Starting phenix.real_space_refine (version: dev) on Wed Apr 6 18:24:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/04_2022/6pw4_20498_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/04_2022/6pw4_20498.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/04_2022/6pw4_20498_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/04_2022/6pw4_20498_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/04_2022/6pw4_20498_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/04_2022/6pw4_20498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/04_2022/6pw4_20498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/04_2022/6pw4_20498_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/04_2022/6pw4_20498_updated.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 21": "OD1" <-> "OD2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ASP 490": "OD1" <-> "OD2" Residue "A ARG 501": "NH1" <-> "NH2" Residue "A ASP 527": "OD1" <-> "OD2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A GLU 757": "OE1" <-> "OE2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A ARG 851": "NH1" <-> "NH2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B ASP 42": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 264": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 439": "OD1" <-> "OD2" Residue "B TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 527": "OD1" <-> "OD2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 562": "OE1" <-> "OE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ASP 604": "OD1" <-> "OD2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 749": "NH1" <-> "NH2" Residue "B GLU 757": "OE1" <-> "OE2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 772": "NH1" <-> "NH2" Residue "B GLU 826": "OE1" <-> "OE2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ASP 840": "OD1" <-> "OD2" Residue "B ARG 846": "NH1" <-> "NH2" Residue "C ASP 21": "OD1" <-> "OD2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 193": "NH1" <-> "NH2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C ASP 384": "OD1" <-> "OD2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C ASP 402": "OD1" <-> "OD2" Residue "C ASP 433": "OD1" <-> "OD2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ASP 490": "OD1" <-> "OD2" Residue "C ARG 501": "NH1" <-> "NH2" Residue "C ASP 527": "OD1" <-> "OD2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C GLU 562": "OE1" <-> "OE2" Residue "C ARG 586": "NH1" <-> "NH2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C GLU 622": "OE1" <-> "OE2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C GLU 757": "OE1" <-> "OE2" Residue "C ARG 759": "NH1" <-> "NH2" Residue "C ARG 771": "NH1" <-> "NH2" Residue "C ARG 809": "NH1" <-> "NH2" Residue "C GLU 812": "OE1" <-> "OE2" Residue "C ARG 851": "NH1" <-> "NH2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D ASP 42": "OD1" <-> "OD2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D ASP 49": "OD1" <-> "OD2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D ASP 226": "OD1" <-> "OD2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 501": "NH1" <-> "NH2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 527": "OD1" <-> "OD2" Residue "D GLU 551": "OE1" <-> "OE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 749": "NH1" <-> "NH2" Residue "D GLU 757": "OE1" <-> "OE2" Residue "D ARG 761": "NH1" <-> "NH2" Residue "D ARG 772": "NH1" <-> "NH2" Residue "D GLU 826": "OE1" <-> "OE2" Residue "D ARG 835": "NH1" <-> "NH2" Residue "D ARG 846": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 22348 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5553 Classifications: {'peptide': 696} Link IDs: {'PTRANS': 24, 'TRANS': 671} Chain breaks: 4 Chain: "B" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5372 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 23, 'TRANS': 651} Chain breaks: 4 Chain: "C" Number of atoms: 5553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5553 Classifications: {'peptide': 696} Link IDs: {'PTRANS': 24, 'TRANS': 671} Chain breaks: 4 Chain: "D" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5372 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 23, 'TRANS': 651} Chain breaks: 4 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'CPL': 1, 'PCW': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 126 Unusual residues: {'PIK': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'CPL': 1, 'PCW': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'CPL:plan-4': 1, 'CPL:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 126 Unusual residues: {'PIK': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.28, per 1000 atoms: 0.55 Number of scatterers: 22348 At special positions: 0 Unit cell: (136.74, 147.34, 114.48, 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 170 16.00 P 22 15.00 O 4060 8.00 N 3634 7.00 C 14462 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.38 Conformation dependent library (CDL) restraints added in 3.8 seconds 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 146 helices and 0 sheets defined 56.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.876A pdb=" N ALA A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.919A pdb=" N GLU A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 removed outlier: 4.052A pdb=" N THR A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.770A pdb=" N ALA A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 4.174A pdb=" N TYR A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 180 through 194 removed outlier: 3.655A pdb=" N GLU A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 219 removed outlier: 4.086A pdb=" N THR A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 239 No H-bonds generated for 'chain 'A' and resid 236 through 239' Processing helix chain 'A' and resid 334 through 347 removed outlier: 3.943A pdb=" N SER A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.536A pdb=" N ILE A 355 " --> pdb=" O CYS A 351 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 385 removed outlier: 3.933A pdb=" N ALA A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.620A pdb=" N ALA A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 419 No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 424 through 432 removed outlier: 4.260A pdb=" N LYS A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 445 through 462 removed outlier: 3.945A pdb=" N CYS A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 473 removed outlier: 3.655A pdb=" N VAL A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 498 through 521 removed outlier: 3.984A pdb=" N LEU A 504 " --> pdb=" O TYR A 500 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 removed outlier: 3.699A pdb=" N CYS A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 577 removed outlier: 3.841A pdb=" N VAL A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 removed outlier: 4.237A pdb=" N LEU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 621 removed outlier: 3.998A pdb=" N LEU A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET A 612 " --> pdb=" O ALA A 608 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 618 " --> pdb=" O TRP A 614 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER A 619 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N PHE A 621 " --> pdb=" O MET A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.604A pdb=" N GLN A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET A 633 " --> pdb=" O PRO A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 661 removed outlier: 3.879A pdb=" N GLY A 655 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 718 through 751 removed outlier: 4.089A pdb=" N PHE A 723 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 727 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 746 " --> pdb=" O MET A 742 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 763 Processing helix chain 'A' and resid 768 through 771 No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 784 through 792 removed outlier: 3.565A pdb=" N ALA A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 789 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 813 No H-bonds generated for 'chain 'A' and resid 810 through 813' Processing helix chain 'A' and resid 824 through 834 removed outlier: 4.011A pdb=" N ARG A 828 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A 831 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A 834 " --> pdb=" O VAL A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 868 removed outlier: 4.273A pdb=" N VAL A 847 " --> pdb=" O ASN A 843 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Proline residue: A 859 - end of helix removed outlier: 4.577A pdb=" N HIS A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A 864 " --> pdb=" O ASN A 860 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 867 " --> pdb=" O HIS A 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 No H-bonds generated for 'chain 'B' and resid 23 through 26' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 65 through 74 removed outlier: 3.680A pdb=" N LYS B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.670A pdb=" N HIS B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 140 through 152 removed outlier: 4.287A pdb=" N TYR B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 177 removed outlier: 3.694A pdb=" N ALA B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 192 removed outlier: 3.631A pdb=" N GLU B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.583A pdb=" N TRP B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.537A pdb=" N VAL B 342 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 3.823A pdb=" N ILE B 355 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 360 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 362 " --> pdb=" O CYS B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.717A pdb=" N ALA B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 416 through 419 No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 424 through 432 removed outlier: 3.531A pdb=" N PHE B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 429 " --> pdb=" O GLN B 425 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 519 removed outlier: 3.873A pdb=" N LEU B 504 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.794A pdb=" N SER B 532 " --> pdb=" O VAL B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 556 removed outlier: 4.455A pdb=" N LEU B 548 " --> pdb=" O CYS B 544 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 565 removed outlier: 4.140A pdb=" N SER B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 590 removed outlier: 3.578A pdb=" N VAL B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 576 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 579 " --> pdb=" O MET B 575 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 587 " --> pdb=" O TYR B 583 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 622 removed outlier: 3.506A pdb=" N MET B 612 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 618 " --> pdb=" O TRP B 614 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER B 619 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE B 621 " --> pdb=" O MET B 617 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU B 622 " --> pdb=" O VAL B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 640 removed outlier: 4.045A pdb=" N LEU B 638 " --> pdb=" O MET B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 661 removed outlier: 3.528A pdb=" N LEU B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 655 " --> pdb=" O VAL B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 752 removed outlier: 3.503A pdb=" N LEU B 725 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 726 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 730 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 745 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG B 749 " --> pdb=" O ASP B 745 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 766 removed outlier: 3.576A pdb=" N ARG B 761 " --> pdb=" O GLU B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 837 removed outlier: 3.596A pdb=" N VAL B 832 " --> pdb=" O ARG B 828 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG B 835 " --> pdb=" O VAL B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 850 removed outlier: 3.971A pdb=" N VAL B 847 " --> pdb=" O ASN B 843 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 850 " --> pdb=" O ARG B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 860 No H-bonds generated for 'chain 'B' and resid 858 through 860' Processing helix chain 'C' and resid 23 through 26 No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 65 through 74 removed outlier: 3.504A pdb=" N ARG C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 removed outlier: 3.875A pdb=" N ALA C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS C 94 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.877A pdb=" N GLU C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU C 108 " --> pdb=" O MET C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 120 removed outlier: 4.038A pdb=" N THR C 117 " --> pdb=" O THR C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.782A pdb=" N ALA C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 152 removed outlier: 4.172A pdb=" N TYR C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 180 through 194 removed outlier: 3.650A pdb=" N GLU C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 219 removed outlier: 4.130A pdb=" N THR C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 239 No H-bonds generated for 'chain 'C' and resid 236 through 239' Processing helix chain 'C' and resid 334 through 347 removed outlier: 3.962A pdb=" N SER C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 365 removed outlier: 3.536A pdb=" N ILE C 355 " --> pdb=" O CYS C 351 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 360 " --> pdb=" O MET C 356 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN C 364 " --> pdb=" O SER C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 385 removed outlier: 3.843A pdb=" N ALA C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 395 removed outlier: 3.621A pdb=" N ALA C 394 " --> pdb=" O GLN C 390 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 419 No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 424 through 432 removed outlier: 4.260A pdb=" N LYS C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 445 through 462 removed outlier: 3.948A pdb=" N CYS C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 473 removed outlier: 3.666A pdb=" N VAL C 470 " --> pdb=" O PRO C 466 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 498 through 521 removed outlier: 3.983A pdb=" N LEU C 504 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 removed outlier: 3.701A pdb=" N CYS C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 577 removed outlier: 3.841A pdb=" N VAL C 573 " --> pdb=" O ASN C 569 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 575 " --> pdb=" O MET C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 587 removed outlier: 4.237A pdb=" N LEU C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 621 removed outlier: 3.999A pdb=" N LEU C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 618 " --> pdb=" O TRP C 614 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER C 619 " --> pdb=" O PHE C 615 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N VAL C 620 " --> pdb=" O ARG C 616 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE C 621 " --> pdb=" O MET C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 636 removed outlier: 3.568A pdb=" N GLN C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET C 633 " --> pdb=" O PRO C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 661 removed outlier: 3.870A pdb=" N GLY C 655 " --> pdb=" O VAL C 651 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 751 removed outlier: 4.107A pdb=" N PHE C 723 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE C 727 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 728 " --> pdb=" O TYR C 724 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 745 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 746 " --> pdb=" O MET C 742 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 748 " --> pdb=" O ALA C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 763 Processing helix chain 'C' and resid 768 through 771 No H-bonds generated for 'chain 'C' and resid 768 through 771' Processing helix chain 'C' and resid 784 through 792 removed outlier: 3.566A pdb=" N ALA C 788 " --> pdb=" O LEU C 784 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 789 " --> pdb=" O VAL C 785 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 791 " --> pdb=" O ALA C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 813 No H-bonds generated for 'chain 'C' and resid 810 through 813' Processing helix chain 'C' and resid 824 through 834 removed outlier: 4.011A pdb=" N ARG C 828 " --> pdb=" O GLU C 825 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL C 831 " --> pdb=" O ARG C 828 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 834 " --> pdb=" O VAL C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 868 removed outlier: 3.520A pdb=" N ARG C 846 " --> pdb=" O LEU C 842 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL C 847 " --> pdb=" O ASN C 843 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 850 " --> pdb=" O ARG C 846 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 856 " --> pdb=" O GLU C 852 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU C 857 " --> pdb=" O LYS C 853 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 858 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Proline residue: C 859 - end of helix removed outlier: 4.607A pdb=" N HIS C 863 " --> pdb=" O PRO C 859 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 864 " --> pdb=" O ASN C 860 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 867 " --> pdb=" O HIS C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 26 No H-bonds generated for 'chain 'D' and resid 23 through 26' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 65 through 74 removed outlier: 3.683A pdb=" N LYS D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 99 through 108 Processing helix chain 'D' and resid 115 through 120 removed outlier: 3.698A pdb=" N HIS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 134 Processing helix chain 'D' and resid 140 through 152 removed outlier: 4.293A pdb=" N TYR D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 removed outlier: 3.691A pdb=" N ALA D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA D 175 " --> pdb=" O MET D 171 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.631A pdb=" N GLU D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL D 185 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.572A pdb=" N TRP D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 215 " --> pdb=" O LEU D 211 " (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 250 through 253 No H-bonds generated for 'chain 'D' and resid 250 through 253' Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 338 through 345 removed outlier: 3.541A pdb=" N VAL D 342 " --> pdb=" O GLN D 338 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER D 343 " --> pdb=" O GLY D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 363 removed outlier: 3.827A pdb=" N ILE D 355 " --> pdb=" O CYS D 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 360 " --> pdb=" O MET D 356 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 362 " --> pdb=" O CYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 383 removed outlier: 3.721A pdb=" N ALA D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN D 374 " --> pdb=" O ASP D 370 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 424 through 432 removed outlier: 3.528A pdb=" N PHE D 428 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR D 429 " --> pdb=" O GLN D 425 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS D 431 " --> pdb=" O ILE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 519 removed outlier: 3.875A pdb=" N LEU D 504 " --> pdb=" O TYR D 500 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.793A pdb=" N SER D 532 " --> pdb=" O VAL D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 558 removed outlier: 4.485A pdb=" N LEU D 548 " --> pdb=" O CYS D 544 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D 558 " --> pdb=" O GLU D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 565 removed outlier: 4.143A pdb=" N SER D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 590 removed outlier: 3.584A pdb=" N VAL D 573 " --> pdb=" O ASN D 569 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR D 579 " --> pdb=" O MET D 575 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D 587 " --> pdb=" O TYR D 583 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 588 " --> pdb=" O ILE D 584 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL D 590 " --> pdb=" O ARG D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 622 removed outlier: 3.539A pdb=" N MET D 612 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 613 " --> pdb=" O ALA D 609 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 618 " --> pdb=" O TRP D 614 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER D 619 " --> pdb=" O PHE D 615 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL D 620 " --> pdb=" O ARG D 616 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE D 621 " --> pdb=" O MET D 617 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 640 removed outlier: 4.046A pdb=" N LEU D 638 " --> pdb=" O MET D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 661 removed outlier: 3.510A pdb=" N LEU D 650 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 651 " --> pdb=" O LEU D 647 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 655 " --> pdb=" O VAL D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 752 removed outlier: 3.506A pdb=" N LEU D 725 " --> pdb=" O VAL D 721 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 730 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 738 " --> pdb=" O LEU D 734 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP D 745 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG D 749 " --> pdb=" O ASP D 745 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 766 removed outlier: 3.576A pdb=" N ARG D 761 " --> pdb=" O GLU D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 850 removed outlier: 3.593A pdb=" N VAL D 832 " --> pdb=" O ARG D 828 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 835 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP D 839 " --> pdb=" O ARG D 835 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL D 847 " --> pdb=" O ASN D 843 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D 850 " --> pdb=" O ARG D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 860 No H-bonds generated for 'chain 'D' and resid 858 through 860' 699 hydrogen bonds defined for protein. 2061 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: 5.68 Time building geometry restraints manager: 10.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3524 1.31 - 1.44: 6111 1.44 - 1.57: 12874 1.57 - 1.70: 33 1.70 - 1.83: 282 Bond restraints: 22824 Sorted by residual: bond pdb=" C31 PCW C1002 " pdb=" O2 PCW C1002 " ideal model delta sigma weight residual 1.333 1.444 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C31 PCW A1002 " pdb=" O2 PCW A1002 " ideal model delta sigma weight residual 1.333 1.444 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C11 PCW A1002 " pdb=" O3 PCW A1002 " ideal model delta sigma weight residual 1.326 1.431 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C11 PCW C1002 " pdb=" O3 PCW C1002 " ideal model delta sigma weight residual 1.326 1.431 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C11 CPL A1003 " pdb=" O3 CPL A1003 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 22819 not shown) Histogram of bond angle deviations from ideal: 97.53 - 104.96: 389 104.96 - 112.38: 11401 112.38 - 119.81: 8866 119.81 - 127.23: 9991 127.23 - 134.65: 293 Bond angle restraints: 30940 Sorted by residual: angle pdb=" N VAL D 246 " pdb=" CA VAL D 246 " pdb=" C VAL D 246 " ideal model delta sigma weight residual 113.71 106.24 7.47 9.50e-01 1.11e+00 6.18e+01 angle pdb=" N VAL B 246 " pdb=" CA VAL B 246 " pdb=" C VAL B 246 " ideal model delta sigma weight residual 113.71 106.24 7.47 9.50e-01 1.11e+00 6.18e+01 angle pdb=" N ILE A 627 " pdb=" CA ILE A 627 " pdb=" C ILE A 627 " ideal model delta sigma weight residual 113.53 105.99 7.54 9.80e-01 1.04e+00 5.93e+01 angle pdb=" N GLN B 114 " pdb=" CA GLN B 114 " pdb=" C GLN B 114 " ideal model delta sigma weight residual 114.04 104.63 9.41 1.24e+00 6.50e-01 5.76e+01 angle pdb=" N GLN D 114 " pdb=" CA GLN D 114 " pdb=" C GLN D 114 " ideal model delta sigma weight residual 114.04 104.68 9.36 1.24e+00 6.50e-01 5.70e+01 ... (remaining 30935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 13150 35.70 - 71.40: 370 71.40 - 107.10: 24 107.10 - 142.81: 4 142.81 - 178.51: 2 Dihedral angle restraints: 13550 sinusoidal: 5484 harmonic: 8066 Sorted by residual: dihedral pdb=" CA SER B 232 " pdb=" C SER B 232 " pdb=" N PHE B 233 " pdb=" CA PHE B 233 " ideal model delta harmonic sigma weight residual 180.00 134.47 45.53 0 5.00e+00 4.00e-02 8.29e+01 dihedral pdb=" CA SER D 232 " pdb=" C SER D 232 " pdb=" N PHE D 233 " pdb=" CA PHE D 233 " ideal model delta harmonic sigma weight residual 180.00 134.49 45.51 0 5.00e+00 4.00e-02 8.28e+01 dihedral pdb=" CA CYS A 776 " pdb=" C CYS A 776 " pdb=" N PRO A 777 " pdb=" CA PRO A 777 " ideal model delta harmonic sigma weight residual 180.00 139.71 40.29 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 13547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2607 0.055 - 0.110: 761 0.110 - 0.166: 135 0.166 - 0.221: 29 0.221 - 0.276: 6 Chirality restraints: 3538 Sorted by residual: chirality pdb=" CB THR A 593 " pdb=" CA THR A 593 " pdb=" OG1 THR A 593 " pdb=" CG2 THR A 593 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB THR C 593 " pdb=" CA THR C 593 " pdb=" OG1 THR C 593 " pdb=" CG2 THR C 593 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL C 775 " pdb=" CA VAL C 775 " pdb=" CG1 VAL C 775 " pdb=" CG2 VAL C 775 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 3535 not shown) Planarity restraints: 3804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 776 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO A 777 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 777 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 777 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 776 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO C 777 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 777 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 777 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 776 " -0.053 5.00e-02 4.00e+02 7.89e-02 9.95e+00 pdb=" N PRO B 777 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 777 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 777 " -0.043 5.00e-02 4.00e+02 ... (remaining 3801 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7051 2.82 - 3.34: 19763 3.34 - 3.86: 35599 3.86 - 4.38: 43365 4.38 - 4.90: 71791 Nonbonded interactions: 177569 Sorted by model distance: nonbonded pdb=" O PHE A 727 " pdb=" OG1 THR A 731 " model vdw 2.302 2.440 nonbonded pdb=" O PHE C 727 " pdb=" OG1 THR C 731 " model vdw 2.303 2.440 nonbonded pdb=" O SER B 565 " pdb=" OG SER B 565 " model vdw 2.308 2.440 nonbonded pdb=" O SER D 565 " pdb=" OG SER D 565 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR B 39 " pdb=" O MET B 44 " model vdw 2.312 2.440 ... (remaining 177564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 325 or resid 327 through 443 or resid 493 throu \ gh 665 or resid 718 through 783 or resid 813 through 867)) selection = (chain 'B' and (resid 17 through 33 or resid 53 through 246 or resid 268 or resi \ d 276 or resid 327 through 867)) selection = (chain 'C' and (resid 17 through 325 or resid 327 through 443 or resid 493 throu \ gh 665 or resid 718 through 783 or resid 813 through 867)) selection = (chain 'D' and (resid 17 through 33 or resid 53 through 246 or resid 268 or resi \ d 276 or resid 327 through 867)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 22 5.49 5 S 170 5.16 5 C 14462 2.51 5 N 3634 2.21 5 O 4060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.760 Check model and map are aligned: 0.380 Convert atoms to be neutral: 0.220 Process input model: 57.520 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.008 0.111 22824 Z= 0.485 Angle : 1.139 15.667 30940 Z= 0.618 Chirality : 0.054 0.276 3538 Planarity : 0.007 0.088 3804 Dihedral : 16.950 178.506 8322 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.66 % Favored : 89.27 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.23 % 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: -6.92 (0.09), residues: 2702 helix: -4.68 (0.05), residues: 1758 sheet: None (None), residues: 0 loop : -3.99 (0.16), residues: 944 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 517 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 526 average time/residue: 0.3612 time to fit residues: 287.1606 Evaluate side-chains 407 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 405 time to evaluate : 2.707 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1943 time to fit residues: 4.5116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 0.5980 chunk 206 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.0020 chunk 213 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN A 363 GLN A 425 GLN A 553 GLN A 665 GLN A 860 ASN B 27 HIS B 98 GLN B 169 ASN B 221 HIS B 359 GLN B 426 GLN B 506 GLN B 636 GLN C 137 GLN C 177 GLN ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 GLN C 363 GLN C 425 GLN C 553 GLN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 665 GLN C 860 ASN D 27 HIS D 98 GLN D 169 ASN D 221 HIS D 359 GLN D 426 GLN D 506 GLN D 636 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 22824 Z= 0.163 Angle : 0.658 15.686 30940 Z= 0.334 Chirality : 0.039 0.144 3538 Planarity : 0.006 0.120 3804 Dihedral : 12.379 165.918 3224 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.23 % 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: -5.27 (0.12), residues: 2702 helix: -3.29 (0.09), residues: 1788 sheet: None (None), residues: 0 loop : -3.58 (0.17), residues: 914 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 464 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 22 residues processed: 492 average time/residue: 0.3252 time to fit residues: 249.3591 Evaluate side-chains 412 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 390 time to evaluate : 2.564 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 2 residues processed: 22 average time/residue: 0.2236 time to fit residues: 12.1240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 247 optimal weight: 4.9990 chunk 267 optimal weight: 0.0170 chunk 220 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 overall best weight: 2.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 GLN A 753 GLN B 179 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 HIS ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 22824 Z= 0.256 Angle : 0.659 9.916 30940 Z= 0.332 Chirality : 0.041 0.156 3538 Planarity : 0.006 0.111 3804 Dihedral : 11.899 157.215 3224 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.23 % 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: -4.19 (0.14), residues: 2702 helix: -2.39 (0.11), residues: 1766 sheet: None (None), residues: 0 loop : -3.30 (0.18), residues: 936 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 406 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 28 residues processed: 432 average time/residue: 0.3276 time to fit residues: 225.3016 Evaluate side-chains 408 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 380 time to evaluate : 2.801 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 2 residues processed: 28 average time/residue: 0.2205 time to fit residues: 14.8578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 0.8980 chunk 186 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 22824 Z= 0.175 Angle : 0.612 14.249 30940 Z= 0.310 Chirality : 0.039 0.197 3538 Planarity : 0.005 0.072 3804 Dihedral : 11.264 150.000 3224 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.23 % 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: -3.41 (0.15), residues: 2702 helix: -1.76 (0.11), residues: 1778 sheet: None (None), residues: 0 loop : -3.05 (0.19), residues: 924 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 427 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 24 residues processed: 455 average time/residue: 0.3213 time to fit residues: 233.9954 Evaluate side-chains 418 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 394 time to evaluate : 2.556 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 2 residues processed: 24 average time/residue: 0.2222 time to fit residues: 13.2491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 22824 Z= 0.259 Angle : 0.661 15.692 30940 Z= 0.328 Chirality : 0.041 0.175 3538 Planarity : 0.006 0.141 3804 Dihedral : 11.243 147.375 3224 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.15 % 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: -3.05 (0.15), residues: 2702 helix: -1.47 (0.12), residues: 1808 sheet: None (None), residues: 0 loop : -3.00 (0.20), residues: 894 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 404 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 27 residues processed: 445 average time/residue: 0.3088 time to fit residues: 219.5455 Evaluate side-chains 410 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 383 time to evaluate : 2.502 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 2 residues processed: 27 average time/residue: 0.2070 time to fit residues: 13.6105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 0.9980 chunk 236 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.876 22824 Z= 0.786 Angle : 1.166 106.098 30940 Z= 0.492 Chirality : 0.042 0.279 3538 Planarity : 0.006 0.198 3804 Dihedral : 11.249 147.346 3224 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.15 % 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: -2.99 (0.15), residues: 2702 helix: -1.42 (0.12), residues: 1802 sheet: None (None), residues: 0 loop : -2.95 (0.20), residues: 900 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 387 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 396 average time/residue: 0.3084 time to fit residues: 197.1879 Evaluate side-chains 395 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 381 time to evaluate : 2.560 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.2245 time to fit residues: 9.0506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 262 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 22824 Z= 0.192 Angle : 0.641 15.269 30940 Z= 0.325 Chirality : 0.040 0.153 3538 Planarity : 0.006 0.164 3804 Dihedral : 10.765 140.861 3224 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.08 % 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 (0.16), residues: 2702 helix: -1.01 (0.12), residues: 1784 sheet: None (None), residues: 0 loop : -2.81 (0.20), residues: 918 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 413 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 431 average time/residue: 0.3180 time to fit residues: 220.0235 Evaluate side-chains 393 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 381 time to evaluate : 2.908 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.2691 time to fit residues: 9.3091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 0.5980 chunk 104 optimal weight: 0.0040 chunk 156 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 178 optimal weight: 0.0470 chunk 129 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.7294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.155 22824 Z= 0.226 Angle : 0.661 19.973 30940 Z= 0.330 Chirality : 0.040 0.154 3538 Planarity : 0.006 0.173 3804 Dihedral : 10.503 136.862 3224 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.18 (0.16), residues: 2702 helix: -0.75 (0.12), residues: 1782 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 920 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 402 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 412 average time/residue: 0.3255 time to fit residues: 212.5811 Evaluate side-chains 385 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 374 time to evaluate : 2.637 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.2383 time to fit residues: 8.1995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 chunk 231 optimal weight: 0.2980 chunk 243 optimal weight: 0.9980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 GLN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.827 22824 Z= 0.583 Angle : 0.966 106.100 30940 Z= 0.432 Chirality : 0.042 0.316 3538 Planarity : 0.006 0.212 3804 Dihedral : 10.507 136.924 3224 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.84 % Favored : 90.08 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.16 (0.16), residues: 2702 helix: -0.74 (0.12), residues: 1782 sheet: None (None), residues: 0 loop : -2.72 (0.20), residues: 920 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 374 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 378 average time/residue: 0.3241 time to fit residues: 194.9506 Evaluate side-chains 370 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 367 time to evaluate : 2.778 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.3040 time to fit residues: 5.2531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 179 optimal weight: 5.9990 chunk 270 optimal weight: 0.8980 chunk 249 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.827 22824 Z= 0.635 Angle : 1.004 106.100 30940 Z= 0.472 Chirality : 0.042 0.316 3538 Planarity : 0.007 0.227 3804 Dihedral : 10.507 136.924 3224 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.84 % Favored : 90.08 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.16 (0.16), residues: 2702 helix: -0.74 (0.12), residues: 1782 sheet: None (None), residues: 0 loop : -2.72 (0.20), residues: 920 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 367 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 367 average time/residue: 0.3170 time to fit residues: 186.0909 Evaluate side-chains 368 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 366 time to evaluate : 2.604 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2744 time to fit residues: 4.4931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.9990 chunk 229 optimal weight: 0.0970 chunk 66 optimal weight: 3.9990 chunk 198 optimal weight: 30.0000 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 221 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.185567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.152199 restraints weight = 27264.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.155168 restraints weight = 17455.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.157101 restraints weight = 13431.865| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.827 22824 Z= 0.635 Angle : 1.004 106.100 30940 Z= 0.472 Chirality : 0.042 0.316 3538 Planarity : 0.007 0.227 3804 Dihedral : 10.507 136.924 3224 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.84 % Favored : 90.08 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.16 (0.16), residues: 2702 helix: -0.74 (0.12), residues: 1782 sheet: None (None), residues: 0 loop : -2.72 (0.20), residues: 920 =============================================================================== Job complete usr+sys time: 4445.86 seconds wall clock time: 81 minutes 41.57 seconds (4901.57 seconds total)