Starting phenix.real_space_refine on Sun Jul 5 21:54:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mdi_23773/07_2026/7mdi_23773.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mdi_23773/07_2026/7mdi_23773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mdi_23773/07_2026/7mdi_23773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mdi_23773/07_2026/7mdi_23773.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mdi_23773/07_2026/7mdi_23773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mdi_23773/07_2026/7mdi_23773.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7mdi_23773/07_2026/7mdi_23773.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mdi_23773/07_2026/7mdi_23773.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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: 7 Type Number sf(0) Gaussians Fe 8 7.16 5 P 32 5.49 5 Mg 8 5.21 5 S 72 5.16 5 C 19572 2.51 5 N 5388 2.21 5 O 5528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30608 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5076 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 28, 'TRANS': 705} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ASP:plan': 35, 'ARG:plan': 11, 'GLU:plan': 32, 'GLN:plan1': 13, 'HIS:plan': 2, 'ASN:plan1': 12, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 429 Chain: "E" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2480 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 3, 'GLN:plan1': 8, 'ASN:plan1': 8, 'ASP:plan': 12, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 231 Chain: "B" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5076 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 28, 'TRANS': 705} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ASP:plan': 35, 'ARG:plan': 11, 'GLU:plan': 32, 'GLN:plan1': 13, 'HIS:plan': 2, 'ASN:plan1': 12, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 429 Chain: "G" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2480 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 3, 'GLN:plan1': 8, 'ASN:plan1': 8, 'ASP:plan': 12, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 231 Chain: "D" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5076 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 28, 'TRANS': 705} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ASP:plan': 35, 'ARG:plan': 11, 'GLU:plan': 32, 'GLN:plan1': 13, 'HIS:plan': 2, 'ASN:plan1': 12, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 429 Chain: "F" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2480 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 3, 'GLN:plan1': 8, 'ASN:plan1': 8, 'ASP:plan': 12, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 231 Chain: "C" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5076 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 217} Link IDs: {'PTRANS': 28, 'TRANS': 705} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 597 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ASP:plan': 35, 'ARG:plan': 11, 'GLU:plan': 32, 'GLN:plan1': 13, 'HIS:plan': 2, 'ASN:plan1': 12, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 429 Chain: "H" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2480 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 3, 'GLN:plan1': 8, 'ASN:plan1': 8, 'ASP:plan': 12, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 231 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'FEO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'FEO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'FEO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 2, 'CDP': 1, 'DTP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'FEO': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 6.27, per 1000 atoms: 0.20 Number of scatterers: 30608 At special positions: 0 Unit cell: (105.587, 223.972, 196.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 8 26.01 S 72 16.00 P 32 15.00 Mg 8 11.99 O 5528 8.00 N 5388 7.00 C 19572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8200 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 24 sheets defined 49.9% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 4.092A pdb=" N VAL A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'A' and resid 79 through 96 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.857A pdb=" N TYR A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.663A pdb=" N ASP A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.820A pdb=" N ARG A 141 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET A 143 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 removed outlier: 4.041A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 4.272A pdb=" N VAL A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 4.167A pdb=" N LYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 235 through 250 Processing helix chain 'A' and resid 279 through 292 removed outlier: 4.235A pdb=" N PHE A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 323 removed outlier: 4.265A pdb=" N VAL A 320 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 322 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.719A pdb=" N ASP A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 387 removed outlier: 3.585A pdb=" N GLU A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.572A pdb=" N LEU A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 496 removed outlier: 4.727A pdb=" N ARG A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 513 removed outlier: 4.296A pdb=" N SER A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 540 through 544 removed outlier: 3.736A pdb=" N ARG A 544 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 removed outlier: 3.651A pdb=" N ILE A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.528A pdb=" N GLY A 578 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 611 removed outlier: 3.815A pdb=" N ARG A 605 " --> pdb=" O TRP A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 676 through 689 removed outlier: 4.314A pdb=" N TYR A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 removed outlier: 3.665A pdb=" N PHE A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 726 removed outlier: 3.612A pdb=" N TYR A 726 " --> pdb=" O THR A 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.762A pdb=" N ILE E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 4.239A pdb=" N ILE E 61 " --> pdb=" O SER E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 87 Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 102 through 128 removed outlier: 3.614A pdb=" N GLU E 106 " --> pdb=" O ILE E 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 138 removed outlier: 3.753A pdb=" N VAL E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE E 138 " --> pdb=" O PRO E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 138' Processing helix chain 'E' and resid 144 through 172 removed outlier: 4.774A pdb=" N ARG E 150 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR E 157 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU E 161 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 205 removed outlier: 3.615A pdb=" N LYS E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 216 removed outlier: 4.043A pdb=" N SER E 212 " --> pdb=" O ARG E 208 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE E 213 " --> pdb=" O PHE E 209 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 254 removed outlier: 3.586A pdb=" N ALA E 229 " --> pdb=" O MET E 225 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE E 235 " --> pdb=" O ILE E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 removed outlier: 4.081A pdb=" N ILE E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 288 Processing helix chain 'E' and resid 302 through 318 removed outlier: 3.743A pdb=" N GLN E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 340 removed outlier: 3.959A pdb=" N ILE E 337 " --> pdb=" O ILE E 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 removed outlier: 4.092A pdb=" N VAL B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 56 through 69 Processing helix chain 'B' and resid 79 through 96 Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.858A pdb=" N TYR B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 135 removed outlier: 3.662A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 removed outlier: 3.820A pdb=" N ARG B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B 143 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 removed outlier: 4.042A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 removed outlier: 4.273A pdb=" N VAL B 176 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 4.167A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 198 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 235 through 250 Processing helix chain 'B' and resid 279 through 292 removed outlier: 4.235A pdb=" N PHE B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 323 removed outlier: 4.265A pdb=" N VAL B 320 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 322 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.719A pdb=" N ASP B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 387 removed outlier: 3.585A pdb=" N GLU B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 removed outlier: 3.573A pdb=" N LEU B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 479 through 496 removed outlier: 4.728A pdb=" N ARG B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 513 removed outlier: 4.296A pdb=" N SER B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 540 through 544 removed outlier: 3.736A pdb=" N ARG B 544 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 562 removed outlier: 3.651A pdb=" N ILE B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.527A pdb=" N GLY B 578 " --> pdb=" O TYR B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 611 removed outlier: 3.814A pdb=" N ARG B 605 " --> pdb=" O TRP B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 674 Processing helix chain 'B' and resid 676 through 689 removed outlier: 4.314A pdb=" N TYR B 680 " --> pdb=" O GLY B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.665A pdb=" N PHE B 706 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 726 removed outlier: 3.612A pdb=" N TYR B 726 " --> pdb=" O THR B 722 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.761A pdb=" N ILE G 54 " --> pdb=" O PRO G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 4.240A pdb=" N ILE G 61 " --> pdb=" O SER G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 87 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 102 through 128 removed outlier: 3.615A pdb=" N GLU G 106 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 138 removed outlier: 3.753A pdb=" N VAL G 137 " --> pdb=" O ASP G 133 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE G 138 " --> pdb=" O PRO G 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 133 through 138' Processing helix chain 'G' and resid 144 through 172 removed outlier: 4.774A pdb=" N ARG G 150 " --> pdb=" O TYR G 146 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR G 157 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU G 161 " --> pdb=" O TYR G 157 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE G 162 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 205 removed outlier: 3.615A pdb=" N LYS G 193 " --> pdb=" O GLY G 189 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS G 197 " --> pdb=" O LYS G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 216 removed outlier: 4.043A pdb=" N SER G 212 " --> pdb=" O ARG G 208 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA G 214 " --> pdb=" O TYR G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 254 removed outlier: 3.586A pdb=" N ALA G 229 " --> pdb=" O MET G 225 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP G 234 " --> pdb=" O LYS G 230 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE G 235 " --> pdb=" O ILE G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 269 removed outlier: 4.082A pdb=" N ILE G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 288 Processing helix chain 'G' and resid 302 through 318 removed outlier: 3.743A pdb=" N GLN G 318 " --> pdb=" O ASN G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 340 removed outlier: 3.960A pdb=" N ILE G 337 " --> pdb=" O ILE G 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 32 removed outlier: 4.092A pdb=" N VAL D 28 " --> pdb=" O ILE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 56 through 69 Processing helix chain 'D' and resid 79 through 96 Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 121 through 125 removed outlier: 3.858A pdb=" N TYR D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 135 removed outlier: 3.662A pdb=" N ASP D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.820A pdb=" N ARG D 141 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET D 143 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 157 removed outlier: 4.042A pdb=" N GLN D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 4.273A pdb=" N VAL D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 204 removed outlier: 4.167A pdb=" N LYS D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE D 198 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 235 through 250 Processing helix chain 'D' and resid 279 through 292 removed outlier: 4.236A pdb=" N PHE D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS D 285 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 4.264A pdb=" N VAL D 320 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS D 322 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 352 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.720A pdb=" N ASP D 373 " --> pdb=" O ALA D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 387 removed outlier: 3.586A pdb=" N GLU D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 412 removed outlier: 3.573A pdb=" N LEU D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 479 through 496 removed outlier: 4.727A pdb=" N ARG D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 513 removed outlier: 4.295A pdb=" N SER D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D 509 " --> pdb=" O ALA D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 530 Processing helix chain 'D' and resid 540 through 544 removed outlier: 3.737A pdb=" N ARG D 544 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 562 removed outlier: 3.650A pdb=" N ILE D 549 " --> pdb=" O THR D 545 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN D 550 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS D 555 " --> pdb=" O TYR D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.527A pdb=" N GLY D 578 " --> pdb=" O TYR D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 611 removed outlier: 3.814A pdb=" N ARG D 605 " --> pdb=" O TRP D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 674 Processing helix chain 'D' and resid 676 through 689 removed outlier: 4.314A pdb=" N TYR D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 706 removed outlier: 3.664A pdb=" N PHE D 706 " --> pdb=" O PRO D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 726 removed outlier: 3.612A pdb=" N TYR D 726 " --> pdb=" O THR D 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.761A pdb=" N ILE F 54 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 removed outlier: 4.240A pdb=" N ILE F 61 " --> pdb=" O SER F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 87 Processing helix chain 'F' and resid 90 through 97 Processing helix chain 'F' and resid 102 through 128 removed outlier: 3.614A pdb=" N GLU F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 3.753A pdb=" N VAL F 137 " --> pdb=" O ASP F 133 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE F 138 " --> pdb=" O PRO F 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 133 through 138' Processing helix chain 'F' and resid 144 through 172 removed outlier: 4.774A pdb=" N ARG F 150 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR F 157 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR F 158 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU F 161 " --> pdb=" O TYR F 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 205 removed outlier: 3.614A pdb=" N LYS F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 216 removed outlier: 4.043A pdb=" N SER F 212 " --> pdb=" O ARG F 208 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE F 213 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA F 214 " --> pdb=" O TYR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 254 removed outlier: 3.586A pdb=" N ALA F 229 " --> pdb=" O MET F 225 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP F 234 " --> pdb=" O LYS F 230 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE F 235 " --> pdb=" O ILE F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 269 removed outlier: 4.080A pdb=" N ILE F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 288 Processing helix chain 'F' and resid 302 through 318 removed outlier: 3.743A pdb=" N GLN F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.092A pdb=" N VAL C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 46 Processing helix chain 'C' and resid 56 through 69 Processing helix chain 'C' and resid 79 through 96 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.857A pdb=" N TYR C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 135 removed outlier: 3.663A pdb=" N ASP C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 135 " --> pdb=" O ASP C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.820A pdb=" N ARG C 141 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET C 143 " --> pdb=" O GLU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 4.042A pdb=" N GLN C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 4.272A pdb=" N VAL C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 204 removed outlier: 4.167A pdb=" N LYS C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE C 198 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 235 through 250 Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.236A pdb=" N PHE C 283 " --> pdb=" O GLY C 279 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 323 removed outlier: 4.265A pdb=" N VAL C 320 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 322 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.719A pdb=" N ASP C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 387 removed outlier: 3.585A pdb=" N GLU C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 412 removed outlier: 3.573A pdb=" N LEU C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 479 through 496 removed outlier: 4.727A pdb=" N ARG C 489 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 513 removed outlier: 4.296A pdb=" N SER C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 509 " --> pdb=" O ALA C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 530 Processing helix chain 'C' and resid 540 through 544 removed outlier: 3.737A pdb=" N ARG C 544 " --> pdb=" O LEU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 562 removed outlier: 3.651A pdb=" N ILE C 549 " --> pdb=" O THR C 545 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS C 555 " --> pdb=" O TYR C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.527A pdb=" N GLY C 578 " --> pdb=" O TYR C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 611 removed outlier: 3.814A pdb=" N ARG C 605 " --> pdb=" O TRP C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 676 through 689 removed outlier: 4.314A pdb=" N TYR C 680 " --> pdb=" O GLY C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 removed outlier: 3.665A pdb=" N PHE C 706 " --> pdb=" O PRO C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 726 removed outlier: 3.612A pdb=" N TYR C 726 " --> pdb=" O THR C 722 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 50 through 54 removed outlier: 3.761A pdb=" N ILE H 54 " --> pdb=" O PRO H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 removed outlier: 4.240A pdb=" N ILE H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 87 Processing helix chain 'H' and resid 90 through 97 Processing helix chain 'H' and resid 102 through 128 removed outlier: 3.614A pdb=" N GLU H 106 " --> pdb=" O ILE H 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP H 108 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 138 removed outlier: 3.753A pdb=" N VAL H 137 " --> pdb=" O ASP H 133 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 133 through 138' Processing helix chain 'H' and resid 144 through 172 removed outlier: 4.774A pdb=" N ARG H 150 " --> pdb=" O TYR H 146 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR H 157 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR H 158 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU H 161 " --> pdb=" O TYR H 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE H 162 " --> pdb=" O TYR H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 205 removed outlier: 3.615A pdb=" N LYS H 193 " --> pdb=" O GLY H 189 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS H 197 " --> pdb=" O LYS H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 216 removed outlier: 4.043A pdb=" N SER H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA H 214 " --> pdb=" O TYR H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 254 removed outlier: 3.587A pdb=" N ALA H 229 " --> pdb=" O MET H 225 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP H 234 " --> pdb=" O LYS H 230 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE H 235 " --> pdb=" O ILE H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 269 removed outlier: 4.081A pdb=" N ILE H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 288 Processing helix chain 'H' and resid 302 through 318 removed outlier: 3.743A pdb=" N GLN H 318 " --> pdb=" O ASN H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 340 removed outlier: 3.959A pdb=" N ILE H 337 " --> pdb=" O ILE H 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 208 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 231 removed outlier: 7.725A pdb=" N VAL A 228 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ASN A 259 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A 230 " --> pdb=" O ASN A 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 341 removed outlier: 6.553A pdb=" N VAL A 339 " --> pdb=" O GLN A 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA5, first strand: chain 'A' and resid 644 through 648 Processing sheet with id=AA6, first strand: chain 'E' and resid 176 through 177 Processing sheet with id=AA7, first strand: chain 'B' and resid 207 through 208 Processing sheet with id=AA8, first strand: chain 'B' and resid 228 through 231 removed outlier: 7.724A pdb=" N VAL B 228 " --> pdb=" O GLY B 257 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN B 259 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 230 " --> pdb=" O ASN B 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 338 through 341 removed outlier: 6.554A pdb=" N VAL B 339 " --> pdb=" O GLN B 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AB2, first strand: chain 'B' and resid 644 through 648 Processing sheet with id=AB3, first strand: chain 'G' and resid 176 through 177 Processing sheet with id=AB4, first strand: chain 'D' and resid 207 through 208 Processing sheet with id=AB5, first strand: chain 'D' and resid 228 through 231 removed outlier: 7.724A pdb=" N VAL D 228 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN D 259 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 230 " --> pdb=" O ASN D 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 338 through 341 removed outlier: 6.554A pdb=" N VAL D 339 " --> pdb=" O GLN D 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 356 through 357 Processing sheet with id=AB8, first strand: chain 'D' and resid 644 through 648 Processing sheet with id=AB9, first strand: chain 'F' and resid 176 through 177 Processing sheet with id=AC1, first strand: chain 'C' and resid 207 through 208 Processing sheet with id=AC2, first strand: chain 'C' and resid 228 through 231 removed outlier: 7.724A pdb=" N VAL C 228 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASN C 259 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 230 " --> pdb=" O ASN C 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 338 through 341 removed outlier: 6.553A pdb=" N VAL C 339 " --> pdb=" O GLN C 417 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AC5, first strand: chain 'C' and resid 644 through 648 Processing sheet with id=AC6, first strand: chain 'H' and resid 176 through 177 1264 hydrogen bonds defined for protein. 3564 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: 6.01 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9807 1.34 - 1.45: 4464 1.45 - 1.57: 16845 1.57 - 1.69: 52 1.69 - 1.81: 120 Bond restraints: 31288 Sorted by residual: bond pdb=" O3A CDP D 801 " pdb=" PB CDP D 801 " ideal model delta sigma weight residual 1.748 1.606 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" O3A CDP A 801 " pdb=" PB CDP A 801 " ideal model delta sigma weight residual 1.748 1.606 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" O3A CDP C 801 " pdb=" PB CDP C 801 " ideal model delta sigma weight residual 1.748 1.606 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" O3A CDP B 801 " pdb=" PB CDP B 801 " ideal model delta sigma weight residual 1.748 1.607 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" N ARG A 391 " pdb=" CA ARG A 391 " ideal model delta sigma weight residual 1.459 1.518 -0.059 1.24e-02 6.50e+03 2.25e+01 ... (remaining 31283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 42729 4.02 - 8.04: 183 8.04 - 12.06: 8 12.06 - 16.09: 4 16.09 - 20.11: 12 Bond angle restraints: 42936 Sorted by residual: angle pdb=" PB DTP A 802 " pdb=" O3B DTP A 802 " pdb=" PG DTP A 802 " ideal model delta sigma weight residual 139.87 119.76 20.11 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB DTP B 802 " pdb=" O3B DTP B 802 " pdb=" PG DTP B 802 " ideal model delta sigma weight residual 139.87 119.78 20.09 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB DTP C 802 " pdb=" O3B DTP C 802 " pdb=" PG DTP C 802 " ideal model delta sigma weight residual 139.87 119.78 20.09 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB DTP D 802 " pdb=" O3B DTP D 802 " pdb=" PG DTP D 802 " ideal model delta sigma weight residual 139.87 119.78 20.09 1.00e+00 1.00e+00 4.03e+02 angle pdb=" PB DTP C 804 " pdb=" O3B DTP C 804 " pdb=" PG DTP C 804 " ideal model delta sigma weight residual 139.87 120.21 19.66 1.00e+00 1.00e+00 3.87e+02 ... (remaining 42931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 17872 34.45 - 68.90: 292 68.90 - 103.35: 24 103.35 - 137.80: 0 137.80 - 172.25: 4 Dihedral angle restraints: 18192 sinusoidal: 5436 harmonic: 12756 Sorted by residual: dihedral pdb=" O1B DTP B 802 " pdb=" O3B DTP B 802 " pdb=" PB DTP B 802 " pdb=" PG DTP B 802 " ideal model delta sinusoidal sigma weight residual -60.07 112.18 -172.25 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1B DTP A 802 " pdb=" O3B DTP A 802 " pdb=" PB DTP A 802 " pdb=" PG DTP A 802 " ideal model delta sinusoidal sigma weight residual -60.07 112.14 -172.21 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1B DTP C 802 " pdb=" O3B DTP C 802 " pdb=" PB DTP C 802 " pdb=" PG DTP C 802 " ideal model delta sinusoidal sigma weight residual -60.07 112.11 -172.18 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 18189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4281 0.059 - 0.117: 614 0.117 - 0.176: 47 0.176 - 0.234: 6 0.234 - 0.293: 4 Chirality restraints: 4952 Sorted by residual: chirality pdb=" C3' CDP D 801 " pdb=" C2' CDP D 801 " pdb=" C4' CDP D 801 " pdb=" O3' CDP D 801 " both_signs ideal model delta sigma weight residual False -2.38 -2.67 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C3' CDP B 801 " pdb=" C2' CDP B 801 " pdb=" C4' CDP B 801 " pdb=" O3' CDP B 801 " both_signs ideal model delta sigma weight residual False -2.38 -2.67 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C3' CDP A 801 " pdb=" C2' CDP A 801 " pdb=" C4' CDP A 801 " pdb=" O3' CDP A 801 " both_signs ideal model delta sigma weight residual False -2.38 -2.67 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 4949 not shown) Planarity restraints: 5564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 384 " -0.015 2.00e-02 2.50e+03 8.30e-03 1.38e+00 pdb=" CG TYR A 384 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 384 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 384 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 384 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 384 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 384 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 384 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 384 " 0.015 2.00e-02 2.50e+03 8.27e-03 1.37e+00 pdb=" CG TYR B 384 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 384 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 384 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 384 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 384 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 384 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 384 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 384 " 0.015 2.00e-02 2.50e+03 8.16e-03 1.33e+00 pdb=" CG TYR D 384 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR D 384 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 384 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 384 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 384 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 384 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 384 " 0.006 2.00e-02 2.50e+03 ... (remaining 5561 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 456 2.65 - 3.21: 30392 3.21 - 3.78: 45465 3.78 - 4.34: 56854 4.34 - 4.90: 89834 Nonbonded interactions: 223001 Sorted by model distance: nonbonded pdb=" O1G DTP A 802 " pdb="MG MG A 803 " model vdw 2.089 2.170 nonbonded pdb=" O1G DTP B 802 " pdb="MG MG B 803 " model vdw 2.089 2.170 nonbonded pdb=" O1G DTP C 802 " pdb="MG MG C 803 " model vdw 2.089 2.170 nonbonded pdb=" O1G DTP D 802 " pdb="MG MG D 803 " model vdw 2.089 2.170 nonbonded pdb=" O1G DTP A 804 " pdb="MG MG A 805 " model vdw 2.090 2.170 ... (remaining 222996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.890 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.006 0.396 31300 Z= 0.515 Angle : 0.756 20.107 42936 Z= 0.546 Chirality : 0.041 0.293 4952 Planarity : 0.003 0.026 5564 Dihedral : 13.932 172.254 9992 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.75 % Favored : 89.15 % Rotamer: Outliers : 0.17 % Allowed : 6.46 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.11), residues: 4324 helix: -1.97 (0.10), residues: 1960 sheet: -3.01 (0.31), residues: 248 loop : -3.71 (0.11), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 316 TYR 0.017 0.001 TYR A 384 PHE 0.008 0.001 PHE G 6 TRP 0.007 0.001 TRP E 108 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.25 (31288) covalent geometry : angle 0.75585 / 0.55 (42936) hydrogen bonds : bond 0.16051 / 11.13 ( 1264) hydrogen bonds : angle 6.42905 / 4.56 ( 3564) Misc. bond : bond 0.25222 / 14.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 420 time to evaluate : 0.927 Fit side-chains REVERT: A 443 GLU cc_start: 0.7938 (pm20) cc_final: 0.7685 (pm20) REVERT: E 29 TYR cc_start: 0.7882 (t80) cc_final: 0.6966 (t80) REVERT: E 48 PHE cc_start: 0.8927 (t80) cc_final: 0.8708 (t80) REVERT: E 90 ARG cc_start: 0.8573 (ptp90) cc_final: 0.8069 (ptt-90) REVERT: E 93 ASN cc_start: 0.8902 (t0) cc_final: 0.8652 (t0) REVERT: E 96 LEU cc_start: 0.8824 (tt) cc_final: 0.8568 (tt) REVERT: E 104 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7661 (tm-30) REVERT: E 291 LEU cc_start: 0.8544 (pt) cc_final: 0.8314 (pt) REVERT: B 229 LEU cc_start: 0.8621 (mm) cc_final: 0.8383 (mm) REVERT: B 239 ILE cc_start: 0.9355 (mt) cc_final: 0.9045 (mm) REVERT: G 29 TYR cc_start: 0.7155 (t80) cc_final: 0.6088 (t80) REVERT: G 85 ASP cc_start: 0.6289 (t0) cc_final: 0.5697 (t0) REVERT: G 116 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7255 (mm-30) REVERT: D 229 LEU cc_start: 0.8882 (mm) cc_final: 0.8681 (mm) REVERT: D 443 GLU cc_start: 0.7993 (pm20) cc_final: 0.7734 (pm20) REVERT: F 32 GLN cc_start: 0.8264 (pm20) cc_final: 0.7774 (pm20) REVERT: F 104 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7584 (tm-30) REVERT: F 116 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6956 (mm-30) REVERT: F 121 ARG cc_start: 0.8945 (ttm-80) cc_final: 0.8744 (ttt-90) REVERT: F 261 GLU cc_start: 0.7555 (tp30) cc_final: 0.7058 (mp0) REVERT: F 291 LEU cc_start: 0.8332 (pt) cc_final: 0.8114 (pt) REVERT: C 443 GLU cc_start: 0.7951 (pm20) cc_final: 0.7706 (pm20) REVERT: H 48 PHE cc_start: 0.8979 (t80) cc_final: 0.8721 (t80) REVERT: H 90 ARG cc_start: 0.8547 (ptp90) cc_final: 0.8061 (ptt-90) REVERT: H 93 ASN cc_start: 0.8882 (t0) cc_final: 0.8576 (t0) REVERT: H 96 LEU cc_start: 0.8798 (tt) cc_final: 0.8575 (tt) REVERT: H 104 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7208 (tm-30) REVERT: H 302 LYS cc_start: 0.9121 (tmtt) cc_final: 0.8918 (tptp) outliers start: 4 outliers final: 0 residues processed: 424 average time/residue: 0.1593 time to fit residues: 112.2293 Evaluate side-chains 298 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 418 ASN B 734 HIS G 242 HIS F 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.089903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.079938 restraints weight = 120876.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.081584 restraints weight = 70782.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.082753 restraints weight = 47351.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083410 restraints weight = 34875.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084048 restraints weight = 28687.593| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 31300 Z= 0.106 Angle : 0.535 5.937 42936 Z= 0.275 Chirality : 0.040 0.206 4952 Planarity : 0.004 0.045 5564 Dihedral : 9.011 179.991 4868 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.12), residues: 4324 helix: -0.52 (0.12), residues: 1908 sheet: -2.62 (0.31), residues: 252 loop : -3.36 (0.12), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 218 TYR 0.015 0.001 TYR E 3 PHE 0.014 0.001 PHE B 546 TRP 0.024 0.001 TRP F 287 HIS 0.003 0.001 HIS C 598 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (31288) covalent geometry : angle 0.53529 / 0.28 (42936) hydrogen bonds : bond 0.03330 / 2.33 ( 1264) hydrogen bonds : angle 4.79762 / 3.37 ( 3564) Misc. bond : bond 0.03974 / 2.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8483 (tm-30) REVERT: E 93 ASN cc_start: 0.8954 (t0) cc_final: 0.8689 (t0) REVERT: E 116 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7616 (mm-30) REVERT: B 239 ILE cc_start: 0.9347 (mt) cc_final: 0.9081 (mm) REVERT: G 29 TYR cc_start: 0.7084 (t80) cc_final: 0.6415 (t80) REVERT: G 96 LEU cc_start: 0.9035 (tt) cc_final: 0.8789 (tt) REVERT: F 121 ARG cc_start: 0.8886 (ttm-80) cc_final: 0.8593 (ttt-90) REVERT: F 261 GLU cc_start: 0.7562 (tp30) cc_final: 0.7017 (mp0) REVERT: H 48 PHE cc_start: 0.8878 (t80) cc_final: 0.8676 (t80) REVERT: H 93 ASN cc_start: 0.8958 (t0) cc_final: 0.8642 (t0) REVERT: H 96 LEU cc_start: 0.9212 (tt) cc_final: 0.9007 (tt) REVERT: H 116 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7518 (mm-30) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.1417 time to fit residues: 91.1479 Evaluate side-chains 292 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 156 optimal weight: 9.9990 chunk 427 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 239 optimal weight: 7.9990 chunk 389 optimal weight: 8.9990 chunk 423 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 369 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN E 247 GLN B 61 HIS B 134 ASN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN G 202 ASN G 247 GLN ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.072117 restraints weight = 124039.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.073623 restraints weight = 72528.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.074666 restraints weight = 48757.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.075448 restraints weight = 36386.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.076017 restraints weight = 29077.316| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.487 31300 Z= 0.286 Angle : 0.734 9.901 42936 Z= 0.389 Chirality : 0.045 0.188 4952 Planarity : 0.005 0.062 5564 Dihedral : 9.596 179.861 4868 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.08 % Favored : 85.82 % Rotamer: Outliers : 0.09 % Allowed : 8.60 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.12), residues: 4324 helix: -0.60 (0.12), residues: 1960 sheet: -2.89 (0.28), residues: 268 loop : -3.34 (0.12), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 121 TYR 0.038 0.003 TYR B 81 PHE 0.042 0.003 PHE G 213 TRP 0.030 0.002 TRP F 287 HIS 0.009 0.002 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.28 (31288) covalent geometry : angle 0.73356 / 0.39 (42936) hydrogen bonds : bond 0.04469 / 3.09 ( 1264) hydrogen bonds : angle 5.38128 / 3.79 ( 3564) Misc. bond : bond 0.22933 / 15.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 PHE cc_start: 0.7235 (p90) cc_final: 0.6980 (p90) REVERT: E 29 TYR cc_start: 0.8220 (t80) cc_final: 0.7989 (t80) REVERT: E 96 LEU cc_start: 0.9269 (tt) cc_final: 0.9029 (tt) REVERT: E 341 LEU cc_start: 0.9144 (tt) cc_final: 0.8858 (tt) REVERT: B 239 ILE cc_start: 0.9579 (mt) cc_final: 0.9312 (mm) REVERT: G 96 LEU cc_start: 0.9186 (tt) cc_final: 0.8898 (tt) REVERT: F 29 TYR cc_start: 0.8587 (t80) cc_final: 0.8136 (t80) REVERT: F 32 GLN cc_start: 0.7641 (pm20) cc_final: 0.7432 (pm20) REVERT: F 121 ARG cc_start: 0.9020 (ttm-80) cc_final: 0.8586 (ttt-90) REVERT: H 96 LEU cc_start: 0.9260 (tt) cc_final: 0.8992 (tt) REVERT: H 239 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8586 (mm-30) outliers start: 2 outliers final: 1 residues processed: 317 average time/residue: 0.1519 time to fit residues: 81.2603 Evaluate side-chains 247 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 59 optimal weight: 0.3980 chunk 389 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 chunk 376 optimal weight: 6.9990 chunk 384 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 303 optimal weight: 6.9990 chunk 254 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS A 134 ASN E 77 ASN B 134 ASN G 77 ASN D 61 HIS D 134 ASN C 61 HIS C 134 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.076208 restraints weight = 120730.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.077809 restraints weight = 70615.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078926 restraints weight = 47224.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.079554 restraints weight = 34973.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080212 restraints weight = 29057.239| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.221 31300 Z= 0.128 Angle : 0.566 6.143 42936 Z= 0.293 Chirality : 0.041 0.161 4952 Planarity : 0.004 0.043 5564 Dihedral : 9.194 174.270 4868 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.13 % Allowed : 5.10 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.13), residues: 4324 helix: -0.16 (0.12), residues: 1944 sheet: -2.27 (0.32), residues: 248 loop : -3.09 (0.12), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 218 TYR 0.025 0.001 TYR C 367 PHE 0.012 0.001 PHE H 19 TRP 0.019 0.001 TRP G 108 HIS 0.005 0.001 HIS H 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (31288) covalent geometry : angle 0.56555 / 0.29 (42936) hydrogen bonds : bond 0.03270 / 2.27 ( 1264) hydrogen bonds : angle 4.72145 / 3.32 ( 3564) Misc. bond : bond 0.09539 / 6.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 349 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7177 (t80) cc_final: 0.6793 (t80) REVERT: E 96 LEU cc_start: 0.9215 (tt) cc_final: 0.8978 (tt) REVERT: B 239 ILE cc_start: 0.9550 (mt) cc_final: 0.9266 (mm) REVERT: G 96 LEU cc_start: 0.9107 (tt) cc_final: 0.8802 (tt) REVERT: D 500 TYR cc_start: 0.8971 (m-80) cc_final: 0.8277 (m-10) REVERT: F 96 LEU cc_start: 0.9150 (tt) cc_final: 0.8864 (tt) REVERT: F 121 ARG cc_start: 0.8931 (ttm-80) cc_final: 0.8725 (ttt-90) REVERT: F 272 GLU cc_start: 0.9035 (pp20) cc_final: 0.8733 (pm20) REVERT: H 96 LEU cc_start: 0.9204 (tt) cc_final: 0.8916 (tt) REVERT: H 241 LEU cc_start: 0.9450 (tt) cc_final: 0.9247 (mt) outliers start: 3 outliers final: 3 residues processed: 352 average time/residue: 0.1499 time to fit residues: 89.7602 Evaluate side-chains 274 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 271 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 260 optimal weight: 8.9990 chunk 242 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 266 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 418 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN D 134 ASN F 202 ASN C 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.076144 restraints weight = 121466.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.077727 restraints weight = 71327.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.078809 restraints weight = 47882.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079633 restraints weight = 35710.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080151 restraints weight = 28675.868| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 31300 Z= 0.135 Angle : 0.567 9.313 42936 Z= 0.293 Chirality : 0.041 0.230 4952 Planarity : 0.004 0.045 5564 Dihedral : 9.204 174.053 4868 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.13), residues: 4324 helix: 0.02 (0.12), residues: 1944 sheet: -2.23 (0.31), residues: 252 loop : -2.96 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 218 TYR 0.016 0.001 TYR B 157 PHE 0.014 0.001 PHE G 74 TRP 0.013 0.001 TRP H 108 HIS 0.003 0.001 HIS E 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (31288) covalent geometry : angle 0.56653 / 0.29 (42936) hydrogen bonds : bond 0.03145 / 2.17 ( 1264) hydrogen bonds : angle 4.64501 / 3.28 ( 3564) Misc. bond : bond 0.07564 / 5.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7153 (t80) cc_final: 0.6756 (t80) REVERT: A 180 MET cc_start: 0.9149 (tpp) cc_final: 0.8876 (tpp) REVERT: A 500 TYR cc_start: 0.8969 (m-80) cc_final: 0.8437 (m-10) REVERT: E 96 LEU cc_start: 0.9229 (tt) cc_final: 0.8958 (tt) REVERT: E 341 LEU cc_start: 0.9161 (tt) cc_final: 0.8942 (tt) REVERT: B 239 ILE cc_start: 0.9569 (mt) cc_final: 0.9306 (mm) REVERT: G 96 LEU cc_start: 0.9203 (tt) cc_final: 0.8855 (tt) REVERT: G 247 GLN cc_start: 0.8527 (tt0) cc_final: 0.7489 (tm-30) REVERT: G 341 LEU cc_start: 0.9199 (tt) cc_final: 0.8940 (tt) REVERT: D 180 MET cc_start: 0.9149 (tpp) cc_final: 0.8880 (tpp) REVERT: D 500 TYR cc_start: 0.8954 (m-80) cc_final: 0.8384 (m-10) REVERT: F 96 LEU cc_start: 0.9219 (tt) cc_final: 0.8919 (tt) REVERT: F 213 PHE cc_start: 0.8391 (m-10) cc_final: 0.8179 (m-10) REVERT: F 341 LEU cc_start: 0.9177 (tt) cc_final: 0.8954 (tt) REVERT: H 29 TYR cc_start: 0.6925 (t80) cc_final: 0.6530 (t80) REVERT: H 96 LEU cc_start: 0.9224 (tt) cc_final: 0.8902 (tt) REVERT: H 341 LEU cc_start: 0.9225 (tt) cc_final: 0.9019 (tt) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.1480 time to fit residues: 84.5878 Evaluate side-chains 269 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 113 optimal weight: 6.9990 chunk 279 optimal weight: 0.0050 chunk 151 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 290 optimal weight: 0.0370 chunk 78 optimal weight: 3.9990 overall best weight: 0.7074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN B 340 GLN D 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.088883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.078706 restraints weight = 120767.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.080334 restraints weight = 71293.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081321 restraints weight = 47860.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082237 restraints weight = 36476.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082699 restraints weight = 28850.310| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 31300 Z= 0.094 Angle : 0.534 7.113 42936 Z= 0.271 Chirality : 0.039 0.206 4952 Planarity : 0.003 0.042 5564 Dihedral : 8.989 172.648 4868 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.04 % Allowed : 2.01 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.13), residues: 4324 helix: 0.19 (0.12), residues: 1944 sheet: -1.99 (0.31), residues: 252 loop : -2.86 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 218 TYR 0.018 0.001 TYR E 29 PHE 0.014 0.001 PHE F 19 TRP 0.018 0.001 TRP G 340 HIS 0.004 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (31288) covalent geometry : angle 0.53438 / 0.27 (42936) hydrogen bonds : bond 0.02730 / 1.90 ( 1264) hydrogen bonds : angle 4.38216 / 3.09 ( 3564) Misc. bond : bond 0.04524 / 2.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.9118 (tpp) cc_final: 0.8819 (tpp) REVERT: A 500 TYR cc_start: 0.8936 (m-80) cc_final: 0.8350 (m-10) REVERT: E 29 TYR cc_start: 0.6588 (t80) cc_final: 0.5944 (t80) REVERT: E 93 ASN cc_start: 0.9020 (t0) cc_final: 0.8818 (t0) REVERT: E 96 LEU cc_start: 0.9209 (tt) cc_final: 0.8909 (tt) REVERT: B 239 ILE cc_start: 0.9568 (mt) cc_final: 0.9306 (mm) REVERT: B 500 TYR cc_start: 0.8951 (m-80) cc_final: 0.8292 (m-10) REVERT: G 29 TYR cc_start: 0.8485 (t80) cc_final: 0.8089 (t80) REVERT: G 96 LEU cc_start: 0.8980 (tt) cc_final: 0.8657 (tt) REVERT: G 104 GLU cc_start: 0.9130 (tp30) cc_final: 0.8681 (tp30) REVERT: G 247 GLN cc_start: 0.8449 (tt0) cc_final: 0.8163 (tp40) REVERT: G 272 GLU cc_start: 0.9102 (pp20) cc_final: 0.8708 (pm20) REVERT: D 180 MET cc_start: 0.9109 (tpp) cc_final: 0.8811 (tpp) REVERT: D 500 TYR cc_start: 0.8956 (m-80) cc_final: 0.8380 (m-10) REVERT: F 96 LEU cc_start: 0.9158 (tt) cc_final: 0.8842 (tt) REVERT: F 302 LYS cc_start: 0.9253 (tptp) cc_final: 0.8946 (tptp) REVERT: H 29 TYR cc_start: 0.6455 (t80) cc_final: 0.6051 (t80) REVERT: H 93 ASN cc_start: 0.9049 (t0) cc_final: 0.8722 (t0) REVERT: H 96 LEU cc_start: 0.9155 (tt) cc_final: 0.8861 (tt) REVERT: H 247 GLN cc_start: 0.8760 (tt0) cc_final: 0.8205 (tp40) REVERT: H 272 GLU cc_start: 0.8988 (pp20) cc_final: 0.8781 (pm20) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.1488 time to fit residues: 96.3254 Evaluate side-chains 293 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 420 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 325 optimal weight: 30.0000 chunk 62 optimal weight: 10.0000 chunk 399 optimal weight: 0.0670 chunk 144 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 395 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN G 247 GLN D 134 ASN C 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.074163 restraints weight = 122648.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.075696 restraints weight = 71708.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.076773 restraints weight = 48132.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.077574 restraints weight = 35789.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.078061 restraints weight = 28675.174| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.295 31300 Z= 0.201 Angle : 0.622 7.811 42936 Z= 0.326 Chirality : 0.042 0.203 4952 Planarity : 0.004 0.045 5564 Dihedral : 9.138 163.236 4868 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.13), residues: 4324 helix: 0.16 (0.12), residues: 1940 sheet: -1.96 (0.32), residues: 248 loop : -2.87 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 121 TYR 0.022 0.002 TYR G 29 PHE 0.020 0.002 PHE E 74 TRP 0.015 0.002 TRP H 112 HIS 0.008 0.001 HIS H 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (31288) covalent geometry : angle 0.62190 / 0.33 (42936) hydrogen bonds : bond 0.03385 / 2.35 ( 1264) hydrogen bonds : angle 4.67577 / 3.30 ( 3564) Misc. bond : bond 0.15113 / 9.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 322 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7164 (t80) cc_final: 0.6903 (t80) REVERT: A 180 MET cc_start: 0.9171 (tpp) cc_final: 0.8968 (tpp) REVERT: A 500 TYR cc_start: 0.9018 (m-80) cc_final: 0.8456 (m-10) REVERT: E 96 LEU cc_start: 0.9301 (tt) cc_final: 0.9026 (tt) REVERT: B 239 ILE cc_start: 0.9625 (mt) cc_final: 0.9380 (mm) REVERT: G 96 LEU cc_start: 0.9167 (tt) cc_final: 0.8909 (tt) REVERT: G 118 ILE cc_start: 0.9592 (mm) cc_final: 0.9337 (tp) REVERT: D 180 MET cc_start: 0.9195 (tpp) cc_final: 0.8960 (tpp) REVERT: D 500 TYR cc_start: 0.8936 (m-80) cc_final: 0.8410 (m-10) REVERT: F 96 LEU cc_start: 0.9234 (tt) cc_final: 0.8932 (tt) REVERT: C 180 MET cc_start: 0.9194 (tpp) cc_final: 0.8886 (tpp) REVERT: H 29 TYR cc_start: 0.6872 (t80) cc_final: 0.6361 (t80) REVERT: H 96 LEU cc_start: 0.9247 (tt) cc_final: 0.9039 (tt) outliers start: 1 outliers final: 0 residues processed: 322 average time/residue: 0.1503 time to fit residues: 82.9920 Evaluate side-chains 251 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 103 optimal weight: 0.5980 chunk 201 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 77 optimal weight: 0.0170 chunk 347 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 219 optimal weight: 0.8980 chunk 408 optimal weight: 3.9990 chunk 269 optimal weight: 9.9990 overall best weight: 1.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076155 restraints weight = 121892.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.077749 restraints weight = 71202.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078870 restraints weight = 47650.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.079631 restraints weight = 35280.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080211 restraints weight = 28380.684| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 31300 Z= 0.118 Angle : 0.567 7.527 42936 Z= 0.290 Chirality : 0.040 0.181 4952 Planarity : 0.003 0.035 5564 Dihedral : 8.798 157.985 4868 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.13), residues: 4324 helix: 0.25 (0.12), residues: 1948 sheet: -1.90 (0.31), residues: 248 loop : -2.81 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 218 TYR 0.019 0.001 TYR C 367 PHE 0.023 0.001 PHE B 401 TRP 0.012 0.001 TRP H 287 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (31288) covalent geometry : angle 0.56692 / 0.29 (42936) hydrogen bonds : bond 0.03026 / 2.10 ( 1264) hydrogen bonds : angle 4.46650 / 3.16 ( 3564) Misc. bond : bond 0.06931 / 4.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.9182 (tpp) cc_final: 0.8870 (tpp) REVERT: A 229 LEU cc_start: 0.8845 (mm) cc_final: 0.8642 (mm) REVERT: A 288 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8418 (tm-30) REVERT: A 500 TYR cc_start: 0.8947 (m-80) cc_final: 0.8319 (m-10) REVERT: E 29 TYR cc_start: 0.6309 (t80) cc_final: 0.6032 (t80) REVERT: E 96 LEU cc_start: 0.9232 (tt) cc_final: 0.8952 (tt) REVERT: G 96 LEU cc_start: 0.9146 (tt) cc_final: 0.8894 (tt) REVERT: G 247 GLN cc_start: 0.8580 (tt0) cc_final: 0.8266 (tp40) REVERT: D 180 MET cc_start: 0.9150 (tpp) cc_final: 0.8852 (tpp) REVERT: D 229 LEU cc_start: 0.8864 (mm) cc_final: 0.8645 (mm) REVERT: D 288 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8411 (tm-30) REVERT: F 96 LEU cc_start: 0.9090 (tt) cc_final: 0.8849 (tt) REVERT: F 302 LYS cc_start: 0.9256 (tptp) cc_final: 0.8923 (tptp) REVERT: F 341 LEU cc_start: 0.9249 (tt) cc_final: 0.8932 (tt) REVERT: C 180 MET cc_start: 0.9221 (tpp) cc_final: 0.8895 (tpp) REVERT: C 288 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8420 (tm-30) REVERT: H 29 TYR cc_start: 0.6442 (t80) cc_final: 0.6085 (t80) REVERT: H 96 LEU cc_start: 0.9215 (tt) cc_final: 0.8970 (tt) REVERT: H 247 GLN cc_start: 0.8713 (tt0) cc_final: 0.8171 (tp40) REVERT: H 262 MET cc_start: 0.6593 (mmp) cc_final: 0.6387 (mmp) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.1476 time to fit residues: 84.5748 Evaluate side-chains 262 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 352 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 368 optimal weight: 4.9990 chunk 229 optimal weight: 10.0000 chunk 406 optimal weight: 0.7980 chunk 314 optimal weight: 5.9990 chunk 338 optimal weight: 10.0000 chunk 362 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN D 134 ASN C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.074023 restraints weight = 122272.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.075575 restraints weight = 71443.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.076616 restraints weight = 47836.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.077425 restraints weight = 35648.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.078015 restraints weight = 28463.834| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.245 31300 Z= 0.192 Angle : 0.631 9.058 42936 Z= 0.328 Chirality : 0.042 0.178 4952 Planarity : 0.004 0.075 5564 Dihedral : 8.550 146.598 4868 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 4324 helix: 0.17 (0.12), residues: 1944 sheet: -2.34 (0.30), residues: 268 loop : -2.81 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 218 TYR 0.018 0.002 TYR A 308 PHE 0.025 0.002 PHE B 401 TRP 0.014 0.002 TRP H 112 HIS 0.007 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (31288) covalent geometry : angle 0.63070 / 0.33 (42936) hydrogen bonds : bond 0.03400 / 2.35 ( 1264) hydrogen bonds : angle 4.70158 / 3.32 ( 3564) Misc. bond : bond 0.14102 / 9.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8468 (tm-30) REVERT: A 367 TYR cc_start: 0.7056 (t80) cc_final: 0.6726 (t80) REVERT: A 469 PHE cc_start: 0.7414 (p90) cc_final: 0.7085 (p90) REVERT: A 500 TYR cc_start: 0.8975 (m-80) cc_final: 0.8452 (m-10) REVERT: E 96 LEU cc_start: 0.9239 (tt) cc_final: 0.8905 (tt) REVERT: B 469 PHE cc_start: 0.7100 (p90) cc_final: 0.6880 (p90) REVERT: G 96 LEU cc_start: 0.9206 (tt) cc_final: 0.8952 (tt) REVERT: G 247 GLN cc_start: 0.8479 (tt0) cc_final: 0.8182 (tp40) REVERT: D 288 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8455 (tm-30) REVERT: D 469 PHE cc_start: 0.7524 (p90) cc_final: 0.7192 (p90) REVERT: F 96 LEU cc_start: 0.9180 (tt) cc_final: 0.8943 (tt) REVERT: C 180 MET cc_start: 0.9178 (tpp) cc_final: 0.8918 (tpp) REVERT: C 288 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8463 (tm-30) REVERT: C 469 PHE cc_start: 0.7416 (p90) cc_final: 0.7064 (p90) REVERT: H 29 TYR cc_start: 0.7056 (t80) cc_final: 0.6635 (t80) REVERT: H 96 LEU cc_start: 0.9166 (tt) cc_final: 0.8927 (tt) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1468 time to fit residues: 78.1609 Evaluate side-chains 252 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 175 optimal weight: 10.0000 chunk 302 optimal weight: 0.0170 chunk 293 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 410 optimal weight: 0.0170 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN C 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.087760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.077591 restraints weight = 120338.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.079173 restraints weight = 69881.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.080367 restraints weight = 47191.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081116 restraints weight = 34921.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081743 restraints weight = 28110.612| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31300 Z= 0.100 Angle : 0.566 7.790 42936 Z= 0.285 Chirality : 0.040 0.178 4952 Planarity : 0.003 0.037 5564 Dihedral : 7.930 136.087 4868 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.13), residues: 4324 helix: 0.34 (0.12), residues: 1936 sheet: -1.84 (0.31), residues: 248 loop : -2.73 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 218 TYR 0.031 0.001 TYR C 157 PHE 0.016 0.001 PHE B 401 TRP 0.016 0.001 TRP G 287 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (31288) covalent geometry : angle 0.56598 / 0.29 (42936) hydrogen bonds : bond 0.02894 / 2.01 ( 1264) hydrogen bonds : angle 4.41994 / 3.12 ( 3564) Misc. bond : bond 0.02137 / 1.49 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8648 Ramachandran restraints generated. 4324 Oldfield, 0 Emsley, 4324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8389 (tm-30) REVERT: A 500 TYR cc_start: 0.9054 (m-80) cc_final: 0.8450 (m-10) REVERT: E 96 LEU cc_start: 0.9141 (tt) cc_final: 0.8817 (tt) REVERT: E 195 TYR cc_start: 0.7913 (t80) cc_final: 0.7651 (t80) REVERT: B 469 PHE cc_start: 0.7331 (p90) cc_final: 0.7122 (p90) REVERT: G 96 LEU cc_start: 0.9118 (tt) cc_final: 0.8831 (tt) REVERT: G 241 LEU cc_start: 0.9361 (tt) cc_final: 0.9154 (mt) REVERT: G 247 GLN cc_start: 0.8510 (tt0) cc_final: 0.8152 (tp40) REVERT: D 288 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8385 (tm-30) REVERT: F 96 LEU cc_start: 0.9070 (tt) cc_final: 0.8808 (tt) REVERT: F 302 LYS cc_start: 0.9271 (tptp) cc_final: 0.8937 (tptp) REVERT: C 180 MET cc_start: 0.9182 (tpp) cc_final: 0.8918 (tpp) REVERT: C 229 LEU cc_start: 0.8783 (mm) cc_final: 0.8543 (mm) REVERT: C 288 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8401 (tm-30) REVERT: H 29 TYR cc_start: 0.6897 (t80) cc_final: 0.6627 (t80) REVERT: H 96 LEU cc_start: 0.9088 (tt) cc_final: 0.8839 (tt) REVERT: H 195 TYR cc_start: 0.7982 (t80) cc_final: 0.7756 (t80) REVERT: H 247 GLN cc_start: 0.8649 (tt0) cc_final: 0.8113 (tp40) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1561 time to fit residues: 91.1719 Evaluate side-chains 275 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 10.0000 chunk 385 optimal weight: 0.0870 chunk 125 optimal weight: 5.9990 chunk 135 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 307 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 420 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.079071 restraints weight = 120306.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.080721 restraints weight = 69859.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081861 restraints weight = 46959.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082767 restraints weight = 34831.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083391 restraints weight = 27508.203| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 31300 Z= 0.091 Angle : 0.549 8.258 42936 Z= 0.274 Chirality : 0.040 0.166 4952 Planarity : 0.003 0.036 5564 Dihedral : 7.081 118.654 4868 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.13), residues: 4324 helix: 0.45 (0.13), residues: 1924 sheet: -1.69 (0.31), residues: 248 loop : -2.52 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 150 TYR 0.022 0.001 TYR E 29 PHE 0.017 0.001 PHE B 401 TRP 0.013 0.001 TRP G 287 HIS 0.005 0.000 HIS H 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (31288) covalent geometry : angle 0.54860 / 0.27 (42936) hydrogen bonds : bond 0.02521 / 1.76 ( 1264) hydrogen bonds : angle 4.19812 / 2.97 ( 3564) Misc. bond : bond 0.02015 / 1.38 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3516.56 seconds wall clock time: 61 minutes 58.33 seconds (3718.33 seconds total)