outliers final: 65 residues processed: 349 average time/residue: 0.2807 time to fit residues: 150.1615 Evaluate side-chains 353 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 284 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 507 ASP Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 365 ASP Chi-restraints excluded: chain F residue 496 ASP Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7951 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18204 Z= 0.167 Angle : 0.620 11.893 24680 Z= 0.300 Chirality : 0.045 0.147 2748 Planarity : 0.005 0.046 3168 Dihedral : 8.748 123.511 2504 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.18 % Favored : 94.64 % Rotamer: Outliers : 4.02 % Allowed : 20.15 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 2220 helix: 0.18 (0.19), residues: 832 sheet: -1.69 (0.29), residues: 324 loop : -1.64 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 285 HIS 0.003 0.001 HIS D 517 PHE 0.017 0.001 PHE D 50 TYR 0.015 0.001 TYR E 42 ARG 0.002 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 302 time to evaluate : 1.962 Fit side-chains REVERT: A 75 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: A 470 ASP cc_start: 0.7310 (t0) cc_final: 0.7092 (t0) REVERT: A 498 SER cc_start: 0.8120 (t) cc_final: 0.7731 (p) REVERT: D 75 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6815 (mt-10) REVERT: D 408 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8104 (tm-30) REVERT: D 436 MET cc_start: 0.8220 (ttm) cc_final: 0.7987 (ttm) REVERT: D 470 ASP cc_start: 0.7341 (t0) cc_final: 0.7102 (t0) REVERT: D 498 SER cc_start: 0.8082 (t) cc_final: 0.7697 (p) REVERT: E 408 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8021 (tm-30) REVERT: E 436 MET cc_start: 0.8191 (ttm) cc_final: 0.7692 (ttm) REVERT: E 470 ASP cc_start: 0.7438 (t0) cc_final: 0.7179 (t0) REVERT: E 498 SER cc_start: 0.8119 (t) cc_final: 0.7724 (p) REVERT: F 408 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8088 (tm-30) REVERT: F 470 ASP cc_start: 0.7430 (t0) cc_final: 0.7178 (t0) REVERT: F 498 SER cc_start: 0.8049 (t) cc_final: 0.7661 (p) outliers start: 78 outliers final: 67 residues processed: 337 average time/residue: 0.2578 time to fit residues: 137.5651 Evaluate side-chains 357 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 288 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 232 MET Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 496 ASP Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 chunk 104 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 192 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 480 HIS E 192 GLN F 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18204 Z= 0.160 Angle : 0.618 9.579 24680 Z= 0.298 Chirality : 0.045 0.140 2748 Planarity : 0.005 0.045 3168 Dihedral : 8.213 109.369 2504 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.73 % Favored : 95.09 % Rotamer: Outliers : 4.28 % Allowed : 19.95 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.28 (0.18), residues: 2220 helix: 0.35 (0.19), residues: 848 sheet: -1.61 (0.29), residues: 324 loop : -1.59 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 285 HIS 0.002 0.001 HIS E 517 PHE 0.018 0.001 PHE D 50 TYR 0.013 0.001 TYR A 42 ARG 0.006 0.000 ARG F 508 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 313 time to evaluate : 1.597 Fit side-chains REVERT: A 368 LEU cc_start: 0.8758 (tp) cc_final: 0.8545 (tt) REVERT: A 408 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7963 (tm-30) REVERT: A 498 SER cc_start: 0.8049 (t) cc_final: 0.7668 (p) REVERT: D 368 LEU cc_start: 0.8775 (tp) cc_final: 0.8562 (tt) REVERT: D 408 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8070 (tm-30) REVERT: D 436 MET cc_start: 0.8289 (ttm) cc_final: 0.8045 (ttm) REVERT: D 470 ASP cc_start: 0.7351 (t0) cc_final: 0.7138 (t0) REVERT: D 498 SER cc_start: 0.8056 (t) cc_final: 0.7699 (p) REVERT: E 40 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7748 (t0) REVERT: E 157 MET cc_start: 0.8161 (mmt) cc_final: 0.7810 (mmt) REVERT: E 294 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7776 (ptt-90) REVERT: E 408 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7973 (tm-30) REVERT: E 436 MET cc_start: 0.8244 (ttm) cc_final: 0.7910 (ttm) REVERT: E 470 ASP cc_start: 0.7438 (t0) cc_final: 0.7195 (t0) REVERT: E 498 SER cc_start: 0.8033 (t) cc_final: 0.7666 (p) REVERT: F 157 MET cc_start: 0.8160 (mmt) cc_final: 0.7806 (mmt) REVERT: F 408 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8041 (tm-30) REVERT: F 470 ASP cc_start: 0.7447 (t0) cc_final: 0.7220 (t0) REVERT: F 498 SER cc_start: 0.7781 (t) cc_final: 0.7391 (p) outliers start: 83 outliers final: 70 residues processed: 349 average time/residue: 0.2484 time to fit residues: 138.7924 Evaluate side-chains 357 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 286 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 496 ASP Chi-restraints excluded: chain F residue 507 ASP Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 186 optimal weight: 0.0970 chunk 196 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 526 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18204 Z= 0.160 Angle : 0.633 13.938 24680 Z= 0.301 Chirality : 0.045 0.141 2748 Planarity : 0.005 0.045 3168 Dihedral : 7.799 83.158 2504 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.14 % Favored : 95.68 % Rotamer: Outliers : 4.02 % Allowed : 20.26 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.19), residues: 2220 helix: 0.51 (0.19), residues: 848 sheet: -1.61 (0.27), residues: 352 loop : -1.54 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 285 HIS 0.002 0.001 HIS E 517 PHE 0.017 0.001 PHE E 50 TYR 0.015 0.001 TYR F 42 ARG 0.007 0.000 ARG F 508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 303 time to evaluate : 2.113 Fit side-chains REVERT: A 408 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 498 SER cc_start: 0.7803 (t) cc_final: 0.7406 (p) REVERT: D 408 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8029 (tm-30) REVERT: D 436 MET cc_start: 0.8261 (ttm) cc_final: 0.8042 (ttm) REVERT: D 498 SER cc_start: 0.7830 (t) cc_final: 0.7471 (p) REVERT: E 368 LEU cc_start: 0.8779 (tp) cc_final: 0.8561 (tt) REVERT: E 408 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7929 (tm-30) REVERT: E 436 MET cc_start: 0.8298 (ttm) cc_final: 0.7863 (ttm) REVERT: E 470 ASP cc_start: 0.7434 (t0) cc_final: 0.7222 (t0) REVERT: E 498 SER cc_start: 0.8034 (t) cc_final: 0.7659 (p) REVERT: F 294 ARG cc_start: 0.8056 (mtm110) cc_final: 0.7840 (ptt-90) REVERT: F 368 LEU cc_start: 0.8758 (tp) cc_final: 0.8540 (tt) REVERT: F 408 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7996 (tm-30) REVERT: F 470 ASP cc_start: 0.7436 (t0) cc_final: 0.7233 (t0) REVERT: F 498 SER cc_start: 0.7679 (t) cc_final: 0.7282 (p) outliers start: 78 outliers final: 69 residues processed: 338 average time/residue: 0.2510 time to fit residues: 135.9213 Evaluate side-chains 339 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 270 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 507 ASP Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 496 ASP Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 99 optimal weight: 0.0370 chunk 145 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 201 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 18 optimal weight: 0.0050 chunk 134 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 138 optimal weight: 0.4980 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 192 GLN A 323 HIS D 128 GLN D 192 GLN D 323 HIS E 128 GLN E 323 HIS ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18204 Z= 0.154 Angle : 0.639 14.764 24680 Z= 0.304 Chirality : 0.044 0.139 2748 Planarity : 0.005 0.045 3168 Dihedral : 7.431 75.738 2504 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.50 % Rotamer: Outliers : 3.66 % Allowed : 21.34 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.02 (0.19), residues: 2220 helix: 0.61 (0.19), residues: 852 sheet: -1.31 (0.29), residues: 324 loop : -1.54 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.003 0.001 HIS D 517 PHE 0.012 0.001 PHE A 50 TYR 0.014 0.001 TYR F 42 ARG 0.009 0.000 ARG D 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 303 time to evaluate : 1.982 Fit side-chains REVERT: A 75 GLU cc_start: 0.7535 (mp0) cc_final: 0.6725 (mt-10) REVERT: A 408 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7953 (tm-30) REVERT: A 498 SER cc_start: 0.7720 (t) cc_final: 0.7341 (p) REVERT: D 75 GLU cc_start: 0.7541 (mp0) cc_final: 0.6728 (mt-10) REVERT: D 298 ILE cc_start: 0.8775 (mm) cc_final: 0.8254 (tp) REVERT: D 368 LEU cc_start: 0.8764 (tp) cc_final: 0.8547 (tt) REVERT: D 408 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7989 (tm-30) REVERT: D 436 MET cc_start: 0.8215 (ttm) cc_final: 0.7981 (ttm) REVERT: D 498 SER cc_start: 0.7740 (t) cc_final: 0.7382 (p) REVERT: E 75 GLU cc_start: 0.7505 (mp0) cc_final: 0.6753 (mt-10) REVERT: E 368 LEU cc_start: 0.8753 (tp) cc_final: 0.8536 (tt) REVERT: E 408 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7914 (tm-30) REVERT: E 436 MET cc_start: 0.8221 (ttm) cc_final: 0.7806 (ttm) REVERT: E 498 SER cc_start: 0.7766 (t) cc_final: 0.7394 (p) REVERT: F 157 MET cc_start: 0.8102 (mmt) cc_final: 0.7600 (mmt) REVERT: F 408 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7961 (tm-30) REVERT: F 498 SER cc_start: 0.7625 (t) cc_final: 0.7246 (p) outliers start: 71 outliers final: 68 residues processed: 334 average time/residue: 0.2749 time to fit residues: 145.5102 Evaluate side-chains 349 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 281 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 496 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 496 ASP Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 496 ASP Chi-restraints excluded: chain E residue 507 ASP Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 496 ASP Chi-restraints excluded: chain F residue 537 SER Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4869 > 50: distance: 40 - 134: 32.172 distance: 43 - 131: 31.783 distance: 75 - 102: 26.215 distance: 78 - 99: 37.562 distance: 94 - 99: 34.116 distance: 99 - 100: 23.719 distance: 100 - 101: 45.718 distance: 100 - 103: 19.724 distance: 101 - 102: 23.900 distance: 101 - 109: 39.283 distance: 103 - 104: 43.676 distance: 104 - 105: 21.590 distance: 104 - 106: 16.735 distance: 106 - 108: 11.193 distance: 107 - 108: 30.009 distance: 109 - 110: 31.953 distance: 110 - 111: 25.400 distance: 110 - 113: 34.764 distance: 111 - 112: 42.171 distance: 113 - 114: 25.108 distance: 114 - 115: 4.519 distance: 115 - 116: 32.792 distance: 116 - 117: 21.413 distance: 117 - 118: 36.482 distance: 117 - 119: 14.785 distance: 120 - 121: 40.744 distance: 121 - 122: 46.019 distance: 121 - 124: 6.357 distance: 122 - 123: 32.421 distance: 122 - 131: 25.184 distance: 124 - 125: 11.118 distance: 125 - 126: 18.779 distance: 125 - 127: 22.959 distance: 126 - 128: 19.039 distance: 127 - 129: 22.667 distance: 128 - 130: 47.152 distance: 129 - 130: 40.281 distance: 131 - 132: 9.673 distance: 132 - 133: 42.806 distance: 132 - 135: 40.384 distance: 133 - 134: 48.559 distance: 133 - 140: 40.191 distance: 136 - 137: 41.982 distance: 137 - 138: 28.350 distance: 137 - 139: 19.830 distance: 140 - 141: 17.933 distance: 141 - 142: 39.606 distance: 141 - 144: 39.545 distance: 142 - 143: 17.275 distance: 142 - 147: 43.869 distance: 144 - 145: 3.136 distance: 144 - 146: 37.698 distance: 147 - 148: 39.951 distance: 148 - 149: 28.160 distance: 148 - 151: 3.964 distance: 149 - 150: 35.693 distance: 149 - 155: 32.195 distance: 151 - 152: 11.166 distance: 152 - 153: 27.747 distance: 152 - 154: 24.332 distance: 155 - 156: 38.699 distance: 155 - 161: 39.651 distance: 156 - 157: 49.650 distance: 156 - 159: 40.179 distance: 157 - 158: 41.374 distance: 157 - 162: 30.611 distance: 159 - 160: 40.815 distance: 160 - 161: 53.587 distance: 162 - 163: 41.988 distance: 163 - 164: 10.976 distance: 163 - 166: 29.914 distance: 164 - 165: 41.425 distance: 166 - 167: 45.836 distance: 167 - 168: 40.524 distance: 167 - 169: 29.739 distance: 171 - 172: 50.114 distance: 171 - 174: 16.213 distance: 172 - 173: 51.714 distance: 172 - 178: 9.011 distance: 174 - 175: 16.586 distance: 175 - 176: 44.252 distance: 175 - 177: 43.442 distance: 178 - 179: 32.052 distance: 179 - 180: 4.902 distance: 179 - 182: 11.654 distance: 180 - 186: 33.732 distance: 182 - 183: 51.827 distance: 182 - 184: 49.581 distance: 183 - 185: 46.629