Starting phenix.real_space_refine on Thu Feb 22 17:38:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlg_24529/02_2024/7rlg_24529_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlg_24529/02_2024/7rlg_24529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlg_24529/02_2024/7rlg_24529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlg_24529/02_2024/7rlg_24529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlg_24529/02_2024/7rlg_24529_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlg_24529/02_2024/7rlg_24529_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 21858 2.51 5 N 6156 2.21 5 O 6642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ASP 304": "OD1" <-> "OD2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ASP 577": "OD1" <-> "OD2" Residue "C ARG 753": "NH1" <-> "NH2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D GLU 546": "OE1" <-> "OE2" Residue "D ASP 577": "OD1" <-> "OD2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E GLU 546": "OE1" <-> "OE2" Residue "E ASP 577": "OD1" <-> "OD2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F ASP 304": "OD1" <-> "OD2" Residue "F GLU 546": "OE1" <-> "OE2" Residue "F ASP 577": "OD1" <-> "OD2" Residue "F ARG 753": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34860 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "B" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "C" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "D" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "E" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "F" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5756 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.45, per 1000 atoms: 0.50 Number of scatterers: 34860 At special positions: 0 Unit cell: (174.96, 176.256, 101.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6642 8.00 N 6156 7.00 C 21858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.32 Conformation dependent library (CDL) restraints added in 6.6 seconds 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 30 sheets defined 39.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.20 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 89 No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 211 through 225 removed outlier: 5.162A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.676A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 removed outlier: 4.030A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.581A pdb=" N LEU A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 408 through 430 removed outlier: 3.700A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.635A pdb=" N ALA A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 458 " --> pdb=" O TRP A 454 " (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 483 through 492 removed outlier: 3.676A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 504 removed outlier: 4.150A pdb=" N LEU A 504 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.952A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.954A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 removed outlier: 3.623A pdb=" N ARG A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A 568 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 4.015A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 650 through 662 removed outlier: 3.634A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.550A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 706 Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 750 through 763 removed outlier: 3.829A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 86 through 89 No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 131 through 134 No H-bonds generated for 'chain 'B' and resid 131 through 134' Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 211 through 225 removed outlier: 5.161A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.675A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 removed outlier: 4.031A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.580A pdb=" N LEU B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 408 through 430 removed outlier: 3.702A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 449 through 458 removed outlier: 3.634A pdb=" N ALA B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B 458 " --> pdb=" O TRP B 454 " (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 483 through 492 removed outlier: 3.676A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 504 removed outlier: 4.151A pdb=" N LEU B 504 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.954A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 removed outlier: 3.956A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 568 removed outlier: 3.624A pdb=" N ARG B 560 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN B 568 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 584 removed outlier: 4.015A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 650 through 662 removed outlier: 3.632A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG B 662 " --> pdb=" O LYS B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.549A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 706 Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 750 through 763 removed outlier: 3.829A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 86 through 89 No H-bonds generated for 'chain 'C' and resid 86 through 89' Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 211 through 225 removed outlier: 5.161A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.675A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 295 removed outlier: 4.031A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.580A pdb=" N LEU C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 408 through 430 removed outlier: 3.700A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 449 through 458 removed outlier: 3.634A pdb=" N ALA C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 458 " --> pdb=" O TRP C 454 " (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 483 through 492 removed outlier: 3.676A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 504 removed outlier: 4.150A pdb=" N LEU C 504 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.954A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 removed outlier: 3.955A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.624A pdb=" N ARG C 560 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN C 568 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 584 removed outlier: 4.016A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS C 584 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 633 No H-bonds generated for 'chain 'C' and resid 631 through 633' Processing helix chain 'C' and resid 650 through 662 removed outlier: 3.633A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 656 " --> pdb=" O SER C 652 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG C 662 " --> pdb=" O LYS C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.549A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 706 Processing helix chain 'C' and resid 733 through 739 Processing helix chain 'C' and resid 750 through 763 removed outlier: 3.829A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 89 No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 131 through 134 No H-bonds generated for 'chain 'D' and resid 131 through 134' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 211 through 225 removed outlier: 5.160A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.675A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 295 removed outlier: 4.031A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 removed outlier: 3.580A pdb=" N LEU D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 408 through 430 removed outlier: 3.702A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 449 through 458 removed outlier: 3.634A pdb=" N ALA D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN D 458 " --> pdb=" O TRP D 454 " (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 483 through 492 removed outlier: 3.676A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 504 removed outlier: 4.151A pdb=" N LEU D 504 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.952A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 552 removed outlier: 3.954A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.623A pdb=" N ARG D 560 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN D 568 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 584 removed outlier: 4.015A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS D 584 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 633 No H-bonds generated for 'chain 'D' and resid 631 through 633' Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.633A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 656 " --> pdb=" O SER D 652 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG D 662 " --> pdb=" O LYS D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.550A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 706 Processing helix chain 'D' and resid 733 through 739 Processing helix chain 'D' and resid 750 through 763 removed outlier: 3.829A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 89 No H-bonds generated for 'chain 'E' and resid 86 through 89' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 211 through 225 removed outlier: 5.161A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.675A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 removed outlier: 4.032A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 removed outlier: 3.580A pdb=" N LEU E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 402 Processing helix chain 'E' and resid 408 through 430 removed outlier: 3.701A pdb=" N ALA E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 449 through 458 removed outlier: 3.635A pdb=" N ALA E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN E 458 " --> pdb=" O TRP E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 492 removed outlier: 3.677A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 504 removed outlier: 4.150A pdb=" N LEU E 504 " --> pdb=" O ASP E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.954A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 552 removed outlier: 3.954A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP E 551 " --> pdb=" O LEU E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 568 removed outlier: 3.624A pdb=" N ARG E 560 " --> pdb=" O ALA E 557 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN E 568 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 584 removed outlier: 4.016A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS E 584 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 633 No H-bonds generated for 'chain 'E' and resid 631 through 633' Processing helix chain 'E' and resid 650 through 662 removed outlier: 3.633A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 656 " --> pdb=" O SER E 652 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG E 662 " --> pdb=" O LYS E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.548A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 706 Processing helix chain 'E' and resid 733 through 739 Processing helix chain 'E' and resid 750 through 763 removed outlier: 3.829A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 89 No H-bonds generated for 'chain 'F' and resid 86 through 89' Processing helix chain 'F' and resid 131 through 134 No H-bonds generated for 'chain 'F' and resid 131 through 134' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 211 through 225 removed outlier: 5.161A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.675A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 295 removed outlier: 4.032A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 removed outlier: 3.581A pdb=" N LEU F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 402 Processing helix chain 'F' and resid 408 through 430 removed outlier: 3.700A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.634A pdb=" N ALA F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN F 458 " --> pdb=" O TRP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 492 removed outlier: 3.676A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 498 No H-bonds generated for 'chain 'F' and resid 495 through 498' Processing helix chain 'F' and resid 500 through 504 removed outlier: 4.150A pdb=" N LEU F 504 " --> pdb=" O ASP F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.954A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 552 removed outlier: 3.954A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 568 removed outlier: 3.624A pdb=" N ARG F 560 " --> pdb=" O ALA F 557 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN F 568 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 584 removed outlier: 4.015A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS F 584 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 650 through 662 removed outlier: 3.634A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 656 " --> pdb=" O SER F 652 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG F 662 " --> pdb=" O LYS F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.549A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 706 Processing helix chain 'F' and resid 733 through 739 Processing helix chain 'F' and resid 750 through 763 removed outlier: 3.829A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 81 through 84 removed outlier: 7.434A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN A 103 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 39 through 42 Processing sheet with id= C, first strand: chain 'A' and resid 151 through 156 removed outlier: 3.607A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 367 removed outlier: 3.634A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.974A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 517 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 81 through 84 removed outlier: 7.435A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 26 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 39 through 42 Processing sheet with id= H, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.606A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 365 through 367 removed outlier: 3.634A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.975A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 517 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 81 through 84 removed outlier: 7.435A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 26 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN C 103 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 39 through 42 Processing sheet with id= M, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.608A pdb=" N PHE C 152 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 365 through 367 removed outlier: 3.634A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.973A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR C 517 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 81 through 84 removed outlier: 7.435A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU D 26 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN D 103 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 39 through 42 Processing sheet with id= R, first strand: chain 'D' and resid 151 through 156 removed outlier: 3.607A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 365 through 367 removed outlier: 3.633A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.975A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR D 517 " --> pdb=" O ILE D 643 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.434A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 26 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN E 103 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 39 through 42 Processing sheet with id= W, first strand: chain 'E' and resid 151 through 156 removed outlier: 3.607A pdb=" N PHE E 152 " --> pdb=" O PHE E 163 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 365 through 367 removed outlier: 3.634A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.976A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 81 through 84 removed outlier: 7.434A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU F 26 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 39 through 42 Processing sheet with id= AB, first strand: chain 'F' and resid 151 through 156 removed outlier: 3.607A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 367 removed outlier: 3.634A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.974A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 954 hydrogen bonds defined for protein. 2628 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: 12.14 Time building geometry restraints manager: 14.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9371 1.33 - 1.45: 5282 1.45 - 1.57: 20483 1.57 - 1.69: 36 1.69 - 1.81: 288 Bond restraints: 35460 Sorted by residual: bond pdb=" C LYS C 136 " pdb=" N PRO C 137 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.20e+01 bond pdb=" C LYS D 136 " pdb=" N PRO D 137 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.20e+01 bond pdb=" C LYS F 136 " pdb=" N PRO F 137 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.16e+01 bond pdb=" C LYS A 136 " pdb=" N PRO A 137 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.16e+01 bond pdb=" C LYS B 136 " pdb=" N PRO B 137 " ideal model delta sigma weight residual 1.334 1.372 -0.039 8.40e-03 1.42e+04 2.12e+01 ... (remaining 35455 not shown) Histogram of bond angle deviations from ideal: 88.49 - 98.02: 6 98.02 - 107.55: 1424 107.55 - 117.08: 23839 117.08 - 126.61: 22299 126.61 - 136.14: 378 Bond angle restraints: 47946 Sorted by residual: angle pdb=" C VAL C 471 " pdb=" N PRO C 472 " pdb=" CA PRO C 472 " ideal model delta sigma weight residual 119.89 131.52 -11.63 1.02e+00 9.61e-01 1.30e+02 angle pdb=" C VAL A 471 " pdb=" N PRO A 472 " pdb=" CA PRO A 472 " ideal model delta sigma weight residual 119.89 130.33 -10.44 1.02e+00 9.61e-01 1.05e+02 angle pdb=" C VAL B 471 " pdb=" N PRO B 472 " pdb=" CA PRO B 472 " ideal model delta sigma weight residual 119.78 130.00 -10.22 1.03e+00 9.43e-01 9.85e+01 angle pdb=" C VAL E 471 " pdb=" N PRO E 472 " pdb=" CA PRO E 472 " ideal model delta sigma weight residual 119.78 129.97 -10.19 1.03e+00 9.43e-01 9.78e+01 angle pdb=" N VAL B 471 " pdb=" CA VAL B 471 " pdb=" C VAL B 471 " ideal model delta sigma weight residual 108.88 88.49 20.39 2.16e+00 2.14e-01 8.91e+01 ... (remaining 47941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 19803 17.88 - 35.76: 1764 35.76 - 53.64: 287 53.64 - 71.52: 40 71.52 - 89.39: 30 Dihedral angle restraints: 21924 sinusoidal: 9240 harmonic: 12684 Sorted by residual: dihedral pdb=" C VAL D 471 " pdb=" N VAL D 471 " pdb=" CA VAL D 471 " pdb=" CB VAL D 471 " ideal model delta harmonic sigma weight residual -122.00 -108.47 -13.53 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" C VAL A 471 " pdb=" N VAL A 471 " pdb=" CA VAL A 471 " pdb=" CB VAL A 471 " ideal model delta harmonic sigma weight residual -122.00 -108.51 -13.49 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" C VAL E 471 " pdb=" N VAL E 471 " pdb=" CA VAL E 471 " pdb=" CB VAL E 471 " ideal model delta harmonic sigma weight residual -122.00 -108.88 -13.12 0 2.50e+00 1.60e-01 2.75e+01 ... (remaining 21921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4951 0.085 - 0.171: 419 0.171 - 0.256: 0 0.256 - 0.342: 0 0.342 - 0.427: 6 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CA VAL A 471 " pdb=" N VAL A 471 " pdb=" C VAL A 471 " pdb=" CB VAL A 471 " both_signs ideal model delta sigma weight residual False 2.44 2.87 -0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CA VAL D 471 " pdb=" N VAL D 471 " pdb=" C VAL D 471 " pdb=" CB VAL D 471 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA VAL E 471 " pdb=" N VAL E 471 " pdb=" C VAL E 471 " pdb=" CB VAL E 471 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 5373 not shown) Planarity restraints: 6300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 630 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO E 631 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 631 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 631 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 630 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO D 631 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 631 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 631 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 630 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO F 631 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 631 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 631 " -0.028 5.00e-02 4.00e+02 ... (remaining 6297 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8052 2.79 - 3.32: 32754 3.32 - 3.84: 57145 3.84 - 4.37: 66662 4.37 - 4.90: 111594 Nonbonded interactions: 276207 Sorted by model distance: nonbonded pdb=" OG SER E 748 " pdb=" OD1 ASN E 750 " model vdw 2.261 2.440 nonbonded pdb=" OG SER C 748 " pdb=" OD1 ASN C 750 " model vdw 2.261 2.440 nonbonded pdb=" OG SER A 748 " pdb=" OD1 ASN A 750 " model vdw 2.261 2.440 nonbonded pdb=" OG SER D 748 " pdb=" OD1 ASN D 750 " model vdw 2.262 2.440 nonbonded pdb=" OG SER F 748 " pdb=" OD1 ASN F 750 " model vdw 2.262 2.440 ... (remaining 276202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 5.600 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 87.890 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.003 0.052 35460 Z= 0.184 Angle : 0.734 20.387 47946 Z= 0.409 Chirality : 0.045 0.427 5376 Planarity : 0.004 0.051 6300 Dihedral : 13.671 89.394 13704 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.16 % Allowed : 0.27 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 4386 helix: -0.20 (0.13), residues: 1566 sheet: -0.34 (0.20), residues: 666 loop : -1.59 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 454 HIS 0.003 0.001 HIS E 183 PHE 0.011 0.001 PHE F 52 TYR 0.016 0.001 TYR D 244 ARG 0.006 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 309 time to evaluate : 4.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8582 (pt0) cc_final: 0.8082 (pp30) REVERT: A 52 PHE cc_start: 0.8221 (m-80) cc_final: 0.7993 (m-80) REVERT: A 332 MET cc_start: 0.9133 (tpt) cc_final: 0.8815 (tpp) REVERT: A 427 MET cc_start: 0.7224 (tpt) cc_final: 0.6472 (tpt) REVERT: A 504 LEU cc_start: 0.8840 (pt) cc_final: 0.7983 (tt) REVERT: B 50 GLN cc_start: 0.8330 (pt0) cc_final: 0.8099 (pp30) REVERT: B 193 ASP cc_start: 0.8906 (t0) cc_final: 0.8465 (p0) REVERT: B 332 MET cc_start: 0.9212 (tpt) cc_final: 0.8990 (tpt) REVERT: B 344 MET cc_start: 0.8884 (mtp) cc_final: 0.8668 (mtp) REVERT: B 427 MET cc_start: 0.7620 (tpt) cc_final: 0.7223 (tpt) REVERT: B 442 MET cc_start: 0.9171 (mmm) cc_final: 0.8937 (mpp) REVERT: B 504 LEU cc_start: 0.8852 (pt) cc_final: 0.8133 (tt) REVERT: C 50 GLN cc_start: 0.8529 (pt0) cc_final: 0.8191 (pp30) REVERT: C 52 PHE cc_start: 0.8359 (m-80) cc_final: 0.8129 (m-80) REVERT: C 79 ASP cc_start: 0.8469 (p0) cc_final: 0.8045 (t0) REVERT: C 193 ASP cc_start: 0.8966 (t0) cc_final: 0.8355 (p0) REVERT: C 275 MET cc_start: 0.8947 (mmm) cc_final: 0.8565 (mmp) REVERT: C 504 LEU cc_start: 0.8857 (pt) cc_final: 0.8287 (tt) REVERT: D 50 GLN cc_start: 0.8435 (pt0) cc_final: 0.8045 (pp30) REVERT: D 52 PHE cc_start: 0.8258 (m-80) cc_final: 0.7969 (m-80) REVERT: D 193 ASP cc_start: 0.8859 (t0) cc_final: 0.8381 (p0) REVERT: D 275 MET cc_start: 0.9103 (mmm) cc_final: 0.8829 (mmm) REVERT: D 427 MET cc_start: 0.7644 (tpt) cc_final: 0.7179 (tpt) REVERT: D 504 LEU cc_start: 0.8830 (pt) cc_final: 0.7996 (tt) REVERT: E 50 GLN cc_start: 0.8316 (pt0) cc_final: 0.8070 (pp30) REVERT: E 193 ASP cc_start: 0.8891 (t0) cc_final: 0.8329 (p0) REVERT: E 324 ILE cc_start: 0.8361 (mt) cc_final: 0.7983 (mm) REVERT: E 344 MET cc_start: 0.8905 (mtp) cc_final: 0.8641 (mtp) REVERT: E 427 MET cc_start: 0.7597 (tpt) cc_final: 0.7209 (tpt) REVERT: E 442 MET cc_start: 0.9311 (mmm) cc_final: 0.9019 (mpp) REVERT: E 504 LEU cc_start: 0.8876 (pt) cc_final: 0.8106 (tt) REVERT: F 50 GLN cc_start: 0.8481 (pt0) cc_final: 0.8244 (pp30) REVERT: F 64 ARG cc_start: 0.9174 (mmm160) cc_final: 0.8931 (mmm160) REVERT: F 79 ASP cc_start: 0.8523 (p0) cc_final: 0.8261 (t0) REVERT: F 193 ASP cc_start: 0.9028 (t0) cc_final: 0.8602 (p0) REVERT: F 219 MET cc_start: 0.8446 (ttm) cc_final: 0.8195 (ttp) REVERT: F 342 ILE cc_start: 0.8752 (mt) cc_final: 0.8530 (mt) REVERT: F 427 MET cc_start: 0.7839 (tpt) cc_final: 0.7384 (tpt) REVERT: F 442 MET cc_start: 0.9169 (mmm) cc_final: 0.8914 (mpp) REVERT: F 504 LEU cc_start: 0.8894 (pt) cc_final: 0.8222 (tt) outliers start: 6 outliers final: 0 residues processed: 315 average time/residue: 0.4886 time to fit residues: 247.1651 Evaluate side-chains 210 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 343 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 255 optimal weight: 0.7980 chunk 397 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 602 ASN B 90 ASN B 401 ASN C 90 ASN C 384 HIS C 401 ASN D 384 HIS D 401 ASN D 602 ASN E 398 GLN F 401 ASN F 602 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35460 Z= 0.355 Angle : 0.692 8.993 47946 Z= 0.333 Chirality : 0.047 0.197 5376 Planarity : 0.005 0.088 6300 Dihedral : 4.277 24.627 4920 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.96 % Allowed : 7.60 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.12), residues: 4386 helix: -0.46 (0.12), residues: 1794 sheet: -0.36 (0.21), residues: 636 loop : -1.47 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 454 HIS 0.004 0.001 HIS B 317 PHE 0.013 0.002 PHE B 563 TYR 0.011 0.002 TYR C 244 ARG 0.007 0.001 ARG F 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 3.959 Fit side-chains REVERT: A 50 GLN cc_start: 0.8714 (pt0) cc_final: 0.8284 (pp30) REVERT: A 64 ARG cc_start: 0.8912 (mmm160) cc_final: 0.8646 (mmm160) REVERT: A 427 MET cc_start: 0.7869 (tpt) cc_final: 0.7304 (tpt) REVERT: A 504 LEU cc_start: 0.9086 (pt) cc_final: 0.8314 (tt) REVERT: B 50 GLN cc_start: 0.8245 (pt0) cc_final: 0.7993 (pp30) REVERT: B 193 ASP cc_start: 0.9017 (t0) cc_final: 0.8529 (p0) REVERT: B 332 MET cc_start: 0.9105 (tpt) cc_final: 0.8863 (tpt) REVERT: B 427 MET cc_start: 0.7669 (tpt) cc_final: 0.7078 (tpp) REVERT: B 608 MET cc_start: 0.8822 (ttm) cc_final: 0.8584 (ttm) REVERT: C 50 GLN cc_start: 0.8481 (pt0) cc_final: 0.8174 (pp30) REVERT: C 79 ASP cc_start: 0.8675 (p0) cc_final: 0.8249 (t0) REVERT: C 193 ASP cc_start: 0.9139 (t0) cc_final: 0.8805 (t70) REVERT: C 504 LEU cc_start: 0.9091 (pt) cc_final: 0.8517 (tt) REVERT: D 50 GLN cc_start: 0.8637 (pt0) cc_final: 0.8260 (pp30) REVERT: D 64 ARG cc_start: 0.8901 (mmm160) cc_final: 0.8547 (mmm160) REVERT: D 193 ASP cc_start: 0.9057 (t0) cc_final: 0.8551 (p0) REVERT: D 427 MET cc_start: 0.8044 (tpt) cc_final: 0.7480 (tpt) REVERT: D 504 LEU cc_start: 0.9021 (pt) cc_final: 0.8181 (tt) REVERT: E 50 GLN cc_start: 0.8321 (pt0) cc_final: 0.8096 (pp30) REVERT: E 79 ASP cc_start: 0.8654 (p0) cc_final: 0.8259 (t0) REVERT: E 84 MET cc_start: 0.7741 (ttm) cc_final: 0.7443 (ttm) REVERT: E 193 ASP cc_start: 0.9054 (t0) cc_final: 0.8563 (p0) REVERT: E 324 ILE cc_start: 0.8755 (mt) cc_final: 0.8431 (mm) REVERT: E 427 MET cc_start: 0.7623 (tpt) cc_final: 0.6886 (tpp) REVERT: E 608 MET cc_start: 0.8834 (ttm) cc_final: 0.8479 (ttm) REVERT: F 64 ARG cc_start: 0.9186 (mmm160) cc_final: 0.8845 (mmm160) REVERT: F 79 ASP cc_start: 0.8692 (p0) cc_final: 0.8386 (t0) REVERT: F 193 ASP cc_start: 0.9126 (t0) cc_final: 0.8828 (t70) REVERT: F 427 MET cc_start: 0.7861 (tpt) cc_final: 0.7471 (tpt) outliers start: 36 outliers final: 22 residues processed: 231 average time/residue: 0.4650 time to fit residues: 177.6458 Evaluate side-chains 204 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 37 SER Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 398 optimal weight: 0.7980 chunk 430 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 395 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 319 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 90 ASN B 398 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN F 36 ASN F 90 ASN F 398 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35460 Z= 0.262 Angle : 0.580 7.977 47946 Z= 0.271 Chirality : 0.044 0.166 5376 Planarity : 0.004 0.078 6300 Dihedral : 4.180 28.155 4920 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.04 % Allowed : 10.43 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 4386 helix: -0.05 (0.12), residues: 1824 sheet: -0.45 (0.21), residues: 648 loop : -1.30 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 454 HIS 0.004 0.001 HIS E 183 PHE 0.012 0.001 PHE E 503 TYR 0.006 0.001 TYR A 517 ARG 0.014 0.000 ARG F 753 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 206 time to evaluate : 4.370 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8677 (pt0) cc_final: 0.8266 (pp30) REVERT: A 64 ARG cc_start: 0.8891 (mmm160) cc_final: 0.8615 (mmm160) REVERT: A 193 ASP cc_start: 0.9050 (t0) cc_final: 0.8738 (t70) REVERT: A 344 MET cc_start: 0.9122 (mtp) cc_final: 0.8869 (mtm) REVERT: A 427 MET cc_start: 0.8188 (tpt) cc_final: 0.7652 (tpt) REVERT: B 50 GLN cc_start: 0.8268 (pt0) cc_final: 0.8005 (pp30) REVERT: B 193 ASP cc_start: 0.9072 (t0) cc_final: 0.8607 (p0) REVERT: B 427 MET cc_start: 0.8020 (tpt) cc_final: 0.7718 (tpt) REVERT: B 608 MET cc_start: 0.8699 (ttm) cc_final: 0.8380 (ttm) REVERT: C 50 GLN cc_start: 0.8498 (pt0) cc_final: 0.8191 (pp30) REVERT: C 79 ASP cc_start: 0.8648 (p0) cc_final: 0.8201 (t0) REVERT: C 193 ASP cc_start: 0.9153 (t0) cc_final: 0.8832 (t70) REVERT: C 740 MET cc_start: 0.8864 (mmm) cc_final: 0.8609 (mmm) REVERT: D 50 GLN cc_start: 0.8711 (pt0) cc_final: 0.8363 (pp30) REVERT: D 79 ASP cc_start: 0.8394 (t0) cc_final: 0.8174 (t0) REVERT: D 193 ASP cc_start: 0.9061 (t0) cc_final: 0.8667 (p0) REVERT: D 427 MET cc_start: 0.8319 (tpt) cc_final: 0.7695 (tpt) REVERT: E 50 GLN cc_start: 0.8494 (pt0) cc_final: 0.8150 (pp30) REVERT: E 79 ASP cc_start: 0.8695 (p0) cc_final: 0.8142 (t0) REVERT: E 193 ASP cc_start: 0.9080 (t0) cc_final: 0.8541 (p0) REVERT: E 427 MET cc_start: 0.7843 (tpt) cc_final: 0.7268 (tpp) REVERT: E 608 MET cc_start: 0.8676 (ttm) cc_final: 0.8325 (ttm) REVERT: F 79 ASP cc_start: 0.8693 (p0) cc_final: 0.8340 (t0) REVERT: F 193 ASP cc_start: 0.9101 (t0) cc_final: 0.8838 (t70) REVERT: F 427 MET cc_start: 0.7997 (tpt) cc_final: 0.7701 (tpt) outliers start: 39 outliers final: 21 residues processed: 235 average time/residue: 0.4494 time to fit residues: 176.6600 Evaluate side-chains 206 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 4.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 1.9990 chunk 299 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 267 optimal weight: 0.6980 chunk 399 optimal weight: 5.9990 chunk 423 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 379 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35460 Z= 0.180 Angle : 0.549 7.247 47946 Z= 0.253 Chirality : 0.043 0.149 5376 Planarity : 0.003 0.044 6300 Dihedral : 4.043 27.904 4920 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.07 % Allowed : 12.11 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.13), residues: 4386 helix: 0.16 (0.13), residues: 1836 sheet: -0.41 (0.20), residues: 648 loop : -1.18 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.005 0.001 HIS E 183 PHE 0.008 0.001 PHE F 363 TYR 0.007 0.001 TYR A 517 ARG 0.007 0.000 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 3.782 Fit side-chains REVERT: A 50 GLN cc_start: 0.8691 (pt0) cc_final: 0.8285 (pp30) REVERT: A 64 ARG cc_start: 0.8924 (mmm160) cc_final: 0.8656 (mmm160) REVERT: A 193 ASP cc_start: 0.9052 (t0) cc_final: 0.8747 (t70) REVERT: A 427 MET cc_start: 0.8180 (tpt) cc_final: 0.7691 (tpt) REVERT: A 504 LEU cc_start: 0.9211 (pt) cc_final: 0.8265 (tt) REVERT: B 193 ASP cc_start: 0.9030 (t0) cc_final: 0.8572 (p0) REVERT: B 427 MET cc_start: 0.8112 (tpt) cc_final: 0.7805 (tpt) REVERT: B 608 MET cc_start: 0.8705 (ttm) cc_final: 0.8354 (ttm) REVERT: C 79 ASP cc_start: 0.8661 (p0) cc_final: 0.8103 (t0) REVERT: C 193 ASP cc_start: 0.9150 (t0) cc_final: 0.8840 (t70) REVERT: C 504 LEU cc_start: 0.9321 (pt) cc_final: 0.8389 (tt) REVERT: C 740 MET cc_start: 0.8874 (mmm) cc_final: 0.8590 (mmm) REVERT: D 50 GLN cc_start: 0.8706 (pt0) cc_final: 0.8360 (pp30) REVERT: D 193 ASP cc_start: 0.9063 (t0) cc_final: 0.8671 (p0) REVERT: D 427 MET cc_start: 0.8165 (tpt) cc_final: 0.7658 (tpt) REVERT: D 504 LEU cc_start: 0.9123 (pt) cc_final: 0.8191 (tt) REVERT: D 574 LEU cc_start: 0.8770 (tp) cc_final: 0.8478 (tp) REVERT: E 50 GLN cc_start: 0.8493 (pt0) cc_final: 0.8156 (pp30) REVERT: E 79 ASP cc_start: 0.8545 (p0) cc_final: 0.8275 (t0) REVERT: E 193 ASP cc_start: 0.9117 (t0) cc_final: 0.8595 (p0) REVERT: E 427 MET cc_start: 0.7861 (tpt) cc_final: 0.7295 (tpp) REVERT: E 608 MET cc_start: 0.8695 (ttm) cc_final: 0.8336 (ttm) REVERT: F 79 ASP cc_start: 0.8701 (p0) cc_final: 0.8211 (t0) REVERT: F 158 MET cc_start: 0.8926 (ttm) cc_final: 0.8648 (ttm) REVERT: F 193 ASP cc_start: 0.9100 (t0) cc_final: 0.8842 (t70) REVERT: F 427 MET cc_start: 0.8059 (tpt) cc_final: 0.7789 (tpt) REVERT: F 574 LEU cc_start: 0.8765 (tp) cc_final: 0.8367 (tp) outliers start: 40 outliers final: 22 residues processed: 232 average time/residue: 0.4360 time to fit residues: 171.2257 Evaluate side-chains 206 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 0.5980 chunk 240 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 315 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 361 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 380 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35460 Z= 0.314 Angle : 0.606 7.076 47946 Z= 0.284 Chirality : 0.044 0.151 5376 Planarity : 0.004 0.046 6300 Dihedral : 4.448 31.962 4920 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.87 % Allowed : 12.61 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4386 helix: 0.21 (0.13), residues: 1842 sheet: -0.43 (0.20), residues: 684 loop : -1.11 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 454 HIS 0.004 0.001 HIS E 183 PHE 0.011 0.001 PHE B 360 TYR 0.007 0.001 TYR B 517 ARG 0.008 0.001 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 176 time to evaluate : 3.902 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8766 (pt0) cc_final: 0.8361 (pp30) REVERT: A 64 ARG cc_start: 0.8862 (mmm160) cc_final: 0.8647 (mmm160) REVERT: A 158 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8700 (mtp) REVERT: A 193 ASP cc_start: 0.9160 (t0) cc_final: 0.8856 (t70) REVERT: A 427 MET cc_start: 0.8293 (tpt) cc_final: 0.7844 (tpt) REVERT: A 449 MET cc_start: 0.8392 (tpp) cc_final: 0.7652 (tpp) REVERT: B 50 GLN cc_start: 0.8487 (pt0) cc_final: 0.8141 (pp30) REVERT: B 60 LYS cc_start: 0.9019 (ttpt) cc_final: 0.8763 (tptt) REVERT: B 291 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: B 427 MET cc_start: 0.8153 (tpt) cc_final: 0.7585 (tpp) REVERT: B 608 MET cc_start: 0.8729 (ttm) cc_final: 0.8318 (ttm) REVERT: C 50 GLN cc_start: 0.8605 (pt0) cc_final: 0.8304 (pp30) REVERT: C 79 ASP cc_start: 0.8525 (p0) cc_final: 0.8103 (t0) REVERT: C 193 ASP cc_start: 0.9138 (t0) cc_final: 0.8913 (t70) REVERT: C 611 MET cc_start: 0.8034 (tpt) cc_final: 0.7807 (tpt) REVERT: C 740 MET cc_start: 0.8907 (mmm) cc_final: 0.8588 (mmm) REVERT: D 50 GLN cc_start: 0.8796 (pt0) cc_final: 0.8467 (pp30) REVERT: D 126 ILE cc_start: 0.9125 (mm) cc_final: 0.8764 (mt) REVERT: D 168 THR cc_start: 0.3633 (OUTLIER) cc_final: 0.3396 (m) REVERT: D 427 MET cc_start: 0.8391 (tpt) cc_final: 0.7889 (tpt) REVERT: D 449 MET cc_start: 0.8387 (tpp) cc_final: 0.7659 (tpp) REVERT: E 50 GLN cc_start: 0.8497 (pt0) cc_final: 0.8238 (pp30) REVERT: E 79 ASP cc_start: 0.8586 (p0) cc_final: 0.8257 (t0) REVERT: E 84 MET cc_start: 0.7772 (ttm) cc_final: 0.7513 (ttm) REVERT: E 193 ASP cc_start: 0.9166 (t0) cc_final: 0.8731 (p0) REVERT: E 291 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: E 344 MET cc_start: 0.9049 (mtp) cc_final: 0.8721 (mtm) REVERT: E 427 MET cc_start: 0.8068 (tpt) cc_final: 0.7444 (tpp) REVERT: E 598 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8277 (p0) REVERT: E 608 MET cc_start: 0.8682 (ttm) cc_final: 0.8189 (ttm) REVERT: F 50 GLN cc_start: 0.8634 (pt0) cc_final: 0.8334 (pp30) REVERT: F 64 ARG cc_start: 0.8632 (mmm160) cc_final: 0.7957 (tpm170) REVERT: F 79 ASP cc_start: 0.8558 (p0) cc_final: 0.8255 (t0) REVERT: F 193 ASP cc_start: 0.9109 (t0) cc_final: 0.8906 (t70) REVERT: F 427 MET cc_start: 0.8096 (tpt) cc_final: 0.7837 (tpt) REVERT: F 611 MET cc_start: 0.8148 (ttp) cc_final: 0.7839 (tpt) outliers start: 70 outliers final: 36 residues processed: 231 average time/residue: 0.4213 time to fit residues: 167.0854 Evaluate side-chains 215 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 174 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 9.9990 chunk 381 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 423 optimal weight: 0.8980 chunk 351 optimal weight: 5.9990 chunk 196 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 222 optimal weight: 9.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 36 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 90 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35460 Z= 0.226 Angle : 0.566 8.197 47946 Z= 0.263 Chirality : 0.044 0.143 5376 Planarity : 0.004 0.044 6300 Dihedral : 4.328 31.037 4920 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.60 % Allowed : 13.60 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4386 helix: 0.28 (0.13), residues: 1830 sheet: -0.42 (0.20), residues: 684 loop : -0.98 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 454 HIS 0.005 0.001 HIS E 183 PHE 0.012 0.001 PHE F 758 TYR 0.006 0.001 TYR A 517 ARG 0.005 0.000 ARG F 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 175 time to evaluate : 4.473 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8832 (pt0) cc_final: 0.8448 (pp30) REVERT: A 64 ARG cc_start: 0.8933 (mmm160) cc_final: 0.8723 (mmm160) REVERT: A 193 ASP cc_start: 0.9168 (t0) cc_final: 0.8886 (t70) REVERT: A 427 MET cc_start: 0.8364 (tpt) cc_final: 0.7967 (tpt) REVERT: A 449 MET cc_start: 0.8410 (tpp) cc_final: 0.7601 (tpp) REVERT: B 50 GLN cc_start: 0.8489 (pt0) cc_final: 0.8140 (pp30) REVERT: B 291 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: B 427 MET cc_start: 0.8170 (tpt) cc_final: 0.7614 (tpp) REVERT: B 608 MET cc_start: 0.8702 (ttm) cc_final: 0.8248 (ttm) REVERT: C 50 GLN cc_start: 0.8635 (pt0) cc_final: 0.8343 (pp30) REVERT: C 64 ARG cc_start: 0.8606 (mmm160) cc_final: 0.8005 (tpm170) REVERT: C 79 ASP cc_start: 0.8533 (p0) cc_final: 0.8170 (t0) REVERT: C 193 ASP cc_start: 0.9133 (t0) cc_final: 0.8918 (t70) REVERT: C 574 LEU cc_start: 0.8719 (tp) cc_final: 0.8415 (tp) REVERT: C 611 MET cc_start: 0.7992 (tpt) cc_final: 0.7790 (tpt) REVERT: C 740 MET cc_start: 0.8913 (mmm) cc_final: 0.8589 (mmm) REVERT: D 50 GLN cc_start: 0.8784 (pt0) cc_final: 0.8469 (pp30) REVERT: D 168 THR cc_start: 0.3847 (OUTLIER) cc_final: 0.3583 (m) REVERT: D 193 ASP cc_start: 0.9086 (t70) cc_final: 0.8758 (t70) REVERT: D 427 MET cc_start: 0.8356 (tpt) cc_final: 0.7925 (tpt) REVERT: D 449 MET cc_start: 0.8405 (tpp) cc_final: 0.7602 (tpp) REVERT: D 574 LEU cc_start: 0.8769 (tp) cc_final: 0.8474 (tp) REVERT: E 50 GLN cc_start: 0.8531 (pt0) cc_final: 0.8228 (pp30) REVERT: E 79 ASP cc_start: 0.8588 (p0) cc_final: 0.8253 (t0) REVERT: E 193 ASP cc_start: 0.9121 (t0) cc_final: 0.8739 (p0) REVERT: E 291 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: E 427 MET cc_start: 0.8209 (tpt) cc_final: 0.7579 (tpp) REVERT: E 442 MET cc_start: 0.9221 (mmm) cc_final: 0.8860 (mpp) REVERT: E 598 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8190 (p0) REVERT: E 608 MET cc_start: 0.8671 (ttm) cc_final: 0.8170 (ttm) REVERT: F 50 GLN cc_start: 0.8654 (pt0) cc_final: 0.8354 (pp30) REVERT: F 79 ASP cc_start: 0.8508 (p0) cc_final: 0.8218 (t0) REVERT: F 84 MET cc_start: 0.7799 (ttp) cc_final: 0.7473 (ttt) REVERT: F 291 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7438 (pm20) REVERT: F 381 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8098 (mt) REVERT: F 574 LEU cc_start: 0.8742 (tp) cc_final: 0.8334 (tp) outliers start: 60 outliers final: 34 residues processed: 223 average time/residue: 0.4302 time to fit residues: 164.9532 Evaluate side-chains 214 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 174 time to evaluate : 4.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 6.9990 chunk 47 optimal weight: 0.0980 chunk 241 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 356 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 422 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 257 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 401 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35460 Z= 0.301 Angle : 0.597 8.973 47946 Z= 0.278 Chirality : 0.044 0.150 5376 Planarity : 0.004 0.045 6300 Dihedral : 4.514 33.432 4920 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.65 % Allowed : 14.05 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4386 helix: 0.30 (0.13), residues: 1830 sheet: -0.43 (0.20), residues: 684 loop : -0.88 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 454 HIS 0.005 0.001 HIS E 183 PHE 0.011 0.001 PHE F 363 TYR 0.006 0.001 TYR B 517 ARG 0.008 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 173 time to evaluate : 3.988 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8688 (pt0) cc_final: 0.8364 (pp30) REVERT: A 193 ASP cc_start: 0.9231 (t0) cc_final: 0.8932 (t70) REVERT: A 427 MET cc_start: 0.8408 (tpt) cc_final: 0.8027 (tpt) REVERT: A 449 MET cc_start: 0.8339 (tpp) cc_final: 0.7388 (tpp) REVERT: B 50 GLN cc_start: 0.8709 (pt0) cc_final: 0.8373 (pp30) REVERT: B 291 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: B 427 MET cc_start: 0.8185 (tpt) cc_final: 0.7654 (tpp) REVERT: B 550 MET cc_start: 0.8602 (mtm) cc_final: 0.8291 (ptp) REVERT: B 608 MET cc_start: 0.8657 (ttm) cc_final: 0.8174 (ttm) REVERT: C 50 GLN cc_start: 0.8742 (pt0) cc_final: 0.8453 (pp30) REVERT: C 79 ASP cc_start: 0.8554 (p0) cc_final: 0.8166 (t0) REVERT: C 291 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: C 574 LEU cc_start: 0.8729 (tp) cc_final: 0.8439 (tp) REVERT: C 740 MET cc_start: 0.8963 (mmm) cc_final: 0.8631 (mmm) REVERT: D 50 GLN cc_start: 0.8831 (pt0) cc_final: 0.8520 (pp30) REVERT: D 168 THR cc_start: 0.4310 (OUTLIER) cc_final: 0.4073 (m) REVERT: D 193 ASP cc_start: 0.9079 (t70) cc_final: 0.8752 (p0) REVERT: D 427 MET cc_start: 0.8402 (tpt) cc_final: 0.8011 (tpt) REVERT: D 449 MET cc_start: 0.8335 (tpp) cc_final: 0.7397 (tpp) REVERT: E 50 GLN cc_start: 0.8667 (pt0) cc_final: 0.8368 (pp30) REVERT: E 291 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: E 344 MET cc_start: 0.9061 (mtp) cc_final: 0.8745 (mtm) REVERT: E 427 MET cc_start: 0.8247 (tpt) cc_final: 0.7663 (tpp) REVERT: E 550 MET cc_start: 0.8593 (mtm) cc_final: 0.8232 (ptp) REVERT: E 598 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8103 (p0) REVERT: E 608 MET cc_start: 0.8679 (ttm) cc_final: 0.8137 (ttm) REVERT: F 50 GLN cc_start: 0.8665 (pt0) cc_final: 0.8423 (pp30) REVERT: F 79 ASP cc_start: 0.8542 (p0) cc_final: 0.8277 (t70) REVERT: F 84 MET cc_start: 0.7910 (ttp) cc_final: 0.7577 (ttt) REVERT: F 193 ASP cc_start: 0.8874 (t70) cc_final: 0.8532 (p0) REVERT: F 291 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: F 427 MET cc_start: 0.8517 (tpt) cc_final: 0.8207 (tpp) REVERT: F 508 MET cc_start: 0.3279 (ptp) cc_final: 0.2643 (ptp) REVERT: F 574 LEU cc_start: 0.8756 (tp) cc_final: 0.8367 (tp) outliers start: 62 outliers final: 36 residues processed: 225 average time/residue: 0.4217 time to fit residues: 162.7117 Evaluate side-chains 211 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 287 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 331 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35460 Z= 0.250 Angle : 0.581 9.145 47946 Z= 0.268 Chirality : 0.044 0.143 5376 Planarity : 0.004 0.046 6300 Dihedral : 4.485 32.378 4920 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.47 % Allowed : 14.75 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 4386 helix: 0.38 (0.13), residues: 1818 sheet: -0.42 (0.20), residues: 696 loop : -0.81 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 454 HIS 0.005 0.001 HIS E 183 PHE 0.015 0.001 PHE C 363 TYR 0.006 0.001 TYR A 517 ARG 0.007 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 163 time to evaluate : 4.404 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8628 (pt0) cc_final: 0.8327 (pp30) REVERT: A 193 ASP cc_start: 0.9225 (t0) cc_final: 0.8935 (t70) REVERT: A 427 MET cc_start: 0.8424 (tpt) cc_final: 0.8047 (tpt) REVERT: A 449 MET cc_start: 0.8348 (tpp) cc_final: 0.7377 (tpp) REVERT: B 50 GLN cc_start: 0.8708 (pt0) cc_final: 0.8421 (pp30) REVERT: B 291 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: B 427 MET cc_start: 0.8197 (tpt) cc_final: 0.7675 (tpp) REVERT: B 608 MET cc_start: 0.8642 (ttm) cc_final: 0.8166 (ttm) REVERT: C 50 GLN cc_start: 0.8682 (pt0) cc_final: 0.8451 (pp30) REVERT: C 79 ASP cc_start: 0.8540 (p0) cc_final: 0.8156 (t0) REVERT: C 291 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: C 574 LEU cc_start: 0.8734 (tp) cc_final: 0.8414 (tp) REVERT: C 740 MET cc_start: 0.8967 (mmm) cc_final: 0.8631 (mmm) REVERT: D 50 GLN cc_start: 0.8839 (pt0) cc_final: 0.8537 (pp30) REVERT: D 168 THR cc_start: 0.4760 (OUTLIER) cc_final: 0.4533 (m) REVERT: D 427 MET cc_start: 0.8413 (tpt) cc_final: 0.8004 (tpt) REVERT: D 449 MET cc_start: 0.8343 (tpp) cc_final: 0.7386 (tpp) REVERT: E 50 GLN cc_start: 0.8735 (pt0) cc_final: 0.8403 (pp30) REVERT: E 193 ASP cc_start: 0.9020 (t70) cc_final: 0.8752 (p0) REVERT: E 291 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: E 427 MET cc_start: 0.8263 (tpt) cc_final: 0.7683 (tpp) REVERT: E 598 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7870 (p0) REVERT: E 608 MET cc_start: 0.8668 (ttm) cc_final: 0.8137 (ttm) REVERT: F 50 GLN cc_start: 0.8677 (pt0) cc_final: 0.8439 (pp30) REVERT: F 79 ASP cc_start: 0.8543 (p0) cc_final: 0.8254 (t70) REVERT: F 84 MET cc_start: 0.7851 (ttp) cc_final: 0.7521 (ttt) REVERT: F 193 ASP cc_start: 0.8870 (t70) cc_final: 0.8553 (p0) REVERT: F 291 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: F 508 MET cc_start: 0.3237 (ptp) cc_final: 0.2734 (ptp) REVERT: F 574 LEU cc_start: 0.8754 (tp) cc_final: 0.8354 (tp) outliers start: 55 outliers final: 39 residues processed: 210 average time/residue: 0.4295 time to fit residues: 155.6877 Evaluate side-chains 208 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 163 time to evaluate : 4.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 0.8980 chunk 404 optimal weight: 5.9990 chunk 368 optimal weight: 10.0000 chunk 393 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 308 optimal weight: 0.3980 chunk 120 optimal weight: 5.9990 chunk 355 optimal weight: 4.9990 chunk 372 optimal weight: 7.9990 chunk 392 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35460 Z= 0.231 Angle : 0.577 9.910 47946 Z= 0.266 Chirality : 0.044 0.153 5376 Planarity : 0.004 0.047 6300 Dihedral : 4.462 32.265 4920 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.28 % Allowed : 15.28 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 4386 helix: 0.38 (0.13), residues: 1848 sheet: -0.39 (0.20), residues: 696 loop : -0.80 (0.16), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 454 HIS 0.005 0.001 HIS E 183 PHE 0.017 0.001 PHE C 363 TYR 0.006 0.001 TYR A 517 ARG 0.008 0.000 ARG F 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 164 time to evaluate : 4.485 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8636 (pt0) cc_final: 0.8319 (pp30) REVERT: A 52 PHE cc_start: 0.8217 (m-10) cc_final: 0.7794 (m-80) REVERT: A 193 ASP cc_start: 0.9229 (t0) cc_final: 0.8942 (t70) REVERT: A 427 MET cc_start: 0.8428 (tpt) cc_final: 0.8058 (tpt) REVERT: A 449 MET cc_start: 0.8348 (tpp) cc_final: 0.7359 (tpp) REVERT: B 50 GLN cc_start: 0.8708 (pt0) cc_final: 0.8494 (pp30) REVERT: B 291 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: B 427 MET cc_start: 0.8214 (tpt) cc_final: 0.7691 (tpp) REVERT: B 550 MET cc_start: 0.8619 (mtm) cc_final: 0.8211 (ptp) REVERT: B 608 MET cc_start: 0.8639 (ttm) cc_final: 0.8150 (ttm) REVERT: C 50 GLN cc_start: 0.8699 (pt0) cc_final: 0.8417 (pp30) REVERT: C 52 PHE cc_start: 0.8182 (m-10) cc_final: 0.7923 (m-80) REVERT: C 79 ASP cc_start: 0.8543 (p0) cc_final: 0.8229 (t70) REVERT: C 193 ASP cc_start: 0.8941 (t70) cc_final: 0.8571 (p0) REVERT: C 291 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: C 574 LEU cc_start: 0.8735 (tp) cc_final: 0.8397 (tp) REVERT: C 740 MET cc_start: 0.8965 (mmm) cc_final: 0.8631 (mmm) REVERT: D 50 GLN cc_start: 0.8821 (pt0) cc_final: 0.8516 (pp30) REVERT: D 168 THR cc_start: 0.4985 (OUTLIER) cc_final: 0.4753 (m) REVERT: D 427 MET cc_start: 0.8419 (tpt) cc_final: 0.8014 (tpt) REVERT: D 449 MET cc_start: 0.8351 (tpp) cc_final: 0.7386 (tpp) REVERT: E 50 GLN cc_start: 0.8685 (pt0) cc_final: 0.8426 (pp30) REVERT: E 193 ASP cc_start: 0.9044 (t70) cc_final: 0.8775 (p0) REVERT: E 291 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: E 344 MET cc_start: 0.9080 (mtp) cc_final: 0.8749 (mtm) REVERT: E 427 MET cc_start: 0.8275 (tpt) cc_final: 0.7699 (tpp) REVERT: E 550 MET cc_start: 0.8614 (mtm) cc_final: 0.8252 (ptp) REVERT: E 598 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7813 (p0) REVERT: E 608 MET cc_start: 0.8666 (ttm) cc_final: 0.8127 (ttm) REVERT: F 50 GLN cc_start: 0.8698 (pt0) cc_final: 0.8477 (pp30) REVERT: F 79 ASP cc_start: 0.8544 (p0) cc_final: 0.8253 (t70) REVERT: F 84 MET cc_start: 0.7814 (ttp) cc_final: 0.7480 (ttt) REVERT: F 193 ASP cc_start: 0.8868 (t70) cc_final: 0.8564 (p0) REVERT: F 291 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: F 508 MET cc_start: 0.3447 (ptp) cc_final: 0.2854 (ptp) REVERT: F 574 LEU cc_start: 0.8761 (tp) cc_final: 0.8363 (tp) outliers start: 48 outliers final: 35 residues processed: 205 average time/residue: 0.4477 time to fit residues: 157.9079 Evaluate side-chains 202 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 5.9990 chunk 415 optimal weight: 0.5980 chunk 253 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 289 optimal weight: 7.9990 chunk 436 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 347 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35460 Z= 0.271 Angle : 0.596 10.021 47946 Z= 0.275 Chirality : 0.044 0.153 5376 Planarity : 0.004 0.053 6300 Dihedral : 4.573 35.507 4920 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.23 % Allowed : 15.44 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4386 helix: 0.37 (0.12), residues: 1854 sheet: -0.27 (0.20), residues: 684 loop : -0.79 (0.16), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 454 HIS 0.005 0.001 HIS E 183 PHE 0.020 0.001 PHE C 363 TYR 0.006 0.001 TYR B 517 ARG 0.009 0.000 ARG C 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 161 time to evaluate : 4.461 Fit side-chains revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8658 (pt0) cc_final: 0.8377 (pp30) REVERT: A 427 MET cc_start: 0.8446 (tpt) cc_final: 0.8079 (tpt) REVERT: A 449 MET cc_start: 0.8333 (tpp) cc_final: 0.7311 (tpp) REVERT: B 50 GLN cc_start: 0.8767 (pt0) cc_final: 0.8527 (pp30) REVERT: B 291 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: B 427 MET cc_start: 0.8235 (tpt) cc_final: 0.7723 (tpp) REVERT: B 550 MET cc_start: 0.8666 (mtm) cc_final: 0.8223 (ptp) REVERT: B 608 MET cc_start: 0.8635 (ttm) cc_final: 0.8142 (ttm) REVERT: C 50 GLN cc_start: 0.8692 (pt0) cc_final: 0.8397 (pp30) REVERT: C 52 PHE cc_start: 0.8079 (m-10) cc_final: 0.7790 (m-80) REVERT: C 79 ASP cc_start: 0.8623 (p0) cc_final: 0.8299 (t70) REVERT: C 193 ASP cc_start: 0.9000 (t70) cc_final: 0.8676 (p0) REVERT: C 291 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7439 (pm20) REVERT: C 574 LEU cc_start: 0.8736 (tp) cc_final: 0.8412 (tp) REVERT: C 740 MET cc_start: 0.8998 (mmm) cc_final: 0.8646 (tmm) REVERT: D 50 GLN cc_start: 0.8695 (pt0) cc_final: 0.8458 (pp30) REVERT: D 52 PHE cc_start: 0.7878 (m-10) cc_final: 0.7652 (m-80) REVERT: D 168 THR cc_start: 0.4970 (OUTLIER) cc_final: 0.4754 (m) REVERT: D 427 MET cc_start: 0.8414 (tpt) cc_final: 0.8023 (tpt) REVERT: D 449 MET cc_start: 0.8339 (tpp) cc_final: 0.7343 (tpp) REVERT: E 50 GLN cc_start: 0.8760 (pt0) cc_final: 0.8496 (pp30) REVERT: E 84 MET cc_start: 0.7415 (ttm) cc_final: 0.7081 (ttt) REVERT: E 193 ASP cc_start: 0.9063 (t70) cc_final: 0.8795 (p0) REVERT: E 291 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: E 427 MET cc_start: 0.8293 (tpt) cc_final: 0.7723 (tpp) REVERT: E 550 MET cc_start: 0.8671 (mtm) cc_final: 0.8195 (ptp) REVERT: E 598 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7791 (p0) REVERT: E 608 MET cc_start: 0.8669 (ttm) cc_final: 0.8096 (ttm) REVERT: F 50 GLN cc_start: 0.8725 (pt0) cc_final: 0.8507 (pp30) REVERT: F 84 MET cc_start: 0.7881 (ttp) cc_final: 0.7538 (ttt) REVERT: F 193 ASP cc_start: 0.8873 (t70) cc_final: 0.8604 (p0) REVERT: F 291 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: F 508 MET cc_start: 0.3560 (ptp) cc_final: 0.2952 (ptp) REVERT: F 574 LEU cc_start: 0.8773 (tp) cc_final: 0.8381 (tp) outliers start: 46 outliers final: 37 residues processed: 200 average time/residue: 0.4323 time to fit residues: 149.2964 Evaluate side-chains 200 residues out of total 3750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 157 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 509 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 509 THR Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 7.9990 chunk 370 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 320 optimal weight: 0.0970 chunk 51 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 348 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 357 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS C 401 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS F 398 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.078637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.054960 restraints weight = 97269.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.056862 restraints weight = 61800.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.058103 restraints weight = 47195.403| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 35460 Z= 0.158 Angle : 0.561 10.337 47946 Z= 0.256 Chirality : 0.043 0.153 5376 Planarity : 0.003 0.046 6300 Dihedral : 4.330 30.636 4920 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.04 % Allowed : 15.87 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4386 helix: 0.49 (0.13), residues: 1848 sheet: -0.21 (0.20), residues: 672 loop : -0.72 (0.16), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 454 HIS 0.006 0.001 HIS E 183 PHE 0.014 0.001 PHE C 363 TYR 0.007 0.001 TYR A 517 ARG 0.008 0.000 ARG C 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4939.48 seconds wall clock time: 92 minutes 48.52 seconds (5568.52 seconds total)