Starting phenix.real_space_refine on Wed Mar 20 01:16:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/03_2024/8ddw_27344.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/03_2024/8ddw_27344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/03_2024/8ddw_27344.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/03_2024/8ddw_27344.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/03_2024/8ddw_27344.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddw_27344/03_2024/8ddw_27344.pdb" } resolution = 4.7 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 175 5.16 5 C 16413 2.51 5 N 4530 2.21 5 O 4751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 351": "OE1" <-> "OE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25869 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5576 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 20, 'TRANS': 674} Chain breaks: 5 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5576 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 20, 'TRANS': 674} Chain breaks: 5 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5576 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 20, 'TRANS': 674} Chain breaks: 5 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 5765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5765 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 23, 'TRANS': 695} Chain breaks: 5 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 2598 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} bond proxies already assigned to first conformer: 2631 Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Time building chain proxies: 14.50, per 1000 atoms: 0.56 Number of scatterers: 25869 At special positions: 0 Unit cell: (145.8, 190.08, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 175 16.00 O 4751 8.00 N 4530 7.00 C 16413 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: 8.90 Conformation dependent library (CDL) restraints added in 5.0 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6134 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 14 sheets defined 55.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.674A pdb=" N LEU A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.930A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.802A pdb=" N HIS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 307 through 322 removed outlier: 4.320A pdb=" N LEU A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 322 " --> pdb=" O HIS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.700A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.648A pdb=" N LYS A 401 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.683A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.613A pdb=" N ILE A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.744A pdb=" N ASN A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 649 removed outlier: 4.100A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 4.006A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 Processing helix chain 'A' and resid 689 through 717 removed outlier: 3.589A pdb=" N GLN A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.527A pdb=" N LEU A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.789A pdb=" N SER A 733 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 752 through 761 removed outlier: 3.700A pdb=" N MET A 757 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 758 " --> pdb=" O CYS A 754 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 removed outlier: 3.568A pdb=" N TYR A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A1001 " --> pdb=" O GLY A 997 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A1002 " --> pdb=" O PRO A 998 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1003 " --> pdb=" O TYR A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1117 removed outlier: 3.608A pdb=" N THR A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1142 removed outlier: 4.668A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1215 Processing helix chain 'A' and resid 1215 through 1240 removed outlier: 3.965A pdb=" N ARG A1240 " --> pdb=" O GLU A1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.561A pdb=" N LEU B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 removed outlier: 4.101A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 4.002A pdb=" N SER B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.622A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.730A pdb=" N LYS B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 removed outlier: 3.966A pdb=" N LYS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.607A pdb=" N LEU B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.598A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 499 removed outlier: 3.753A pdb=" N VAL B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.658A pdb=" N ILE B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 636 through 648 removed outlier: 4.313A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.938A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 685 Processing helix chain 'B' and resid 689 through 717 removed outlier: 4.320A pdb=" N GLN B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 729 through 733 removed outlier: 4.163A pdb=" N SER B 733 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 745 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 752 through 762 removed outlier: 3.752A pdb=" N LEU B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 761 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1007 Processing helix chain 'B' and resid 1110 through 1117 Processing helix chain 'B' and resid 1118 through 1142 removed outlier: 4.520A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 removed outlier: 3.864A pdb=" N ARG B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.666A pdb=" N UNK F 5 " --> pdb=" O UNK F 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 175 removed outlier: 3.836A pdb=" N LEU C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 216 removed outlier: 3.738A pdb=" N VAL C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 244 removed outlier: 4.161A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 344 through 355 Processing helix chain 'C' and resid 369 through 379 removed outlier: 4.106A pdb=" N LYS C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 413 through 423 removed outlier: 4.230A pdb=" N LYS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 451 removed outlier: 3.752A pdb=" N LEU C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'C' and resid 468 through 476 removed outlier: 3.733A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 497 removed outlier: 3.767A pdb=" N GLN C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 556 through 569 Processing helix chain 'C' and resid 574 through 577 Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.776A pdb=" N ASN C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 649 removed outlier: 4.102A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.552A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 Processing helix chain 'C' and resid 689 through 717 Processing helix chain 'C' and resid 718 through 724 Processing helix chain 'C' and resid 729 through 733 removed outlier: 3.962A pdb=" N SER C 733 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 745 Processing helix chain 'C' and resid 746 through 751 Processing helix chain 'C' and resid 752 through 760 removed outlier: 4.322A pdb=" N LEU C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1007 removed outlier: 3.920A pdb=" N TYR C 999 " --> pdb=" O TYR C 995 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET C1001 " --> pdb=" O GLY C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1116 Processing helix chain 'C' and resid 1118 through 1142 removed outlier: 4.535A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1215 removed outlier: 3.609A pdb=" N SER C1215 " --> pdb=" O ARG C1211 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1240 removed outlier: 3.557A pdb=" N ARG C1240 " --> pdb=" O GLU C1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 removed outlier: 3.877A pdb=" N LEU D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 216 removed outlier: 4.177A pdb=" N PHE D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'D' and resid 308 through 322 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 365 through 368 removed outlier: 3.871A pdb=" N GLY D 368 " --> pdb=" O ASP D 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 368' Processing helix chain 'D' and resid 369 through 379 removed outlier: 4.237A pdb=" N LYS D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 removed outlier: 4.943A pdb=" N GLU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 451 removed outlier: 3.533A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 475 Processing helix chain 'D' and resid 486 through 499 Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 578 through 588 Processing helix chain 'D' and resid 596 through 601 removed outlier: 3.920A pdb=" N LEU D 600 " --> pdb=" O ALA D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 3.750A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 Processing helix chain 'D' and resid 663 through 685 removed outlier: 3.529A pdb=" N ASN D 685 " --> pdb=" O GLU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 717 removed outlier: 4.254A pdb=" N GLN D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 725 removed outlier: 3.873A pdb=" N LEU D 725 " --> pdb=" O ALA D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 745 Processing helix chain 'D' and resid 746 through 752 Processing helix chain 'D' and resid 752 through 761 removed outlier: 3.914A pdb=" N ASP D 761 " --> pdb=" O MET D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1005 removed outlier: 4.008A pdb=" N TYR D 999 " --> pdb=" O TYR D 995 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET D1001 " --> pdb=" O GLY D 997 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D1003 " --> pdb=" O TYR D 999 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D1005 " --> pdb=" O MET D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1117 Processing helix chain 'D' and resid 1118 through 1142 removed outlier: 4.890A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 removed outlier: 4.000A pdb=" N ARG D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 26 removed outlier: 3.814A pdb=" N GLN I 9 " --> pdb=" O ASP I 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN I 17 " --> pdb=" O GLN I 13 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 34 removed outlier: 3.642A pdb=" N ILE I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 29 through 34' Processing helix chain 'J' and resid 9 through 24 removed outlier: 3.652A pdb=" N ARG J 13 " --> pdb=" O ILE J 9 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET J 21 " --> pdb=" O GLU J 17 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN J 24 " --> pdb=" O LYS J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 39 removed outlier: 3.638A pdb=" N ALA J 35 " --> pdb=" O SER J 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 137 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 275 removed outlier: 4.046A pdb=" N VAL A 270 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 143 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 272 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 155 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE A 294 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N MET A 156 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU A 296 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 158 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP A 298 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 160 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR A 250 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE A 295 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY A 252 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA A 297 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA A 254 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE A 253 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR A 222 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 364 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL A 361 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE A 430 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 363 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 270 through 275 removed outlier: 3.818A pdb=" N VAL B 270 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 143 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 145 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 157 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE B 294 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET B 156 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU B 296 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 158 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP B 298 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 160 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL B 339 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS B 189 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N VAL B 362 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 336 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N CYS B 364 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 338 " --> pdb=" O CYS B 364 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 361 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE B 430 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 363 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 273 through 275 removed outlier: 8.553A pdb=" N TYR C 274 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU C 145 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 155 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE C 294 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N MET C 156 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C 296 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL C 158 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP C 298 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL C 160 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLY C 300 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASN C 299 " --> pdb=" O TRP C 256 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE C 251 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 253 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 222 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 185 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU C 337 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N VAL C 362 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA C 336 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N CYS C 364 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE C 338 " --> pdb=" O CYS C 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 133 through 137 removed outlier: 3.793A pdb=" N SER D 136 " --> pdb=" O UNK H 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 271 through 275 removed outlier: 8.094A pdb=" N ARG D 272 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR D 143 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR D 274 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU D 145 " --> pdb=" O TYR D 274 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 157 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 155 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE D 294 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N MET D 156 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU D 296 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL D 158 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP D 298 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL D 160 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE D 220 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 253 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR D 222 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL D 361 " --> pdb=" O THR D 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 46 through 50 removed outlier: 6.367A pdb=" N ILE I 338 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR I 50 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU I 336 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL I 327 " --> pdb=" O TRP I 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 58 through 63 removed outlier: 7.293A pdb=" N ALA I 73 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N MET I 61 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL I 71 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP I 63 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU I 69 " --> pdb=" O TRP I 63 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE I 80 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER I 74 " --> pdb=" O LYS I 78 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS I 78 " --> pdb=" O SER I 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS I 91 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP I 83 " --> pdb=" O LYS I 89 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS I 89 " --> pdb=" O ASP I 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 100 through 105 removed outlier: 3.835A pdb=" N GLY I 115 " --> pdb=" O THR I 102 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N CYS I 121 " --> pdb=" O GLU I 138 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU I 138 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE I 123 " --> pdb=" O SER I 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 146 through 151 removed outlier: 4.000A pdb=" N CYS I 148 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER I 161 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR I 165 " --> pdb=" O SER I 161 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU I 168 " --> pdb=" O THR I 178 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR I 178 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP I 170 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN I 176 " --> pdb=" O ASP I 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 187 through 192 removed outlier: 4.004A pdb=" N SER I 201 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS I 209 " --> pdb=" O SER I 201 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA I 203 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER I 207 " --> pdb=" O ALA I 203 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA I 208 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR I 221 " --> pdb=" O ALA I 208 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU I 210 " --> pdb=" O ARG I 219 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET I 217 " --> pdb=" O ASP I 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 231 through 234 removed outlier: 3.854A pdb=" N PHE I 241 " --> pdb=" O PHE I 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE I 253 " --> pdb=" O PHE I 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 273 through 277 Processing sheet with id=AB5, first strand: chain 'I' and resid 294 through 295 removed outlier: 4.045A pdb=" N CYS I 294 " --> pdb=" O LEU I 308 " (cutoff:3.500A) 1230 hydrogen bonds defined for protein. 3641 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: 8.39 Time building geometry restraints manager: 9.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8353 1.34 - 1.45: 3435 1.45 - 1.57: 14279 1.57 - 1.69: 0 1.69 - 1.81: 297 Bond restraints: 26364 Sorted by residual: bond pdb=" CA PRO D 629 " pdb=" C PRO D 629 " ideal model delta sigma weight residual 1.526 1.492 0.034 8.50e-03 1.38e+04 1.62e+01 bond pdb=" CA ASN D 632 " pdb=" C ASN D 632 " ideal model delta sigma weight residual 1.526 1.479 0.047 1.29e-02 6.01e+03 1.33e+01 bond pdb=" N HIS D 633 " pdb=" CA HIS D 633 " ideal model delta sigma weight residual 1.458 1.419 0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N PHE D 634 " pdb=" CA PHE D 634 " ideal model delta sigma weight residual 1.456 1.419 0.036 1.13e-02 7.83e+03 1.04e+01 bond pdb=" CA HIS D 633 " pdb=" C HIS D 633 " ideal model delta sigma weight residual 1.520 1.487 0.034 1.17e-02 7.31e+03 8.31e+00 ... (remaining 26359 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.26: 608 106.26 - 113.19: 14518 113.19 - 120.13: 8817 120.13 - 127.06: 11350 127.06 - 133.99: 291 Bond angle restraints: 35584 Sorted by residual: angle pdb=" N ASN D 632 " pdb=" CA ASN D 632 " pdb=" C ASN D 632 " ideal model delta sigma weight residual 111.54 99.89 11.65 1.36e+00 5.41e-01 7.34e+01 angle pdb=" N GLU D 630 " pdb=" CA GLU D 630 " pdb=" C GLU D 630 " ideal model delta sigma weight residual 110.80 100.69 10.11 2.13e+00 2.20e-01 2.25e+01 angle pdb=" C ASN D 632 " pdb=" N HIS D 633 " pdb=" CA HIS D 633 " ideal model delta sigma weight residual 122.77 117.10 5.67 1.41e+00 5.03e-01 1.62e+01 angle pdb=" N PRO A 357 " pdb=" CA PRO A 357 " pdb=" C PRO A 357 " ideal model delta sigma weight residual 110.70 105.88 4.82 1.22e+00 6.72e-01 1.56e+01 angle pdb=" C ASP I 195 " pdb=" N THR I 196 " pdb=" CA THR I 196 " ideal model delta sigma weight residual 121.54 128.08 -6.54 1.91e+00 2.74e-01 1.17e+01 ... (remaining 35579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 14369 17.45 - 34.89: 1084 34.89 - 52.34: 315 52.34 - 69.79: 90 69.79 - 87.23: 18 Dihedral angle restraints: 15876 sinusoidal: 6409 harmonic: 9467 Sorted by residual: dihedral pdb=" CA PRO J 55 " pdb=" C PRO J 55 " pdb=" N ALA J 56 " pdb=" CA ALA J 56 " ideal model delta harmonic sigma weight residual 180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE I 151 " pdb=" C PHE I 151 " pdb=" N LEU I 152 " pdb=" CA LEU I 152 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 15873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3378 0.054 - 0.107: 553 0.107 - 0.161: 60 0.161 - 0.214: 1 0.214 - 0.268: 1 Chirality restraints: 3993 Sorted by residual: chirality pdb=" CA HIS D 633 " pdb=" N HIS D 633 " pdb=" C HIS D 633 " pdb=" CB HIS D 633 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE D 631 " pdb=" N ILE D 631 " pdb=" C ILE D 631 " pdb=" CB ILE D 631 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE I 120 " pdb=" N ILE I 120 " pdb=" C ILE I 120 " pdb=" CB ILE I 120 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 3990 not shown) Planarity restraints: 4551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 634 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO D 635 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO D 635 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO D 635 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 357 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 358 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 59 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO J 60 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO J 60 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 60 " -0.027 5.00e-02 4.00e+02 ... (remaining 4548 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1339 2.72 - 3.27: 27630 3.27 - 3.81: 44530 3.81 - 4.36: 51123 4.36 - 4.90: 83189 Nonbonded interactions: 207811 Sorted by model distance: nonbonded pdb=" OG SER C 556 " pdb=" OD1 ASP C 559 " model vdw 2.179 2.440 nonbonded pdb=" OH TYR I 264 " pdb=" O ALA I 299 " model vdw 2.185 2.440 nonbonded pdb=" OE2 GLU C 565 " pdb=" OG1 THR C 577 " model vdw 2.187 2.440 nonbonded pdb=" O ILE A 248 " pdb=" OG SER A 292 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR C 402 " pdb=" OE1 GLN C 409 " model vdw 2.216 2.440 ... (remaining 207806 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' and (resid 129 through 588 or resid 632 through 1009 or resid 1109 th \ rough 1243)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.770 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 65.790 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 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 0.048 26364 Z= 0.179 Angle : 0.529 11.653 35584 Z= 0.298 Chirality : 0.038 0.268 3993 Planarity : 0.004 0.106 4551 Dihedral : 14.465 87.234 9742 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 8.35 % Allowed : 10.33 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.15), residues: 3148 helix: 1.52 (0.13), residues: 1602 sheet: -0.66 (0.28), residues: 359 loop : -1.67 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 483 HIS 0.008 0.001 HIS D 633 PHE 0.013 0.001 PHE B 376 TYR 0.016 0.001 TYR A 380 ARG 0.003 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 867 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 HIS cc_start: 0.6300 (m-70) cc_final: 0.5568 (m-70) REVERT: A 156 MET cc_start: 0.7836 (mmt) cc_final: 0.7514 (mtp) REVERT: A 275 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.6105 (tp40) REVERT: A 296 LEU cc_start: -0.1325 (OUTLIER) cc_final: -0.2171 (mt) REVERT: A 350 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8684 (tp) REVERT: A 407 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7893 (mmp-170) REVERT: A 417 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.4204 (pp) REVERT: A 471 ILE cc_start: 0.9024 (mm) cc_final: 0.8805 (pt) REVERT: A 489 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8391 (mt-10) REVERT: A 516 ARG cc_start: 0.8952 (mtp-110) cc_final: 0.8614 (mmp-170) REVERT: A 559 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: A 633 HIS cc_start: 0.5343 (OUTLIER) cc_final: 0.4928 (t70) REVERT: A 662 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 704 GLN cc_start: 0.9013 (tp40) cc_final: 0.8675 (tp40) REVERT: A 708 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8451 (mt-10) REVERT: A 709 LEU cc_start: 0.8785 (tp) cc_final: 0.8511 (tp) REVERT: A 712 GLN cc_start: 0.8107 (tp40) cc_final: 0.6447 (tm-30) REVERT: A 722 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8624 (mmm) REVERT: A 729 LEU cc_start: 0.9306 (mt) cc_final: 0.8962 (mt) REVERT: A 732 TRP cc_start: 0.6206 (m100) cc_final: 0.4591 (m100) REVERT: A 1186 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.7996 (p) REVERT: A 1194 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8253 (m-70) REVERT: A 1204 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8720 (t80) REVERT: A 1230 MET cc_start: 0.7838 (ttm) cc_final: 0.7242 (ttm) REVERT: B 156 MET cc_start: 0.7783 (mmt) cc_final: 0.7386 (mmp) REVERT: B 171 HIS cc_start: 0.6503 (t-90) cc_final: 0.6268 (t70) REVERT: B 245 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6982 (mmm160) REVERT: B 275 GLN cc_start: -0.1222 (OUTLIER) cc_final: -0.1436 (tp-100) REVERT: B 291 HIS cc_start: 0.4914 (m-70) cc_final: 0.4200 (m-70) REVERT: B 350 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7494 (mp) REVERT: B 412 HIS cc_start: 0.2917 (OUTLIER) cc_final: 0.2547 (t70) REVERT: B 440 ILE cc_start: 0.8316 (mm) cc_final: 0.7994 (mp) REVERT: B 445 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6587 (mm) REVERT: B 450 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7864 (mmpt) REVERT: B 469 VAL cc_start: 0.6950 (p) cc_final: 0.6719 (p) REVERT: B 471 ILE cc_start: 0.9262 (mm) cc_final: 0.9018 (pt) REVERT: B 492 MET cc_start: 0.7732 (tpp) cc_final: 0.6600 (tpp) REVERT: B 501 VAL cc_start: 0.7217 (t) cc_final: 0.6657 (t) REVERT: B 580 ARG cc_start: 0.6804 (ttt90) cc_final: 0.6173 (tpt170) REVERT: B 636 PHE cc_start: 0.7251 (m-80) cc_final: 0.6750 (m-10) REVERT: B 656 PHE cc_start: 0.8156 (t80) cc_final: 0.7609 (t80) REVERT: B 657 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: B 670 VAL cc_start: 0.8444 (t) cc_final: 0.8096 (t) REVERT: B 694 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7986 (tm-30) REVERT: B 720 LEU cc_start: 0.8819 (mt) cc_final: 0.8267 (tt) REVERT: B 722 MET cc_start: 0.8797 (mtm) cc_final: 0.8292 (mpp) REVERT: B 746 HIS cc_start: 0.7598 (t-90) cc_final: 0.6731 (t70) REVERT: B 748 ASP cc_start: 0.8915 (m-30) cc_final: 0.8631 (m-30) REVERT: B 752 HIS cc_start: 0.7021 (t-90) cc_final: 0.6807 (t-90) REVERT: B 754 CYS cc_start: 0.9161 (t) cc_final: 0.8869 (t) REVERT: B 756 GLN cc_start: 0.9268 (mm-40) cc_final: 0.9049 (mt0) REVERT: B 1182 LYS cc_start: 0.7533 (mttp) cc_final: 0.7133 (mmmm) REVERT: B 1190 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8438 (mt) REVERT: B 1202 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 1213 ASN cc_start: 0.8536 (m-40) cc_final: 0.8260 (m-40) REVERT: B 1226 ARG cc_start: 0.8520 (mtt180) cc_final: 0.8254 (mtm-85) REVERT: C 158 VAL cc_start: 0.9360 (t) cc_final: 0.9150 (m) REVERT: C 186 ILE cc_start: 0.8059 (mt) cc_final: 0.7749 (mp) REVERT: C 248 ILE cc_start: 0.6914 (mt) cc_final: 0.6616 (tp) REVERT: C 291 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6534 (m170) REVERT: C 293 HIS cc_start: 0.7615 (m90) cc_final: 0.7170 (m-70) REVERT: C 294 PHE cc_start: 0.5479 (OUTLIER) cc_final: 0.4926 (t80) REVERT: C 345 VAL cc_start: 0.8183 (p) cc_final: 0.7916 (m) REVERT: C 414 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6476 (m-80) REVERT: C 479 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7350 (m-10) REVERT: C 494 ASP cc_start: 0.7984 (m-30) cc_final: 0.7403 (m-30) REVERT: C 499 ASP cc_start: 0.6693 (t0) cc_final: 0.5988 (t0) REVERT: C 559 ASP cc_start: 0.4183 (OUTLIER) cc_final: 0.3957 (p0) REVERT: C 646 VAL cc_start: 0.7936 (t) cc_final: 0.7547 (p) REVERT: C 672 CYS cc_start: 0.8928 (t) cc_final: 0.8612 (t) REVERT: C 681 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8016 (mm-30) REVERT: D 131 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7399 (mmmt) REVERT: D 179 LEU cc_start: 0.7711 (mt) cc_final: 0.7282 (mt) REVERT: D 181 LEU cc_start: 0.9057 (mt) cc_final: 0.8604 (pt) REVERT: D 261 ASN cc_start: 0.5803 (OUTLIER) cc_final: 0.5281 (m-40) REVERT: D 277 MET cc_start: 0.5539 (tmm) cc_final: 0.5267 (pmm) REVERT: D 278 SER cc_start: 0.4649 (t) cc_final: 0.3809 (m) REVERT: D 417 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5158 (mt) REVERT: D 431 ARG cc_start: 0.5347 (ptp-110) cc_final: 0.5031 (mtt180) REVERT: D 459 GLN cc_start: 0.8817 (mt0) cc_final: 0.8537 (mm-40) REVERT: D 469 VAL cc_start: 0.8465 (p) cc_final: 0.8206 (p) REVERT: D 474 SER cc_start: 0.8548 (m) cc_final: 0.8342 (p) REVERT: D 506 LEU cc_start: 0.8903 (tp) cc_final: 0.8356 (tp) REVERT: D 526 LEU cc_start: 0.8802 (mt) cc_final: 0.8463 (mt) REVERT: D 542 ARG cc_start: 0.8359 (ttp-110) cc_final: 0.7668 (ttp-110) REVERT: D 564 ILE cc_start: 0.9444 (mt) cc_final: 0.9146 (mt) REVERT: D 567 LEU cc_start: 0.8931 (mt) cc_final: 0.8470 (mt) REVERT: D 642 MET cc_start: 0.8436 (ttt) cc_final: 0.7746 (mtp) REVERT: D 689 ASP cc_start: 0.8185 (m-30) cc_final: 0.7856 (m-30) REVERT: D 690 ASP cc_start: 0.8438 (p0) cc_final: 0.8154 (p0) REVERT: D 711 ASP cc_start: 0.9244 (t0) cc_final: 0.8918 (p0) REVERT: D 724 LEU cc_start: 0.9455 (tp) cc_final: 0.9165 (tp) REVERT: D 727 TYR cc_start: 0.8188 (p90) cc_final: 0.7602 (t80) REVERT: D 740 LEU cc_start: 0.9147 (mt) cc_final: 0.8930 (mm) REVERT: D 1130 LYS cc_start: 0.8087 (mttt) cc_final: 0.7800 (mttt) REVERT: D 1195 ASP cc_start: 0.9179 (m-30) cc_final: 0.8955 (m-30) REVERT: D 1202 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: D 1235 GLU cc_start: 0.8873 (tp30) cc_final: 0.8671 (mm-30) REVERT: I 101 MET cc_start: 0.8686 (mmm) cc_final: 0.8200 (mmm) REVERT: I 145 TYR cc_start: 0.3088 (p90) cc_final: 0.2793 (p90) REVERT: I 178 THR cc_start: -0.4195 (OUTLIER) cc_final: -0.4584 (t) REVERT: I 187 VAL cc_start: 0.6235 (OUTLIER) cc_final: 0.5512 (p) REVERT: I 217 MET cc_start: 0.2206 (tpt) cc_final: 0.1814 (tmm) REVERT: I 232 ILE cc_start: 0.5496 (tt) cc_final: 0.4785 (mt) outliers start: 233 outliers final: 49 residues processed: 1037 average time/residue: 0.3966 time to fit residues: 627.8254 Evaluate side-chains 625 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 544 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 129 optimal weight: 30.0000 chunk 250 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 186 optimal weight: 0.0980 chunk 290 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN A 314 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 412 HIS A 490 GLN A 510 ASN ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN A 696 ASN A 697 HIS A 739 GLN A1116 ASN B 134 GLN B 198 GLN ** B 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1116 ASN ** B1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS C 232 HIS ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS C 330 GLN C 378 HIS C 539 HIS C 696 ASN ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN C 719 GLN C 746 HIS C1126 ASN D 232 HIS D 299 ASN D 411 GLN D 535 ASN D 548 ASN ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 ASN ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 734 ASN D 739 GLN D1115 ASN I 44 GLN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26364 Z= 0.259 Angle : 0.696 9.551 35584 Z= 0.367 Chirality : 0.044 0.194 3993 Planarity : 0.005 0.070 4551 Dihedral : 4.941 27.297 3504 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 0.22 % Allowed : 4.70 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.15), residues: 3148 helix: 1.09 (0.13), residues: 1665 sheet: -0.55 (0.28), residues: 366 loop : -1.78 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 219 HIS 0.019 0.002 HIS I 142 PHE 0.042 0.002 PHE B 376 TYR 0.017 0.002 TYR C 576 ARG 0.011 0.001 ARG C 700 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 640 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8545 (tp) cc_final: 0.8040 (pt) REVERT: A 156 MET cc_start: 0.8090 (mmt) cc_final: 0.7554 (mmt) REVERT: A 197 LEU cc_start: 0.7462 (mt) cc_final: 0.7244 (mt) REVERT: A 251 ILE cc_start: 0.8335 (mt) cc_final: 0.8021 (mt) REVERT: A 321 LEU cc_start: 0.8490 (tp) cc_final: 0.8152 (mt) REVERT: A 363 VAL cc_start: 0.9141 (t) cc_final: 0.8933 (p) REVERT: A 418 MET cc_start: 0.7839 (tpt) cc_final: 0.7606 (tpt) REVERT: A 489 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8469 (mt-10) REVERT: A 492 MET cc_start: 0.8780 (tpp) cc_final: 0.8354 (tpp) REVERT: A 516 ARG cc_start: 0.8930 (tpp80) cc_final: 0.8694 (mmp-170) REVERT: A 524 GLU cc_start: 0.8740 (mt-10) cc_final: 0.7751 (mm-30) REVERT: A 691 ILE cc_start: 0.7679 (mt) cc_final: 0.7153 (mt) REVERT: A 708 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8152 (pt0) REVERT: A 712 GLN cc_start: 0.6999 (tp40) cc_final: 0.6627 (tm-30) REVERT: A 728 GLU cc_start: 0.7981 (tt0) cc_final: 0.6938 (pm20) REVERT: A 729 LEU cc_start: 0.9087 (mt) cc_final: 0.8744 (mp) REVERT: A 1206 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7769 (mtm-85) REVERT: A 1218 GLU cc_start: 0.8091 (tp30) cc_final: 0.7638 (tp30) REVERT: B 144 ILE cc_start: 0.7929 (mm) cc_final: 0.7268 (tp) REVERT: B 418 MET cc_start: 0.3898 (mmm) cc_final: 0.3598 (tmm) REVERT: B 492 MET cc_start: 0.8023 (tpp) cc_final: 0.7118 (tpp) REVERT: B 545 LYS cc_start: 0.8936 (tptm) cc_final: 0.8348 (ptmt) REVERT: B 568 MET cc_start: 0.5459 (mtm) cc_final: 0.5098 (mtm) REVERT: B 580 ARG cc_start: 0.7189 (ttt90) cc_final: 0.6598 (tpt170) REVERT: B 752 HIS cc_start: 0.6903 (t-90) cc_final: 0.6020 (t-90) REVERT: B 754 CYS cc_start: 0.8842 (t) cc_final: 0.8626 (t) REVERT: B 756 GLN cc_start: 0.9317 (mm-40) cc_final: 0.9032 (tm-30) REVERT: B 1179 TYR cc_start: 0.8890 (t80) cc_final: 0.8134 (t80) REVERT: B 1182 LYS cc_start: 0.7322 (mttp) cc_final: 0.6986 (mmmm) REVERT: B 1202 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8456 (tm-30) REVERT: C 158 VAL cc_start: 0.9351 (t) cc_final: 0.9118 (p) REVERT: C 248 ILE cc_start: 0.7744 (mt) cc_final: 0.7445 (tp) REVERT: C 290 MET cc_start: 0.7245 (mmp) cc_final: 0.7039 (mmp) REVERT: C 317 LYS cc_start: 0.7882 (mttm) cc_final: 0.7502 (tptt) REVERT: C 492 MET cc_start: 0.4654 (ttm) cc_final: 0.4358 (ptm) REVERT: C 494 ASP cc_start: 0.8127 (m-30) cc_final: 0.7585 (m-30) REVERT: C 672 CYS cc_start: 0.8968 (t) cc_final: 0.8407 (t) REVERT: C 675 CYS cc_start: 0.8183 (m) cc_final: 0.7682 (m) REVERT: C 694 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8565 (tt0) REVERT: C 708 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7933 (mt-10) REVERT: C 728 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6770 (pm20) REVERT: C 730 LYS cc_start: 0.7973 (tptt) cc_final: 0.7721 (ttmm) REVERT: C 742 VAL cc_start: 0.8750 (t) cc_final: 0.8472 (t) REVERT: C 757 MET cc_start: 0.8553 (tmm) cc_final: 0.8137 (tmm) REVERT: C 1185 ILE cc_start: 0.6723 (tp) cc_final: 0.6398 (tp) REVERT: C 1230 MET cc_start: 0.8890 (mtp) cc_final: 0.8658 (mtm) REVERT: C 1234 LEU cc_start: 0.8680 (tt) cc_final: 0.8346 (tp) REVERT: D 156 MET cc_start: 0.8043 (mmt) cc_final: 0.7356 (mpp) REVERT: D 181 LEU cc_start: 0.9389 (mt) cc_final: 0.8887 (pt) REVERT: D 278 SER cc_start: 0.3927 (t) cc_final: 0.3671 (m) REVERT: D 290 MET cc_start: 0.8350 (mmm) cc_final: 0.7831 (mmm) REVERT: D 327 ARG cc_start: 0.6427 (mmp-170) cc_final: 0.6200 (mtm-85) REVERT: D 418 MET cc_start: 0.6091 (mmm) cc_final: 0.5858 (mmm) REVERT: D 476 ILE cc_start: 0.7910 (tp) cc_final: 0.7150 (tp) REVERT: D 494 ASP cc_start: 0.9005 (m-30) cc_final: 0.8726 (m-30) REVERT: D 540 LEU cc_start: 0.8718 (mt) cc_final: 0.8456 (mt) REVERT: D 641 LEU cc_start: 0.8809 (mm) cc_final: 0.8519 (mt) REVERT: D 642 MET cc_start: 0.8902 (ttt) cc_final: 0.8537 (tmm) REVERT: D 646 VAL cc_start: 0.8953 (t) cc_final: 0.8459 (p) REVERT: D 689 ASP cc_start: 0.8539 (m-30) cc_final: 0.8241 (t0) REVERT: D 711 ASP cc_start: 0.9240 (t0) cc_final: 0.8893 (p0) REVERT: D 720 LEU cc_start: 0.8204 (mt) cc_final: 0.7842 (tp) REVERT: D 722 MET cc_start: 0.7338 (ttm) cc_final: 0.6812 (ttm) REVERT: D 727 TYR cc_start: 0.8074 (p90) cc_final: 0.7672 (t80) REVERT: D 1127 GLN cc_start: 0.8385 (tt0) cc_final: 0.8145 (tt0) REVERT: D 1129 TRP cc_start: 0.8356 (t60) cc_final: 0.8126 (t60) REVERT: D 1130 LYS cc_start: 0.8266 (mttt) cc_final: 0.7985 (mttt) REVERT: D 1199 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8247 (pp30) REVERT: D 1202 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7968 (tm-30) REVERT: I 101 MET cc_start: 0.8397 (mmm) cc_final: 0.8123 (mmt) REVERT: I 188 MET cc_start: 0.7489 (mmp) cc_final: 0.6532 (mpp) REVERT: I 217 MET cc_start: 0.1398 (tpt) cc_final: 0.0728 (ttt) REVERT: I 312 ASP cc_start: 0.7734 (p0) cc_final: 0.7442 (p0) outliers start: 6 outliers final: 3 residues processed: 643 average time/residue: 0.3830 time to fit residues: 384.3924 Evaluate side-chains 465 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 461 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 241 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 291 optimal weight: 0.9980 chunk 314 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 233 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 HIS ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS A 639 HIS A1115 ASN A1199 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN B 696 ASN ** B 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 GLN C 151 HIS ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 232 HIS C 240 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 GLN C 660 HIS ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 HIS C1135 GLN C1213 ASN D 378 HIS D 459 GLN D 539 HIS ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26364 Z= 0.224 Angle : 0.614 8.572 35584 Z= 0.323 Chirality : 0.041 0.189 3993 Planarity : 0.004 0.052 4551 Dihedral : 4.664 27.147 3504 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 0.14 % Allowed : 4.66 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.15), residues: 3148 helix: 1.18 (0.13), residues: 1676 sheet: -0.35 (0.28), residues: 353 loop : -1.75 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP I 332 HIS 0.011 0.001 HIS C 639 PHE 0.023 0.002 PHE C 636 TYR 0.015 0.002 TYR I 105 ARG 0.015 0.001 ARG C 700 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 594 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8509 (tp) cc_final: 0.8111 (pt) REVERT: A 181 LEU cc_start: 0.7505 (mt) cc_final: 0.6530 (pt) REVERT: A 378 HIS cc_start: 0.7978 (t-90) cc_final: 0.7573 (t70) REVERT: A 421 MET cc_start: 0.7980 (mmp) cc_final: 0.7549 (mmp) REVERT: A 492 MET cc_start: 0.8889 (tpp) cc_final: 0.8546 (tpp) REVERT: A 516 ARG cc_start: 0.8915 (tpp80) cc_final: 0.8646 (mmp-170) REVERT: A 687 MET cc_start: 0.8117 (mmp) cc_final: 0.7700 (mmm) REVERT: A 704 GLN cc_start: 0.8964 (tp40) cc_final: 0.8398 (tp40) REVERT: A 708 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8402 (mt-10) REVERT: A 728 GLU cc_start: 0.7411 (tt0) cc_final: 0.6743 (pm20) REVERT: A 729 LEU cc_start: 0.9046 (mt) cc_final: 0.8764 (mp) REVERT: A 1218 GLU cc_start: 0.8079 (tp30) cc_final: 0.7679 (tt0) REVERT: B 144 ILE cc_start: 0.8300 (mm) cc_final: 0.7782 (tp) REVERT: B 193 GLN cc_start: 0.8593 (tp40) cc_final: 0.7927 (tm-30) REVERT: B 492 MET cc_start: 0.8196 (tpp) cc_final: 0.7363 (tpp) REVERT: B 523 LEU cc_start: 0.9058 (mt) cc_final: 0.8797 (mt) REVERT: B 568 MET cc_start: 0.6065 (mtm) cc_final: 0.5219 (mtm) REVERT: B 580 ARG cc_start: 0.7348 (ttt90) cc_final: 0.6775 (tpt170) REVERT: B 688 VAL cc_start: 0.8892 (t) cc_final: 0.8496 (t) REVERT: B 702 PHE cc_start: 0.8416 (m-80) cc_final: 0.8117 (m-80) REVERT: B 720 LEU cc_start: 0.8989 (mt) cc_final: 0.8485 (tp) REVERT: B 1179 TYR cc_start: 0.8845 (t80) cc_final: 0.7989 (t80) REVERT: B 1202 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8597 (tm-30) REVERT: B 1203 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8898 (tm-30) REVERT: B 1230 MET cc_start: 0.8013 (mtp) cc_final: 0.7717 (tpp) REVERT: C 183 LYS cc_start: 0.6983 (mttt) cc_final: 0.6307 (mmtt) REVERT: C 248 ILE cc_start: 0.7875 (mt) cc_final: 0.7654 (tp) REVERT: C 492 MET cc_start: 0.5643 (ttm) cc_final: 0.5139 (ptp) REVERT: C 526 LEU cc_start: 0.8689 (mt) cc_final: 0.8479 (mt) REVERT: C 672 CYS cc_start: 0.9221 (t) cc_final: 0.8833 (t) REVERT: C 694 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8597 (tt0) REVERT: C 728 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6980 (pm20) REVERT: C 730 LYS cc_start: 0.8274 (tptt) cc_final: 0.7975 (ttmm) REVERT: C 742 VAL cc_start: 0.8959 (t) cc_final: 0.8660 (t) REVERT: C 757 MET cc_start: 0.8707 (tmm) cc_final: 0.8361 (tmm) REVERT: D 156 MET cc_start: 0.7956 (mmt) cc_final: 0.7603 (mpp) REVERT: D 173 MET cc_start: 0.9047 (mtm) cc_final: 0.8839 (mtp) REVERT: D 181 LEU cc_start: 0.9383 (mt) cc_final: 0.8913 (pt) REVERT: D 290 MET cc_start: 0.8325 (mmm) cc_final: 0.7887 (mmm) REVERT: D 462 LEU cc_start: 0.9250 (mt) cc_final: 0.8871 (mt) REVERT: D 494 ASP cc_start: 0.9058 (m-30) cc_final: 0.8807 (t0) REVERT: D 595 LYS cc_start: 0.8654 (pptt) cc_final: 0.8410 (tmmt) REVERT: D 641 LEU cc_start: 0.8893 (mm) cc_final: 0.8610 (mt) REVERT: D 642 MET cc_start: 0.8993 (ttt) cc_final: 0.8770 (tmm) REVERT: D 646 VAL cc_start: 0.9020 (t) cc_final: 0.8689 (p) REVERT: D 727 TYR cc_start: 0.8166 (p90) cc_final: 0.7781 (t80) REVERT: D 729 LEU cc_start: 0.9611 (mt) cc_final: 0.9215 (mt) REVERT: D 757 MET cc_start: 0.8386 (ptm) cc_final: 0.8100 (ptt) REVERT: D 1129 TRP cc_start: 0.8340 (t60) cc_final: 0.8066 (t60) REVERT: D 1130 LYS cc_start: 0.8301 (mttt) cc_final: 0.8061 (mttt) REVERT: D 1199 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8514 (pp30) REVERT: D 1232 MET cc_start: 0.8676 (mtp) cc_final: 0.7995 (mtp) REVERT: I 61 MET cc_start: 0.4627 (ptm) cc_final: 0.4390 (ptm) REVERT: I 110 ASN cc_start: 0.6902 (m-40) cc_final: 0.6217 (m-40) REVERT: I 111 TYR cc_start: 0.7790 (m-80) cc_final: 0.7558 (m-80) REVERT: I 186 ASP cc_start: 0.9340 (m-30) cc_final: 0.9084 (t0) REVERT: I 188 MET cc_start: 0.7416 (mmp) cc_final: 0.6869 (mpp) REVERT: I 217 MET cc_start: 0.1855 (tpt) cc_final: 0.1340 (ttt) REVERT: I 292 PHE cc_start: 0.6652 (m-80) cc_final: 0.6309 (m-10) REVERT: I 293 ASN cc_start: 0.8265 (m-40) cc_final: 0.7412 (p0) REVERT: I 312 ASP cc_start: 0.7957 (p0) cc_final: 0.6741 (t70) outliers start: 4 outliers final: 0 residues processed: 597 average time/residue: 0.3834 time to fit residues: 354.7576 Evaluate side-chains 449 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 448 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 287 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 309 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN A 704 GLN ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN B 318 HIS B 330 GLN B 378 HIS ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 HIS ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS C 178 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 HIS ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN C1135 GLN C1199 GLN C1213 ASN C1229 ASN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 734 ASN ** I 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 GLN I 225 HIS I 268 ASN ** J 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 1.0472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 26364 Z= 0.526 Angle : 1.115 13.563 35584 Z= 0.586 Chirality : 0.056 0.314 3993 Planarity : 0.008 0.078 4551 Dihedral : 6.898 42.078 3504 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 33.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.65 % Favored : 91.32 % Rotamer: Outliers : 0.47 % Allowed : 8.25 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.03 % 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: -1.95 (0.14), residues: 3148 helix: -0.62 (0.12), residues: 1645 sheet: -1.14 (0.30), residues: 302 loop : -2.18 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP B 219 HIS 0.024 0.004 HIS D 639 PHE 0.047 0.004 PHE C 221 TYR 0.068 0.004 TYR B 527 ARG 0.023 0.002 ARG C 700 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 516 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8995 (mt) cc_final: 0.8206 (pt) REVERT: A 237 LEU cc_start: 0.9444 (mt) cc_final: 0.9187 (mp) REVERT: A 256 TRP cc_start: 0.5738 (OUTLIER) cc_final: 0.4854 (t-100) REVERT: A 378 HIS cc_start: 0.7413 (t-90) cc_final: 0.7004 (t70) REVERT: A 418 MET cc_start: 0.7986 (tpt) cc_final: 0.7430 (tpt) REVERT: A 419 GLU cc_start: 0.8577 (pt0) cc_final: 0.8305 (pt0) REVERT: A 427 ILE cc_start: 0.7635 (mt) cc_final: 0.7382 (mt) REVERT: A 467 ASN cc_start: 0.8963 (t0) cc_final: 0.8742 (t0) REVERT: A 502 ASP cc_start: 0.9289 (m-30) cc_final: 0.9065 (p0) REVERT: A 525 GLU cc_start: 0.8692 (mp0) cc_final: 0.8365 (mp0) REVERT: A 727 TYR cc_start: 0.8766 (p90) cc_final: 0.8193 (p90) REVERT: A 728 GLU cc_start: 0.8410 (tt0) cc_final: 0.7967 (pm20) REVERT: A 1195 ASP cc_start: 0.8901 (t0) cc_final: 0.8680 (t0) REVERT: A 1230 MET cc_start: 0.8343 (ttm) cc_final: 0.8118 (ttm) REVERT: A 1232 MET cc_start: 0.9094 (mmp) cc_final: 0.8854 (mmp) REVERT: B 376 PHE cc_start: 0.8191 (m-80) cc_final: 0.7740 (m-80) REVERT: B 407 ARG cc_start: 0.8896 (ttp-170) cc_final: 0.8265 (mpt180) REVERT: B 418 MET cc_start: 0.6729 (tmm) cc_final: 0.6200 (tpp) REVERT: B 492 MET cc_start: 0.8623 (tpp) cc_final: 0.8370 (tpp) REVERT: B 523 LEU cc_start: 0.9082 (mt) cc_final: 0.8801 (mt) REVERT: B 585 TYR cc_start: 0.8470 (t80) cc_final: 0.8155 (t80) REVERT: B 711 ASP cc_start: 0.8703 (m-30) cc_final: 0.8302 (m-30) REVERT: B 756 GLN cc_start: 0.9367 (mm-40) cc_final: 0.9051 (tm-30) REVERT: B 1138 MET cc_start: 0.5319 (mmm) cc_final: 0.4933 (mmm) REVERT: B 1203 GLU cc_start: 0.9520 (tm-30) cc_final: 0.9250 (tm-30) REVERT: B 1233 ARG cc_start: 0.8525 (ttm170) cc_final: 0.8277 (ttm170) REVERT: C 151 HIS cc_start: 0.3675 (t-90) cc_final: 0.3177 (t-170) REVERT: C 156 MET cc_start: 0.8231 (mtp) cc_final: 0.7569 (mtp) REVERT: C 214 MET cc_start: 0.9158 (mmm) cc_final: 0.8910 (mmp) REVERT: C 235 ASP cc_start: 0.9224 (m-30) cc_final: 0.8898 (t70) REVERT: C 277 MET cc_start: 0.6516 (pmm) cc_final: 0.5718 (pmm) REVERT: C 317 LYS cc_start: 0.8524 (mttm) cc_final: 0.8220 (tptt) REVERT: C 418 MET cc_start: 0.7023 (tmm) cc_final: 0.6745 (tmm) REVERT: C 421 MET cc_start: 0.3618 (mmm) cc_final: 0.3268 (mmt) REVERT: C 513 SER cc_start: 0.8513 (t) cc_final: 0.8311 (m) REVERT: C 527 TYR cc_start: 0.7537 (m-80) cc_final: 0.7123 (m-80) REVERT: C 560 ILE cc_start: 0.9427 (mm) cc_final: 0.9164 (mm) REVERT: C 717 ASP cc_start: 0.9034 (t70) cc_final: 0.8714 (t70) REVERT: C 730 LYS cc_start: 0.8693 (tptt) cc_final: 0.8446 (ttmm) REVERT: C 731 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8861 (t0) REVERT: C 757 MET cc_start: 0.9116 (tmm) cc_final: 0.8649 (tmm) REVERT: C 1202 GLU cc_start: 0.8804 (tt0) cc_final: 0.8585 (mt-10) REVERT: C 1209 ASP cc_start: 0.8895 (m-30) cc_final: 0.8662 (m-30) REVERT: C 1230 MET cc_start: 0.8951 (mtp) cc_final: 0.8494 (mmm) REVERT: D 156 MET cc_start: 0.8529 (mmt) cc_final: 0.8280 (mpp) REVERT: D 181 LEU cc_start: 0.9494 (mt) cc_final: 0.9076 (pt) REVERT: D 441 ASP cc_start: 0.9148 (t70) cc_final: 0.8337 (t0) REVERT: D 518 LEU cc_start: 0.9460 (tp) cc_final: 0.9215 (tt) REVERT: D 538 TYR cc_start: 0.9119 (t80) cc_final: 0.8884 (t80) REVERT: D 597 LEU cc_start: 0.8196 (mm) cc_final: 0.7897 (mm) REVERT: D 632 ASN cc_start: 0.7436 (t0) cc_final: 0.6689 (t0) REVERT: D 646 VAL cc_start: 0.9262 (t) cc_final: 0.8969 (t) REVERT: D 730 LYS cc_start: 0.9429 (mmtt) cc_final: 0.8969 (mmmt) REVERT: D 1195 ASP cc_start: 0.9418 (m-30) cc_final: 0.9156 (m-30) REVERT: D 1199 GLN cc_start: 0.8823 (pm20) cc_final: 0.8288 (pp30) REVERT: I 61 MET cc_start: 0.6010 (ptm) cc_final: 0.5770 (ptm) REVERT: I 217 MET cc_start: 0.1391 (tpt) cc_final: 0.0563 (ttt) outliers start: 13 outliers final: 4 residues processed: 525 average time/residue: 0.3835 time to fit residues: 315.4938 Evaluate side-chains 374 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 368 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 257 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 263 optimal weight: 0.5980 chunk 213 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN A 548 ASN A1229 ASN B 171 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 696 ASN ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 HIS C 438 GLN ** C 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 698 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 HIS D 293 HIS ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN D1127 GLN I 62 HIS ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 268 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 1.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26364 Z= 0.214 Angle : 0.661 10.270 35584 Z= 0.348 Chirality : 0.043 0.204 3993 Planarity : 0.004 0.092 4551 Dihedral : 5.529 33.310 3504 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.10 % Rotamer: Outliers : 0.07 % Allowed : 3.01 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -0.81 (0.15), residues: 3148 helix: 0.55 (0.12), residues: 1668 sheet: -0.89 (0.28), residues: 356 loop : -2.04 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 177 HIS 0.013 0.001 HIS C 240 PHE 0.031 0.002 PHE C1184 TYR 0.024 0.002 TYR I 289 ARG 0.009 0.001 ARG C 700 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 553 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8862 (mt) cc_final: 0.8187 (pt) REVERT: A 198 GLN cc_start: 0.8689 (mp10) cc_final: 0.7692 (tm-30) REVERT: A 249 CYS cc_start: 0.7148 (t) cc_final: 0.6776 (t) REVERT: A 418 MET cc_start: 0.7903 (tpt) cc_final: 0.7325 (tpp) REVERT: A 419 GLU cc_start: 0.8511 (pt0) cc_final: 0.8247 (pt0) REVERT: A 473 ARG cc_start: 0.9518 (ttm-80) cc_final: 0.9242 (ttp80) REVERT: A 704 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8254 (tp40) REVERT: A 727 TYR cc_start: 0.8471 (p90) cc_final: 0.7732 (p90) REVERT: A 728 GLU cc_start: 0.8316 (tt0) cc_final: 0.7660 (pm20) REVERT: A 1209 ASP cc_start: 0.8852 (m-30) cc_final: 0.8582 (p0) REVERT: B 183 LYS cc_start: 0.7685 (mttt) cc_final: 0.7413 (mtpt) REVERT: B 243 LYS cc_start: 0.8445 (mppt) cc_final: 0.8182 (tppp) REVERT: B 290 MET cc_start: 0.7111 (mmp) cc_final: 0.5611 (mmt) REVERT: B 376 PHE cc_start: 0.8072 (m-80) cc_final: 0.7611 (m-80) REVERT: B 407 ARG cc_start: 0.8843 (ttp-170) cc_final: 0.8208 (mpt180) REVERT: B 418 MET cc_start: 0.7230 (tmm) cc_final: 0.7028 (tpp) REVERT: B 424 LYS cc_start: 0.5740 (ptmt) cc_final: 0.5206 (mtmt) REVERT: B 442 LEU cc_start: 0.8618 (mt) cc_final: 0.8261 (tp) REVERT: B 492 MET cc_start: 0.8591 (tpp) cc_final: 0.8216 (tpp) REVERT: B 540 LEU cc_start: 0.8588 (mt) cc_final: 0.8220 (pp) REVERT: B 557 LEU cc_start: 0.9096 (mt) cc_final: 0.8857 (tp) REVERT: B 675 CYS cc_start: 0.8831 (m) cc_final: 0.8228 (m) REVERT: B 690 ASP cc_start: 0.8903 (m-30) cc_final: 0.8166 (t0) REVERT: B 702 PHE cc_start: 0.8704 (m-80) cc_final: 0.8387 (m-80) REVERT: B 1191 LYS cc_start: 0.8477 (mttt) cc_final: 0.8111 (mttp) REVERT: B 1203 GLU cc_start: 0.9444 (tm-30) cc_final: 0.9237 (tm-30) REVERT: C 156 MET cc_start: 0.8242 (mtp) cc_final: 0.7168 (ttm) REVERT: C 173 MET cc_start: 0.9017 (mpp) cc_final: 0.8637 (ptp) REVERT: C 177 TRP cc_start: 0.7971 (m-10) cc_final: 0.7733 (m100) REVERT: C 235 ASP cc_start: 0.9229 (m-30) cc_final: 0.8848 (t0) REVERT: C 239 ASP cc_start: 0.8163 (m-30) cc_final: 0.7883 (m-30) REVERT: C 432 MET cc_start: 0.8069 (mpp) cc_final: 0.7638 (tpt) REVERT: C 449 LEU cc_start: 0.9303 (mp) cc_final: 0.8990 (mp) REVERT: C 462 LEU cc_start: 0.9181 (mm) cc_final: 0.8670 (tp) REVERT: C 513 SER cc_start: 0.8444 (t) cc_final: 0.8150 (m) REVERT: C 514 MET cc_start: 0.8400 (tpp) cc_final: 0.7892 (tpp) REVERT: C 527 TYR cc_start: 0.7825 (m-80) cc_final: 0.7265 (m-80) REVERT: C 560 ILE cc_start: 0.9446 (mm) cc_final: 0.9161 (mm) REVERT: C 566 TYR cc_start: 0.9257 (t80) cc_final: 0.9045 (t80) REVERT: C 665 MET cc_start: 0.8661 (ttm) cc_final: 0.8114 (tmm) REVERT: C 717 ASP cc_start: 0.8966 (t70) cc_final: 0.8634 (t70) REVERT: C 722 MET cc_start: 0.8484 (ptp) cc_final: 0.8150 (ptt) REVERT: C 730 LYS cc_start: 0.8675 (tptt) cc_final: 0.8454 (ttmm) REVERT: C 757 MET cc_start: 0.8967 (tmm) cc_final: 0.8625 (tmm) REVERT: C 1225 GLU cc_start: 0.8814 (mp0) cc_final: 0.8566 (mp0) REVERT: C 1230 MET cc_start: 0.8809 (mtp) cc_final: 0.8491 (mmm) REVERT: D 156 MET cc_start: 0.8162 (mpp) cc_final: 0.7681 (mpp) REVERT: D 181 LEU cc_start: 0.9435 (mt) cc_final: 0.8963 (pt) REVERT: D 196 GLU cc_start: 0.8888 (pm20) cc_final: 0.8113 (tp30) REVERT: D 290 MET cc_start: 0.8199 (mmm) cc_final: 0.7669 (mmm) REVERT: D 441 ASP cc_start: 0.8883 (t70) cc_final: 0.8380 (t0) REVERT: D 525 GLU cc_start: 0.9201 (mp0) cc_final: 0.8933 (mp0) REVERT: D 641 LEU cc_start: 0.9104 (mt) cc_final: 0.8887 (mt) REVERT: D 722 MET cc_start: 0.8642 (tmm) cc_final: 0.8351 (tmm) REVERT: D 730 LYS cc_start: 0.9504 (mmtt) cc_final: 0.9003 (mmmt) REVERT: D 749 PHE cc_start: 0.9263 (t80) cc_final: 0.9057 (t80) REVERT: D 754 CYS cc_start: 0.8927 (t) cc_final: 0.8714 (t) REVERT: I 16 ASN cc_start: 0.8416 (m110) cc_final: 0.8124 (m110) REVERT: I 217 MET cc_start: 0.1539 (tpt) cc_final: 0.0902 (ttt) outliers start: 2 outliers final: 0 residues processed: 555 average time/residue: 0.3792 time to fit residues: 325.0717 Evaluate side-chains 407 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 104 optimal weight: 0.8980 chunk 278 optimal weight: 0.0770 chunk 61 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 chunk 257 optimal weight: 0.4980 chunk 143 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 162 optimal weight: 4.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 ASN B1229 ASN C 151 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 HIS C 660 HIS C 731 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 1.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26364 Z= 0.181 Angle : 0.617 8.462 35584 Z= 0.322 Chirality : 0.041 0.222 3993 Planarity : 0.004 0.055 4551 Dihedral : 4.947 29.874 3504 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 0.07 % Allowed : 1.69 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.15), residues: 3148 helix: 0.98 (0.13), residues: 1654 sheet: -0.63 (0.28), residues: 346 loop : -1.84 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 256 HIS 0.010 0.001 HIS D 240 PHE 0.015 0.001 PHE A1205 TYR 0.023 0.001 TYR B 157 ARG 0.010 0.001 ARG C 700 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 515 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8845 (mt) cc_final: 0.8170 (pt) REVERT: A 237 LEU cc_start: 0.9495 (mt) cc_final: 0.9294 (mt) REVERT: A 249 CYS cc_start: 0.7144 (t) cc_final: 0.6765 (t) REVERT: A 418 MET cc_start: 0.7780 (tpt) cc_final: 0.7197 (tpp) REVERT: A 419 GLU cc_start: 0.8459 (pt0) cc_final: 0.8185 (pt0) REVERT: A 525 GLU cc_start: 0.8872 (mp0) cc_final: 0.8581 (mp0) REVERT: A 704 GLN cc_start: 0.8789 (tp-100) cc_final: 0.8251 (tp40) REVERT: A 727 TYR cc_start: 0.8336 (p90) cc_final: 0.7511 (p90) REVERT: A 728 GLU cc_start: 0.8401 (tt0) cc_final: 0.7306 (pm20) REVERT: A 758 LEU cc_start: 0.8050 (tp) cc_final: 0.7800 (tp) REVERT: A 1230 MET cc_start: 0.7947 (ttm) cc_final: 0.7682 (ttm) REVERT: B 144 ILE cc_start: 0.8351 (mm) cc_final: 0.7873 (tp) REVERT: B 183 LYS cc_start: 0.7524 (mttt) cc_final: 0.7260 (mtpt) REVERT: B 290 MET cc_start: 0.7150 (mmp) cc_final: 0.6002 (tpt) REVERT: B 376 PHE cc_start: 0.8146 (m-80) cc_final: 0.7680 (m-80) REVERT: B 407 ARG cc_start: 0.8862 (ttp-170) cc_final: 0.8213 (mtt90) REVERT: B 418 MET cc_start: 0.7171 (tmm) cc_final: 0.6932 (tpp) REVERT: B 492 MET cc_start: 0.8486 (tpp) cc_final: 0.8258 (tpp) REVERT: B 540 LEU cc_start: 0.8619 (mt) cc_final: 0.8262 (pp) REVERT: B 665 MET cc_start: 0.8872 (ttm) cc_final: 0.8474 (ttm) REVERT: B 675 CYS cc_start: 0.8842 (m) cc_final: 0.8172 (m) REVERT: B 701 ASP cc_start: 0.8917 (m-30) cc_final: 0.8665 (m-30) REVERT: B 702 PHE cc_start: 0.8717 (m-80) cc_final: 0.8345 (m-80) REVERT: B 722 MET cc_start: 0.8922 (ptp) cc_final: 0.8690 (ptp) REVERT: B 1203 GLU cc_start: 0.9339 (tm-30) cc_final: 0.9114 (tm-30) REVERT: B 1211 ARG cc_start: 0.8308 (ttm170) cc_final: 0.8069 (ttp-110) REVERT: C 143 THR cc_start: 0.6861 (p) cc_final: 0.6258 (p) REVERT: C 177 TRP cc_start: 0.7920 (m-10) cc_final: 0.7575 (m-10) REVERT: C 235 ASP cc_start: 0.9201 (m-30) cc_final: 0.8797 (t0) REVERT: C 239 ASP cc_start: 0.8098 (m-30) cc_final: 0.7793 (m-30) REVERT: C 432 MET cc_start: 0.8097 (mpp) cc_final: 0.7759 (tpt) REVERT: C 462 LEU cc_start: 0.9159 (mm) cc_final: 0.8825 (tp) REVERT: C 468 ARG cc_start: 0.8082 (tpm170) cc_final: 0.7842 (tpm170) REVERT: C 479 TYR cc_start: 0.7690 (t80) cc_final: 0.7478 (t80) REVERT: C 526 LEU cc_start: 0.9006 (mt) cc_final: 0.8718 (mt) REVERT: C 527 TYR cc_start: 0.7826 (m-80) cc_final: 0.7392 (m-80) REVERT: C 560 ILE cc_start: 0.9463 (mm) cc_final: 0.9200 (mm) REVERT: C 648 MET cc_start: 0.9366 (mmp) cc_final: 0.9116 (mmm) REVERT: C 665 MET cc_start: 0.8730 (ttt) cc_final: 0.8511 (tmm) REVERT: C 722 MET cc_start: 0.8488 (ptp) cc_final: 0.8123 (ppp) REVERT: C 730 LYS cc_start: 0.8668 (tptt) cc_final: 0.8416 (ttmm) REVERT: C 757 MET cc_start: 0.8966 (tmm) cc_final: 0.8617 (tmm) REVERT: C 1203 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 1209 ASP cc_start: 0.8718 (m-30) cc_final: 0.8428 (p0) REVERT: D 156 MET cc_start: 0.8132 (mpp) cc_final: 0.7640 (mpp) REVERT: D 181 LEU cc_start: 0.9407 (mt) cc_final: 0.8930 (pt) REVERT: D 196 GLU cc_start: 0.8802 (pm20) cc_final: 0.7932 (tp30) REVERT: D 290 MET cc_start: 0.8194 (mmm) cc_final: 0.7660 (mmm) REVERT: D 441 ASP cc_start: 0.8765 (t70) cc_final: 0.7826 (t0) REVERT: D 536 THR cc_start: 0.9434 (p) cc_final: 0.9160 (p) REVERT: D 659 GLN cc_start: 0.9108 (pt0) cc_final: 0.8693 (tm-30) REVERT: D 714 TYR cc_start: 0.8939 (t80) cc_final: 0.8434 (t80) REVERT: D 730 LYS cc_start: 0.9489 (mmtt) cc_final: 0.8999 (mmmt) REVERT: D 749 PHE cc_start: 0.9391 (t80) cc_final: 0.9177 (t80) REVERT: D 1195 ASP cc_start: 0.9403 (m-30) cc_final: 0.9179 (m-30) REVERT: D 1199 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8314 (pp30) REVERT: D 1203 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8474 (mm-30) REVERT: I 186 ASP cc_start: 0.9318 (m-30) cc_final: 0.9115 (m-30) REVERT: I 217 MET cc_start: 0.1841 (tpt) cc_final: 0.1159 (ttt) REVERT: I 293 ASN cc_start: 0.8273 (m-40) cc_final: 0.7467 (p0) REVERT: I 325 MET cc_start: 0.8609 (mtm) cc_final: 0.8086 (mtm) outliers start: 2 outliers final: 0 residues processed: 517 average time/residue: 0.3709 time to fit residues: 301.6826 Evaluate side-chains 396 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 395 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 298 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 226 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 260 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 GLN ** B 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 ASN C 151 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS D1115 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 1.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26364 Z= 0.198 Angle : 0.632 11.732 35584 Z= 0.328 Chirality : 0.041 0.198 3993 Planarity : 0.004 0.069 4551 Dihedral : 4.780 27.946 3504 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.37 % Rotamer: Outliers : 0.07 % Allowed : 1.72 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.21 (0.15), residues: 3148 helix: 1.05 (0.13), residues: 1658 sheet: -0.52 (0.33), residues: 266 loop : -1.72 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 658 HIS 0.016 0.001 HIS B 171 PHE 0.024 0.001 PHE C1184 TYR 0.018 0.001 TYR C1134 ARG 0.011 0.001 ARG C 700 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 487 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8988 (pm20) cc_final: 0.8693 (mp10) REVERT: A 181 LEU cc_start: 0.8884 (mt) cc_final: 0.8220 (pt) REVERT: A 316 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9098 (mt-10) REVERT: A 418 MET cc_start: 0.7777 (tpt) cc_final: 0.7158 (tpp) REVERT: A 419 GLU cc_start: 0.8511 (pt0) cc_final: 0.8216 (pt0) REVERT: A 525 GLU cc_start: 0.8831 (mp0) cc_final: 0.8500 (mp0) REVERT: A 704 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8180 (tp40) REVERT: A 708 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8155 (mt-10) REVERT: A 724 LEU cc_start: 0.9469 (tp) cc_final: 0.9231 (tp) REVERT: A 727 TYR cc_start: 0.8330 (p90) cc_final: 0.7742 (p90) REVERT: A 728 GLU cc_start: 0.8454 (tt0) cc_final: 0.7473 (pm20) REVERT: A 758 LEU cc_start: 0.7672 (tp) cc_final: 0.7281 (tp) REVERT: A 1198 GLU cc_start: 0.8552 (mp0) cc_final: 0.8229 (mp0) REVERT: A 1230 MET cc_start: 0.8018 (ttm) cc_final: 0.7818 (ttm) REVERT: B 144 ILE cc_start: 0.8459 (mm) cc_final: 0.7999 (tp) REVERT: B 183 LYS cc_start: 0.7469 (mttt) cc_final: 0.7127 (mtpt) REVERT: B 290 MET cc_start: 0.7223 (mmp) cc_final: 0.6205 (mmt) REVERT: B 376 PHE cc_start: 0.8172 (m-80) cc_final: 0.7710 (m-80) REVERT: B 407 ARG cc_start: 0.9017 (ttp-170) cc_final: 0.8338 (mtt90) REVERT: B 409 GLN cc_start: 0.5499 (tt0) cc_final: 0.5189 (tp40) REVERT: B 418 MET cc_start: 0.7157 (tmm) cc_final: 0.6938 (tpt) REVERT: B 492 MET cc_start: 0.8467 (tpp) cc_final: 0.8061 (tpp) REVERT: B 514 MET cc_start: 0.8939 (mmp) cc_final: 0.8715 (mmp) REVERT: B 538 TYR cc_start: 0.8343 (t80) cc_final: 0.8034 (m-80) REVERT: B 665 MET cc_start: 0.8931 (ttm) cc_final: 0.8530 (ttm) REVERT: B 675 CYS cc_start: 0.8939 (m) cc_final: 0.8251 (m) REVERT: B 701 ASP cc_start: 0.8930 (m-30) cc_final: 0.8658 (m-30) REVERT: B 702 PHE cc_start: 0.8825 (m-80) cc_final: 0.8460 (m-80) REVERT: B 722 MET cc_start: 0.8888 (ptp) cc_final: 0.8678 (ptp) REVERT: B 1191 LYS cc_start: 0.8515 (mttt) cc_final: 0.8063 (mttp) REVERT: B 1203 GLU cc_start: 0.9396 (tm-30) cc_final: 0.9045 (tm-30) REVERT: C 151 HIS cc_start: 0.3381 (OUTLIER) cc_final: 0.3024 (t-170) REVERT: C 156 MET cc_start: 0.7822 (mmm) cc_final: 0.7463 (mmm) REVERT: C 235 ASP cc_start: 0.9201 (m-30) cc_final: 0.8799 (t0) REVERT: C 239 ASP cc_start: 0.8148 (m-30) cc_final: 0.7829 (m-30) REVERT: C 275 GLN cc_start: 0.8013 (mm-40) cc_final: 0.6784 (pm20) REVERT: C 462 LEU cc_start: 0.9237 (mm) cc_final: 0.8905 (tp) REVERT: C 526 LEU cc_start: 0.9011 (mt) cc_final: 0.8723 (mt) REVERT: C 527 TYR cc_start: 0.7873 (m-80) cc_final: 0.7449 (m-80) REVERT: C 560 ILE cc_start: 0.9462 (mm) cc_final: 0.9178 (mm) REVERT: C 648 MET cc_start: 0.9356 (mmp) cc_final: 0.9114 (mmt) REVERT: C 698 ASN cc_start: 0.8244 (m-40) cc_final: 0.7770 (m-40) REVERT: C 722 MET cc_start: 0.8571 (ptp) cc_final: 0.8103 (ppp) REVERT: C 730 LYS cc_start: 0.8646 (tptt) cc_final: 0.8436 (ttmm) REVERT: C 757 MET cc_start: 0.8965 (tmm) cc_final: 0.8657 (tmm) REVERT: C 1192 LYS cc_start: 0.8778 (tttt) cc_final: 0.8389 (tptp) REVERT: C 1209 ASP cc_start: 0.8741 (m-30) cc_final: 0.8484 (p0) REVERT: D 156 MET cc_start: 0.8164 (mpp) cc_final: 0.7686 (mpp) REVERT: D 181 LEU cc_start: 0.9434 (mt) cc_final: 0.8936 (pt) REVERT: D 196 GLU cc_start: 0.8784 (pm20) cc_final: 0.7900 (tp30) REVERT: D 290 MET cc_start: 0.8233 (mmm) cc_final: 0.7704 (mmm) REVERT: D 441 ASP cc_start: 0.8541 (t70) cc_final: 0.7967 (t0) REVERT: D 492 MET cc_start: 0.8743 (tpt) cc_final: 0.8253 (tpp) REVERT: D 536 THR cc_start: 0.9418 (p) cc_final: 0.9172 (p) REVERT: D 659 GLN cc_start: 0.9144 (pt0) cc_final: 0.8735 (tm-30) REVERT: D 687 MET cc_start: 0.5936 (tmm) cc_final: 0.5294 (mmm) REVERT: D 696 ASN cc_start: 0.8718 (m110) cc_final: 0.8443 (t0) REVERT: D 700 ARG cc_start: 0.8503 (mmp80) cc_final: 0.8070 (mmp80) REVERT: D 714 TYR cc_start: 0.8921 (t80) cc_final: 0.8395 (t80) REVERT: D 725 LEU cc_start: 0.8513 (tp) cc_final: 0.8309 (tp) REVERT: D 730 LYS cc_start: 0.9473 (mmtt) cc_final: 0.8966 (mmmt) REVERT: D 749 PHE cc_start: 0.9304 (t80) cc_final: 0.9083 (t80) REVERT: I 217 MET cc_start: 0.1914 (tpt) cc_final: 0.1527 (ttt) REVERT: I 260 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6068 (mm-30) REVERT: I 293 ASN cc_start: 0.8337 (m-40) cc_final: 0.7551 (p0) REVERT: I 325 MET cc_start: 0.8424 (mtm) cc_final: 0.7976 (mtm) outliers start: 2 outliers final: 0 residues processed: 488 average time/residue: 0.3569 time to fit residues: 276.6136 Evaluate side-chains 379 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 378 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 190 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 chunk 184 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 50.0000 chunk 59 optimal weight: 30.0000 chunk 196 optimal weight: 0.6980 chunk 210 optimal weight: 9.9990 chunk 152 optimal weight: 0.0060 chunk 28 optimal weight: 4.9990 chunk 242 optimal weight: 0.9980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1194 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS C 712 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 HIS D1115 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 1.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26364 Z= 0.195 Angle : 0.625 10.236 35584 Z= 0.324 Chirality : 0.041 0.195 3993 Planarity : 0.004 0.076 4551 Dihedral : 4.672 26.128 3504 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 0.04 % Allowed : 1.11 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.15), residues: 3148 helix: 1.02 (0.13), residues: 1663 sheet: -0.38 (0.29), residues: 340 loop : -1.74 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 177 HIS 0.016 0.001 HIS B 171 PHE 0.018 0.001 PHE I 278 TYR 0.017 0.001 TYR C1134 ARG 0.008 0.001 ARG C 700 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8889 (mt) cc_final: 0.8190 (pt) REVERT: A 418 MET cc_start: 0.7773 (tpt) cc_final: 0.7167 (tpp) REVERT: A 419 GLU cc_start: 0.8513 (pt0) cc_final: 0.8212 (pt0) REVERT: A 524 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7804 (mm-30) REVERT: A 704 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8175 (tp40) REVERT: A 708 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 728 GLU cc_start: 0.8325 (tt0) cc_final: 0.7109 (pm20) REVERT: A 1225 GLU cc_start: 0.8695 (tp30) cc_final: 0.7637 (tp30) REVERT: A 1230 MET cc_start: 0.7912 (ttm) cc_final: 0.7667 (ttm) REVERT: B 183 LYS cc_start: 0.7394 (mttt) cc_final: 0.7048 (mtpt) REVERT: B 290 MET cc_start: 0.7299 (mmp) cc_final: 0.6279 (mmt) REVERT: B 376 PHE cc_start: 0.8129 (m-10) cc_final: 0.7640 (m-80) REVERT: B 407 ARG cc_start: 0.9071 (ttp-170) cc_final: 0.8368 (mtt90) REVERT: B 409 GLN cc_start: 0.5491 (tt0) cc_final: 0.5170 (tp40) REVERT: B 418 MET cc_start: 0.7109 (tmm) cc_final: 0.6891 (tpt) REVERT: B 492 MET cc_start: 0.8480 (tpp) cc_final: 0.8087 (tpp) REVERT: B 514 MET cc_start: 0.8964 (mmp) cc_final: 0.8750 (mmp) REVERT: B 538 TYR cc_start: 0.8368 (t80) cc_final: 0.8091 (m-80) REVERT: B 665 MET cc_start: 0.8938 (ttm) cc_final: 0.8641 (ttm) REVERT: B 675 CYS cc_start: 0.8775 (m) cc_final: 0.7893 (m) REVERT: B 690 ASP cc_start: 0.8901 (m-30) cc_final: 0.8520 (t0) REVERT: B 701 ASP cc_start: 0.9017 (m-30) cc_final: 0.8783 (m-30) REVERT: B 702 PHE cc_start: 0.8861 (m-80) cc_final: 0.8482 (m-80) REVERT: B 711 ASP cc_start: 0.9143 (t70) cc_final: 0.8863 (t0) REVERT: B 712 GLN cc_start: 0.9136 (tp40) cc_final: 0.8899 (tm-30) REVERT: B 722 MET cc_start: 0.8888 (ptp) cc_final: 0.8661 (ptp) REVERT: B 1191 LYS cc_start: 0.8475 (mttt) cc_final: 0.8182 (mttt) REVERT: B 1203 GLU cc_start: 0.9370 (tm-30) cc_final: 0.9122 (tm-30) REVERT: C 173 MET cc_start: 0.9044 (mpp) cc_final: 0.8796 (ptp) REVERT: C 235 ASP cc_start: 0.9229 (m-30) cc_final: 0.8859 (t70) REVERT: C 239 ASP cc_start: 0.8139 (m-30) cc_final: 0.7854 (m-30) REVERT: C 275 GLN cc_start: 0.8036 (mm-40) cc_final: 0.6852 (pm20) REVERT: C 432 MET cc_start: 0.8295 (mpp) cc_final: 0.7997 (tpt) REVERT: C 462 LEU cc_start: 0.9232 (mm) cc_final: 0.8856 (tp) REVERT: C 479 TYR cc_start: 0.7646 (t80) cc_final: 0.7327 (t80) REVERT: C 514 MET cc_start: 0.9035 (tpp) cc_final: 0.8449 (mmt) REVERT: C 526 LEU cc_start: 0.9067 (mt) cc_final: 0.8813 (mt) REVERT: C 527 TYR cc_start: 0.7968 (m-80) cc_final: 0.7571 (m-80) REVERT: C 560 ILE cc_start: 0.9490 (mm) cc_final: 0.9238 (mm) REVERT: C 694 GLU cc_start: 0.9199 (mp0) cc_final: 0.8864 (mp0) REVERT: C 698 ASN cc_start: 0.8310 (m-40) cc_final: 0.7935 (m110) REVERT: C 722 MET cc_start: 0.8535 (ptp) cc_final: 0.8107 (ppp) REVERT: C 757 MET cc_start: 0.8996 (tmm) cc_final: 0.8690 (tmm) REVERT: C 1184 PHE cc_start: 0.5908 (m-10) cc_final: 0.5707 (m-10) REVERT: D 156 MET cc_start: 0.8150 (mpp) cc_final: 0.7686 (mpp) REVERT: D 181 LEU cc_start: 0.9429 (mt) cc_final: 0.8941 (pt) REVERT: D 196 GLU cc_start: 0.8782 (pm20) cc_final: 0.7922 (tp30) REVERT: D 290 MET cc_start: 0.8193 (mmm) cc_final: 0.7629 (mmm) REVERT: D 441 ASP cc_start: 0.8530 (t70) cc_final: 0.7917 (t0) REVERT: D 687 MET cc_start: 0.5919 (tmm) cc_final: 0.5279 (mmm) REVERT: D 696 ASN cc_start: 0.8726 (m110) cc_final: 0.8433 (t0) REVERT: D 700 ARG cc_start: 0.8600 (mmp80) cc_final: 0.8175 (mmp80) REVERT: D 725 LEU cc_start: 0.8498 (tp) cc_final: 0.8264 (tp) REVERT: D 730 LYS cc_start: 0.9469 (mmtt) cc_final: 0.8963 (mmmt) REVERT: D 749 PHE cc_start: 0.9309 (t80) cc_final: 0.9048 (t80) REVERT: I 188 MET cc_start: 0.7020 (mmp) cc_final: 0.6819 (mmm) REVERT: I 217 MET cc_start: 0.2335 (tpt) cc_final: 0.1772 (ttt) REVERT: I 293 ASN cc_start: 0.8376 (m-40) cc_final: 0.7579 (p0) REVERT: I 325 MET cc_start: 0.8519 (mtm) cc_final: 0.8044 (mtm) outliers start: 1 outliers final: 0 residues processed: 477 average time/residue: 0.3622 time to fit residues: 270.7910 Evaluate side-chains 374 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 280 optimal weight: 1.9990 chunk 295 optimal weight: 7.9990 chunk 269 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 225 optimal weight: 0.1980 chunk 88 optimal weight: 0.9980 chunk 259 optimal weight: 0.7980 chunk 271 optimal weight: 30.0000 chunk 286 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 HIS D1115 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 1.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26364 Z= 0.210 Angle : 0.642 9.738 35584 Z= 0.331 Chirality : 0.042 0.253 3993 Planarity : 0.004 0.066 4551 Dihedral : 4.694 25.555 3504 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 0.07 % Allowed : 0.86 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.15), residues: 3148 helix: 1.08 (0.13), residues: 1665 sheet: -0.43 (0.29), residues: 347 loop : -1.71 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 177 HIS 0.017 0.001 HIS D 660 PHE 0.018 0.001 PHE I 278 TYR 0.016 0.001 TYR C1134 ARG 0.010 0.001 ARG C1226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 464 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8876 (mt) cc_final: 0.8189 (pt) REVERT: A 418 MET cc_start: 0.7802 (tpt) cc_final: 0.7193 (tpp) REVERT: A 419 GLU cc_start: 0.8530 (pt0) cc_final: 0.8224 (pt0) REVERT: A 524 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7813 (mm-30) REVERT: A 525 GLU cc_start: 0.8928 (mp0) cc_final: 0.8674 (mp0) REVERT: A 687 MET cc_start: 0.8466 (mmp) cc_final: 0.8138 (mmm) REVERT: A 704 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8210 (tp40) REVERT: A 708 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8151 (mt-10) REVERT: A 728 GLU cc_start: 0.8332 (tt0) cc_final: 0.7213 (pm20) REVERT: A 1198 GLU cc_start: 0.8553 (mp0) cc_final: 0.8187 (mp0) REVERT: A 1225 GLU cc_start: 0.8427 (tp30) cc_final: 0.8070 (tp30) REVERT: A 1229 ASN cc_start: 0.8236 (m-40) cc_final: 0.7936 (m-40) REVERT: A 1230 MET cc_start: 0.7703 (ttm) cc_final: 0.7470 (ttm) REVERT: B 183 LYS cc_start: 0.7360 (mttt) cc_final: 0.7047 (mtpt) REVERT: B 245 ARG cc_start: 0.6286 (mmm-85) cc_final: 0.5968 (mmm-85) REVERT: B 290 MET cc_start: 0.7378 (mmp) cc_final: 0.6466 (mmt) REVERT: B 317 LYS cc_start: 0.8923 (ptpp) cc_final: 0.8699 (pttt) REVERT: B 376 PHE cc_start: 0.8191 (m-10) cc_final: 0.7696 (m-80) REVERT: B 407 ARG cc_start: 0.9053 (ttp-170) cc_final: 0.8338 (mtt90) REVERT: B 409 GLN cc_start: 0.5549 (tt0) cc_final: 0.5225 (tp40) REVERT: B 418 MET cc_start: 0.7178 (tmm) cc_final: 0.6948 (tpp) REVERT: B 421 MET cc_start: 0.1732 (mmt) cc_final: 0.1086 (mmt) REVERT: B 492 MET cc_start: 0.8567 (tpp) cc_final: 0.8210 (tpp) REVERT: B 538 TYR cc_start: 0.8403 (t80) cc_final: 0.8144 (m-80) REVERT: B 557 LEU cc_start: 0.8938 (mt) cc_final: 0.8496 (tp) REVERT: B 665 MET cc_start: 0.9006 (ttm) cc_final: 0.8698 (ttm) REVERT: B 675 CYS cc_start: 0.8799 (m) cc_final: 0.7958 (m) REVERT: B 687 MET cc_start: 0.8691 (tpp) cc_final: 0.8202 (tpp) REVERT: B 690 ASP cc_start: 0.8900 (m-30) cc_final: 0.8634 (t0) REVERT: B 701 ASP cc_start: 0.9034 (m-30) cc_final: 0.8796 (m-30) REVERT: B 702 PHE cc_start: 0.8869 (m-80) cc_final: 0.8440 (m-80) REVERT: B 711 ASP cc_start: 0.9160 (t70) cc_final: 0.8914 (t0) REVERT: B 712 GLN cc_start: 0.9140 (tp40) cc_final: 0.8904 (tm-30) REVERT: B 722 MET cc_start: 0.8888 (ptp) cc_final: 0.8653 (ptp) REVERT: B 1191 LYS cc_start: 0.8506 (mttt) cc_final: 0.8259 (mttt) REVERT: B 1203 GLU cc_start: 0.9459 (tm-30) cc_final: 0.9248 (tm-30) REVERT: C 235 ASP cc_start: 0.9248 (m-30) cc_final: 0.8835 (t70) REVERT: C 239 ASP cc_start: 0.8140 (m-30) cc_final: 0.7841 (m-30) REVERT: C 275 GLN cc_start: 0.8066 (mm-40) cc_final: 0.6893 (pm20) REVERT: C 462 LEU cc_start: 0.9244 (mm) cc_final: 0.8860 (tp) REVERT: C 479 TYR cc_start: 0.7598 (t80) cc_final: 0.7353 (t80) REVERT: C 527 TYR cc_start: 0.7758 (m-80) cc_final: 0.7289 (m-80) REVERT: C 560 ILE cc_start: 0.9513 (mm) cc_final: 0.9246 (mm) REVERT: C 722 MET cc_start: 0.8533 (ptp) cc_final: 0.8090 (ppp) REVERT: C 757 MET cc_start: 0.8906 (tmm) cc_final: 0.8630 (tmm) REVERT: C 1225 GLU cc_start: 0.8602 (mp0) cc_final: 0.8331 (mp0) REVERT: D 156 MET cc_start: 0.8153 (mpp) cc_final: 0.7695 (mpp) REVERT: D 181 LEU cc_start: 0.9433 (mt) cc_final: 0.8964 (pt) REVERT: D 196 GLU cc_start: 0.8768 (pm20) cc_final: 0.7880 (tp30) REVERT: D 290 MET cc_start: 0.8180 (mmm) cc_final: 0.7619 (mmm) REVERT: D 441 ASP cc_start: 0.8529 (t70) cc_final: 0.7908 (t0) REVERT: D 687 MET cc_start: 0.5875 (tmm) cc_final: 0.5313 (mmm) REVERT: D 696 ASN cc_start: 0.8730 (m110) cc_final: 0.8464 (t0) REVERT: D 714 TYR cc_start: 0.8959 (t80) cc_final: 0.8692 (t80) REVERT: D 725 LEU cc_start: 0.8538 (tp) cc_final: 0.8243 (tp) REVERT: D 730 LYS cc_start: 0.9487 (mmtt) cc_final: 0.8975 (mmmt) REVERT: I 18 ILE cc_start: 0.8764 (tt) cc_final: 0.8415 (tt) REVERT: I 188 MET cc_start: 0.7024 (mmp) cc_final: 0.6812 (mmm) REVERT: I 217 MET cc_start: 0.2197 (tpt) cc_final: 0.1763 (ttt) outliers start: 2 outliers final: 0 residues processed: 466 average time/residue: 0.3592 time to fit residues: 266.5322 Evaluate side-chains 371 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 188 optimal weight: 0.6980 chunk 303 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 211 optimal weight: 0.9980 chunk 318 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 HIS ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 ASN B1213 ASN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 1.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26364 Z= 0.200 Angle : 0.644 9.511 35584 Z= 0.333 Chirality : 0.042 0.237 3993 Planarity : 0.004 0.083 4551 Dihedral : 4.631 24.749 3504 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.15), residues: 3148 helix: 1.09 (0.13), residues: 1666 sheet: -0.45 (0.28), residues: 354 loop : -1.68 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 644 HIS 0.017 0.001 HIS B 171 PHE 0.018 0.001 PHE I 278 TYR 0.016 0.001 TYR C1134 ARG 0.010 0.001 ARG C1226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8894 (mt) cc_final: 0.8208 (pt) REVERT: A 418 MET cc_start: 0.7853 (tpt) cc_final: 0.7231 (tpp) REVERT: A 419 GLU cc_start: 0.8532 (pt0) cc_final: 0.8213 (pt0) REVERT: A 524 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7559 (mm-30) REVERT: A 687 MET cc_start: 0.8430 (mmp) cc_final: 0.8108 (mmm) REVERT: A 704 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8088 (tp40) REVERT: A 708 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8112 (mt-10) REVERT: A 728 GLU cc_start: 0.8438 (tt0) cc_final: 0.7437 (pm20) REVERT: A 1198 GLU cc_start: 0.8569 (mp0) cc_final: 0.8211 (mp0) REVERT: A 1225 GLU cc_start: 0.8402 (tp30) cc_final: 0.8031 (tp30) REVERT: A 1229 ASN cc_start: 0.8335 (m-40) cc_final: 0.7979 (m-40) REVERT: A 1230 MET cc_start: 0.7820 (ttm) cc_final: 0.7582 (ttm) REVERT: B 183 LYS cc_start: 0.7335 (mttt) cc_final: 0.7090 (mtpt) REVERT: B 237 LEU cc_start: 0.9220 (tt) cc_final: 0.9012 (tt) REVERT: B 290 MET cc_start: 0.7484 (mmp) cc_final: 0.6444 (mmt) REVERT: B 376 PHE cc_start: 0.8210 (m-10) cc_final: 0.7675 (m-80) REVERT: B 407 ARG cc_start: 0.9055 (ttp-170) cc_final: 0.8313 (mtt90) REVERT: B 418 MET cc_start: 0.7196 (tmm) cc_final: 0.6965 (tpp) REVERT: B 492 MET cc_start: 0.8577 (tpp) cc_final: 0.8177 (tpp) REVERT: B 498 LEU cc_start: 0.8200 (mt) cc_final: 0.7975 (mt) REVERT: B 538 TYR cc_start: 0.8424 (t80) cc_final: 0.8118 (m-80) REVERT: B 557 LEU cc_start: 0.8904 (mt) cc_final: 0.8448 (tp) REVERT: B 675 CYS cc_start: 0.8792 (m) cc_final: 0.7948 (m) REVERT: B 701 ASP cc_start: 0.9028 (m-30) cc_final: 0.8796 (m-30) REVERT: B 702 PHE cc_start: 0.8900 (m-80) cc_final: 0.8481 (m-80) REVERT: B 711 ASP cc_start: 0.9142 (t70) cc_final: 0.8918 (t0) REVERT: B 712 GLN cc_start: 0.9089 (tp40) cc_final: 0.8863 (tm-30) REVERT: B 722 MET cc_start: 0.8894 (ptp) cc_final: 0.8665 (ptp) REVERT: B 1191 LYS cc_start: 0.8505 (mttt) cc_final: 0.8291 (mttt) REVERT: B 1203 GLU cc_start: 0.9450 (tm-30) cc_final: 0.9239 (tm-30) REVERT: C 235 ASP cc_start: 0.9233 (m-30) cc_final: 0.8830 (t0) REVERT: C 239 ASP cc_start: 0.8155 (m-30) cc_final: 0.7792 (m-30) REVERT: C 275 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7003 (pm20) REVERT: C 462 LEU cc_start: 0.9207 (mm) cc_final: 0.8800 (tp) REVERT: C 479 TYR cc_start: 0.7626 (t80) cc_final: 0.7402 (t80) REVERT: C 526 LEU cc_start: 0.9036 (mt) cc_final: 0.8804 (mt) REVERT: C 527 TYR cc_start: 0.7804 (m-80) cc_final: 0.7300 (m-80) REVERT: C 560 ILE cc_start: 0.9508 (mm) cc_final: 0.9272 (mm) REVERT: C 694 GLU cc_start: 0.9237 (mp0) cc_final: 0.9017 (mp0) REVERT: C 722 MET cc_start: 0.8557 (ptp) cc_final: 0.8103 (ppp) REVERT: C 757 MET cc_start: 0.8863 (tmm) cc_final: 0.8572 (tmm) REVERT: C 1184 PHE cc_start: 0.6028 (m-10) cc_final: 0.5825 (m-10) REVERT: C 1198 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8897 (mm-30) REVERT: D 156 MET cc_start: 0.8170 (mpp) cc_final: 0.7721 (mpp) REVERT: D 181 LEU cc_start: 0.9424 (mt) cc_final: 0.8962 (pt) REVERT: D 196 GLU cc_start: 0.8760 (pm20) cc_final: 0.7872 (tp30) REVERT: D 290 MET cc_start: 0.8163 (mmm) cc_final: 0.7585 (mmm) REVERT: D 441 ASP cc_start: 0.8482 (t70) cc_final: 0.7869 (t0) REVERT: D 687 MET cc_start: 0.5852 (tmm) cc_final: 0.5292 (mmm) REVERT: D 696 ASN cc_start: 0.8730 (m110) cc_final: 0.8483 (t0) REVERT: D 714 TYR cc_start: 0.8941 (t80) cc_final: 0.8661 (t80) REVERT: D 725 LEU cc_start: 0.8539 (tp) cc_final: 0.8202 (tp) REVERT: D 730 LYS cc_start: 0.9515 (mmtt) cc_final: 0.9029 (mmmt) REVERT: D 749 PHE cc_start: 0.9324 (t80) cc_final: 0.9082 (t80) REVERT: D 1203 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8715 (mm-30) REVERT: I 61 MET cc_start: 0.4992 (ptm) cc_final: 0.4625 (ptm) REVERT: I 186 ASP cc_start: 0.9283 (m-30) cc_final: 0.9072 (m-30) REVERT: I 217 MET cc_start: 0.2014 (tpt) cc_final: 0.1526 (ttt) REVERT: I 325 MET cc_start: 0.8327 (mtp) cc_final: 0.7915 (mtm) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.3435 time to fit residues: 251.3947 Evaluate side-chains 365 residues out of total 2785 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 201 optimal weight: 0.7980 chunk 270 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 234 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 254 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 539 HIS ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.097306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068535 restraints weight = 163869.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.070441 restraints weight = 114894.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071897 restraints weight = 90430.679| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 1.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26364 Z= 0.182 Angle : 0.634 10.264 35584 Z= 0.325 Chirality : 0.041 0.184 3993 Planarity : 0.004 0.066 4551 Dihedral : 4.549 24.496 3504 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.15), residues: 3148 helix: 1.12 (0.13), residues: 1664 sheet: -0.37 (0.29), residues: 347 loop : -1.66 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 63 HIS 0.017 0.001 HIS B 171 PHE 0.017 0.001 PHE C1114 TYR 0.019 0.001 TYR I 289 ARG 0.017 0.001 ARG C1226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6449.54 seconds wall clock time: 117 minutes 39.79 seconds (7059.79 seconds total)