Starting phenix.real_space_refine on Tue Dec 12 19:09:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/12_2023/6pw4_20498_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/12_2023/6pw4_20498.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/12_2023/6pw4_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_20498/12_2023/6pw4_20498_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/12_2023/6pw4_20498_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/12_2023/6pw4_20498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/12_2023/6pw4_20498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/12_2023/6pw4_20498_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw4_20498/12_2023/6pw4_20498_updated.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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-1.21rc1-5172/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: 12.00, per 1000 atoms: 0.54 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: 8.10 Conformation dependent library (CDL) restraints added in 4.1 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: 4.97 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: 6.70 Time building geometry restraints manager: 8.83 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: 13201 35.70 - 71.40: 411 71.40 - 107.10: 28 107.10 - 142.81: 2 142.81 - 178.51: 4 Dihedral angle restraints: 13646 sinusoidal: 5580 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 13643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2602 0.055 - 0.110: 766 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 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: 0.440 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: 3.100 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 59.610 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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= 0.506 Angle : 1.139 15.667 30940 Z= 0.618 Chirality : 0.055 0.276 3538 Planarity : 0.007 0.088 3804 Dihedral : 17.521 178.506 8418 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 % Allowed : 10.28 % Favored : 89.34 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 543 HIS 0.007 0.002 HIS A 179 PHE 0.022 0.002 PHE B 841 TYR 0.027 0.002 TYR D 22 ARG 0.007 0.001 ARG B 851 *********************** 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 : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 526 average time/residue: 0.3684 time to fit residues: 291.6803 Evaluate side-chains 409 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 407 time to evaluate : 2.437 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2008 time to fit residues: 4.1682 ------------------------------------------------------------------------------- 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 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: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22824 Z= 0.161 Angle : 0.652 14.580 30940 Z= 0.332 Chirality : 0.039 0.143 3538 Planarity : 0.006 0.077 3804 Dihedral : 13.979 175.337 3320 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 2.23 % Allowed : 17.40 % Favored : 80.37 % 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: -5.29 (0.12), residues: 2702 helix: -3.31 (0.09), residues: 1788 sheet: None (None), residues: 0 loop : -3.58 (0.17), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 568 HIS 0.003 0.001 HIS B 221 PHE 0.015 0.001 PHE C 821 TYR 0.019 0.001 TYR C 747 ARG 0.005 0.000 ARG C 32 *********************** 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 514 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 461 time to evaluate : 2.379 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: 53 outliers final: 20 residues processed: 489 average time/residue: 0.3500 time to fit residues: 266.4412 Evaluate side-chains 409 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 389 time to evaluate : 2.493 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 4 residues processed: 20 average time/residue: 0.2379 time to fit residues: 11.9126 ------------------------------------------------------------------------------- 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: 0.2980 chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 168 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 chunk 247 optimal weight: 10.0000 chunk 267 optimal weight: 0.1980 chunk 220 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 198 optimal weight: 0.0670 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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 753 GLN B 636 GLN ** 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 496 HIS D 636 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22824 Z= 0.136 Angle : 0.599 10.798 30940 Z= 0.300 Chirality : 0.039 0.146 3538 Planarity : 0.005 0.070 3804 Dihedral : 12.798 165.951 3320 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 1.73 % Allowed : 19.92 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.14), residues: 2702 helix: -2.22 (0.11), residues: 1762 sheet: None (None), residues: 0 loop : -3.19 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.009 0.001 HIS B 496 PHE 0.022 0.001 PHE B 233 TYR 0.022 0.001 TYR C 747 ARG 0.006 0.000 ARG C 32 *********************** 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 462 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 421 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 16 residues processed: 443 average time/residue: 0.3210 time to fit residues: 228.7660 Evaluate side-chains 396 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 380 time to evaluate : 2.585 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 16 average time/residue: 0.2331 time to fit residues: 10.1678 ------------------------------------------------------------------------------- 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: 0.9990 chunk 186 optimal weight: 1.9990 chunk 128 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 811 ASN ** 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 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 811 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22824 Z= 0.176 Angle : 0.607 13.804 30940 Z= 0.302 Chirality : 0.040 0.197 3538 Planarity : 0.004 0.067 3804 Dihedral : 12.553 166.629 3320 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 1.47 % Allowed : 21.57 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.15), residues: 2702 helix: -1.73 (0.11), residues: 1816 sheet: None (None), residues: 0 loop : -3.08 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 432 HIS 0.007 0.001 HIS B 496 PHE 0.016 0.001 PHE B 233 TYR 0.018 0.001 TYR C 747 ARG 0.006 0.000 ARG C 32 *********************** 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 439 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 404 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 424 average time/residue: 0.3086 time to fit residues: 213.7413 Evaluate side-chains 400 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 380 time to evaluate : 2.595 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.2483 time to fit residues: 12.2875 ------------------------------------------------------------------------------- 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: 6.9990 chunk 3 optimal weight: 0.0770 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 224 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.5344 ------------------------------------------------------------------------------- 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 A 553 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 553 GLN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22824 Z= 0.274 Angle : 0.662 9.785 30940 Z= 0.329 Chirality : 0.042 0.165 3538 Planarity : 0.005 0.063 3804 Dihedral : 12.510 167.055 3320 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 2.65 % Allowed : 22.20 % Favored : 75.15 % 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: -2.97 (0.15), residues: 2702 helix: -1.43 (0.12), residues: 1802 sheet: None (None), residues: 0 loop : -2.88 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 432 HIS 0.008 0.001 HIS B 496 PHE 0.018 0.001 PHE B 233 TYR 0.017 0.002 TYR C 747 ARG 0.006 0.000 ARG C 32 *********************** 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 454 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 391 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 30 residues processed: 427 average time/residue: 0.3205 time to fit residues: 219.9759 Evaluate side-chains 404 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 374 time to evaluate : 2.411 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 2 residues processed: 30 average time/residue: 0.2155 time to fit residues: 15.4690 ------------------------------------------------------------------------------- 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: 0.9990 chunk 236 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 0.0370 chunk 138 optimal weight: 10.0000 overall best weight: 0.9664 ------------------------------------------------------------------------------- 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 103 GLN ** B 152 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** D 103 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22824 Z= 0.168 Angle : 0.620 16.602 30940 Z= 0.305 Chirality : 0.040 0.147 3538 Planarity : 0.004 0.063 3804 Dihedral : 12.178 166.040 3320 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 1.39 % Allowed : 22.66 % Favored : 75.95 % 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: -2.50 (0.16), residues: 2702 helix: -1.02 (0.12), residues: 1796 sheet: None (None), residues: 0 loop : -2.82 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 432 HIS 0.007 0.001 HIS B 496 PHE 0.019 0.001 PHE B 233 TYR 0.017 0.001 TYR C 747 ARG 0.006 0.000 ARG C 32 *********************** 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 438 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 405 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 426 average time/residue: 0.3198 time to fit residues: 219.6612 Evaluate side-chains 400 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 383 time to evaluate : 2.922 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 17 average time/residue: 0.2432 time to fit residues: 10.9182 ------------------------------------------------------------------------------- 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: 0.6980 chunk 29 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 148 optimal weight: 0.0470 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 HIS B 632 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22824 Z= 0.154 Angle : 0.606 12.654 30940 Z= 0.299 Chirality : 0.040 0.153 3538 Planarity : 0.004 0.065 3804 Dihedral : 11.803 163.001 3320 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 1.10 % Allowed : 23.72 % Favored : 75.19 % 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: -2.12 (0.16), residues: 2702 helix: -0.70 (0.12), residues: 1790 sheet: None (None), residues: 0 loop : -2.72 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 432 HIS 0.012 0.001 HIS B 496 PHE 0.021 0.001 PHE B 233 TYR 0.016 0.001 TYR C 555 ARG 0.006 0.000 ARG C 32 *********************** 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 442 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 416 time to evaluate : 2.458 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: 26 outliers final: 10 residues processed: 433 average time/residue: 0.3465 time to fit residues: 235.7280 Evaluate side-chains 399 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 389 time to evaluate : 2.503 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.2556 time to fit residues: 8.1867 ------------------------------------------------------------------------------- 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: 1.9990 chunk 104 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 178 optimal weight: 0.0470 chunk 129 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- 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 27 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22824 Z= 0.210 Angle : 0.644 11.756 30940 Z= 0.315 Chirality : 0.041 0.247 3538 Planarity : 0.004 0.065 3804 Dihedral : 11.734 159.296 3320 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 0.80 % Allowed : 24.26 % Favored : 74.94 % 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: -1.98 (0.16), residues: 2702 helix: -0.58 (0.13), residues: 1794 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 432 HIS 0.004 0.001 HIS B 221 PHE 0.023 0.001 PHE D 739 TYR 0.022 0.001 TYR C 747 ARG 0.007 0.000 ARG C 32 *********************** 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 412 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 393 time to evaluate : 2.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 405 average time/residue: 0.3262 time to fit residues: 211.3799 Evaluate side-chains 390 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 379 time to evaluate : 2.390 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.2401 time to fit residues: 7.9760 ------------------------------------------------------------------------------- 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: 3.9990 chunk 229 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 603 ASN ** 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 D 569 ASN D 632 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22824 Z= 0.263 Angle : 0.686 22.874 30940 Z= 0.334 Chirality : 0.043 0.249 3538 Planarity : 0.005 0.066 3804 Dihedral : 11.788 155.309 3320 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 0.46 % Allowed : 24.73 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2702 helix: -0.60 (0.12), residues: 1782 sheet: None (None), residues: 0 loop : -2.64 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 432 HIS 0.004 0.001 HIS B 221 PHE 0.017 0.001 PHE B 233 TYR 0.019 0.001 TYR A 518 ARG 0.007 0.000 ARG C 32 *********************** 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 391 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 380 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 387 average time/residue: 0.3170 time to fit residues: 196.4088 Evaluate side-chains 377 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 369 time to evaluate : 2.387 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.2591 time to fit residues: 6.9149 ------------------------------------------------------------------------------- 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: 0.7980 chunk 258 optimal weight: 3.9990 chunk 157 optimal weight: 0.0770 chunk 122 optimal weight: 0.3980 chunk 179 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 132 optimal weight: 0.0170 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ** 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 359 GLN B 582 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22824 Z= 0.160 Angle : 0.659 24.082 30940 Z= 0.316 Chirality : 0.041 0.245 3538 Planarity : 0.004 0.061 3804 Dihedral : 11.428 168.132 3320 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.29 % Allowed : 25.02 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2702 helix: -0.28 (0.13), residues: 1774 sheet: None (None), residues: 0 loop : -2.59 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 432 HIS 0.004 0.001 HIS B 221 PHE 0.024 0.001 PHE D 233 TYR 0.016 0.001 TYR A 518 ARG 0.007 0.000 ARG C 32 ********************** 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 411 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 404 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 406 average time/residue: 0.3384 time to fit residues: 217.2356 Evaluate side-chains 382 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 377 time to evaluate : 2.379 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.2973 time to fit residues: 6.0718 ------------------------------------------------------------------------------- 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: 6.9990 chunk 66 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ** 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 359 GLN ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 GLN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 665 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.184600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.151864 restraints weight = 27246.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.154468 restraints weight = 18511.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.156138 restraints weight = 14721.865| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22824 Z= 0.216 Angle : 0.701 26.785 30940 Z= 0.337 Chirality : 0.043 0.244 3538 Planarity : 0.005 0.065 3804 Dihedral : 11.402 162.316 3320 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.46 % Allowed : 25.48 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.17), residues: 2702 helix: -0.27 (0.13), residues: 1764 sheet: None (None), residues: 0 loop : -2.47 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 432 HIS 0.005 0.001 HIS B 582 PHE 0.032 0.001 PHE D 739 TYR 0.023 0.001 TYR A 518 ARG 0.007 0.000 ARG C 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4749.11 seconds wall clock time: 87 minutes 34.84 seconds (5254.84 seconds total)