Starting phenix.real_space_refine on Fri Sep 19 03:43:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xli_38449/09_2025/8xli_38449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xli_38449/09_2025/8xli_38449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xli_38449/09_2025/8xli_38449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xli_38449/09_2025/8xli_38449.map" model { file = "/net/cci-nas-00/data/ceres_data/8xli_38449/09_2025/8xli_38449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xli_38449/09_2025/8xli_38449.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 151 5.16 5 C 15057 2.51 5 N 3711 2.21 5 O 4105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23024 Number of models: 1 Model: "" Number of chains: 20 Chain: "a" Number of atoms: 5728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5728 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 31, 'TRANS': 729} Chain breaks: 2 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 15, 'ARG:plan': 14, 'GLU:plan': 19, 'GLN:plan1': 5, 'ASN:plan1': 9, 'ASP:plan': 5, 'TRP:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 337 Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "c" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1631 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 195} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "d" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2768 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "e" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "f" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 683 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 85} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.49, per 1000 atoms: 0.24 Number of scatterers: 23024 At special positions: 0 Unit cell: (149.94, 121.023, 133.875, 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 151 16.00 O 4105 8.00 N 3711 7.00 C 15057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 1 " - " ASN c 261 " " NAG B 1 " - " ASN c 303 " " NAG C 1 " - " ASN c 273 " " NAG D 1 " - " ASN c 350 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 6 sheets defined 75.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'a' and resid 20 through 33 removed outlier: 4.048A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 76 Processing helix chain 'a' and resid 91 through 143 removed outlier: 4.075A pdb=" N ASP a 96 " --> pdb=" O ARG a 92 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU a 97 " --> pdb=" O ASP a 93 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN a 137 " --> pdb=" O ARG a 133 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE a 139 " --> pdb=" O THR a 135 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP a 140 " --> pdb=" O GLN a 136 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU a 141 " --> pdb=" O GLN a 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 188 Processing helix chain 'a' and resid 226 through 241 Processing helix chain 'a' and resid 251 through 310 removed outlier: 4.360A pdb=" N LYS a 255 " --> pdb=" O PRO a 251 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA a 285 " --> pdb=" O ARG a 281 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS a 288 " --> pdb=" O GLN a 284 " (cutoff:3.500A) Processing helix chain 'a' and resid 329 through 343 Processing helix chain 'a' and resid 371 through 379 removed outlier: 3.702A pdb=" N GLN a 375 " --> pdb=" O THR a 371 " (cutoff:3.500A) Processing helix chain 'a' and resid 385 through 389 removed outlier: 3.708A pdb=" N ILE a 389 " --> pdb=" O TYR a 386 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 396 removed outlier: 3.640A pdb=" N THR a 395 " --> pdb=" O PRO a 391 " (cutoff:3.500A) Processing helix chain 'a' and resid 410 through 426 Processing helix chain 'a' and resid 426 through 433 Processing helix chain 'a' and resid 437 through 465 removed outlier: 5.430A pdb=" N TYR a 448 " --> pdb=" O PHE a 444 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE a 449 " --> pdb=" O SER a 445 " (cutoff:3.500A) Processing helix chain 'a' and resid 466 through 470 removed outlier: 4.068A pdb=" N SER a 469 " --> pdb=" O ASP a 466 " (cutoff:3.500A) Processing helix chain 'a' and resid 481 through 487 Processing helix chain 'a' and resid 520 through 526 removed outlier: 3.906A pdb=" N ASN a 524 " --> pdb=" O ASP a 520 " (cutoff:3.500A) Processing helix chain 'a' and resid 528 through 563 removed outlier: 3.797A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE a 563 " --> pdb=" O ASN a 559 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 572 Processing helix chain 'a' and resid 573 through 597 removed outlier: 4.768A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU a 587 " --> pdb=" O LEU a 583 " (cutoff:3.500A) Processing helix chain 'a' and resid 599 through 603 removed outlier: 4.210A pdb=" N SER a 603 " --> pdb=" O ALA a 600 " (cutoff:3.500A) Processing helix chain 'a' and resid 632 through 645 Processing helix chain 'a' and resid 647 through 652 Processing helix chain 'a' and resid 655 through 667 removed outlier: 4.069A pdb=" N LEU a 659 " --> pdb=" O LYS a 655 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN a 662 " --> pdb=" O ILE a 658 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS a 667 " --> pdb=" O TYR a 663 " (cutoff:3.500A) Processing helix chain 'a' and resid 713 through 739 removed outlier: 3.518A pdb=" N THR a 717 " --> pdb=" O ASP a 713 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE a 733 " --> pdb=" O CYS a 729 " (cutoff:3.500A) Processing helix chain 'a' and resid 740 through 765 removed outlier: 3.711A pdb=" N ALA a 744 " --> pdb=" O LEU a 740 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N HIS a 762 " --> pdb=" O THR a 758 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE a 763 " --> pdb=" O MET a 759 " (cutoff:3.500A) Processing helix chain 'a' and resid 768 through 775 removed outlier: 4.454A pdb=" N GLY a 775 " --> pdb=" O ALA a 771 " (cutoff:3.500A) Processing helix chain 'a' and resid 775 through 790 Processing helix chain 'a' and resid 793 through 810 removed outlier: 3.620A pdb=" N GLU a 810 " --> pdb=" O LEU a 806 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 29 Processing helix chain 'b' and resid 36 through 44 removed outlier: 3.559A pdb=" N PHE b 40 " --> pdb=" O ASP b 36 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 80 removed outlier: 3.852A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 90 removed outlier: 3.743A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN b 90 " --> pdb=" O ILE b 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 85 through 90' Processing helix chain 'b' and resid 91 through 93 No H-bonds generated for 'chain 'b' and resid 91 through 93' Processing helix chain 'b' and resid 94 through 113 removed outlier: 3.672A pdb=" N GLY b 104 " --> pdb=" O VAL b 100 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE b 105 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET b 107 " --> pdb=" O TYR b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 167 Processing helix chain 'b' and resid 172 through 177 Processing helix chain 'b' and resid 177 through 198 removed outlier: 3.542A pdb=" N ILE b 181 " --> pdb=" O LEU b 177 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR b 198 " --> pdb=" O ALA b 194 " (cutoff:3.500A) Processing helix chain 'c' and resid 285 through 290 Processing helix chain 'c' and resid 422 through 448 Processing helix chain 'd' and resid 8 through 12 removed outlier: 4.186A pdb=" N ASP d 12 " --> pdb=" O PHE d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 25 removed outlier: 3.840A pdb=" N ALA d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 38 removed outlier: 4.309A pdb=" N GLN d 38 " --> pdb=" O LEU d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 51 removed outlier: 3.953A pdb=" N SER d 51 " --> pdb=" O LEU d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 88 removed outlier: 3.578A pdb=" N HIS d 88 " --> pdb=" O HIS d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 119 removed outlier: 4.012A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU d 112 " --> pdb=" O ASN d 108 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU d 117 " --> pdb=" O ILE d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 152 Processing helix chain 'd' and resid 160 through 165 Processing helix chain 'd' and resid 179 through 200 removed outlier: 3.532A pdb=" N ASN d 183 " --> pdb=" O GLU d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 202 through 229 Proline residue: d 210 - end of helix removed outlier: 4.401A pdb=" N GLY d 229 " --> pdb=" O ILE d 225 " (cutoff:3.500A) Processing helix chain 'd' and resid 233 through 241 Processing helix chain 'd' and resid 251 through 258 Processing helix chain 'd' and resid 260 through 269 Processing helix chain 'd' and resid 271 through 281 removed outlier: 3.553A pdb=" N ALA d 281 " --> pdb=" O LEU d 277 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 306 through 308 No H-bonds generated for 'chain 'd' and resid 306 through 308' Processing helix chain 'd' and resid 312 through 338 removed outlier: 4.338A pdb=" N TYR d 316 " --> pdb=" O PHE d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 343 through 347 removed outlier: 3.633A pdb=" N TYR d 347 " --> pdb=" O ILE d 344 " (cutoff:3.500A) Processing helix chain 'e' and resid 6 through 22 Processing helix chain 'e' and resid 34 through 60 Processing helix chain 'e' and resid 72 through 77 Processing helix chain 'f' and resid 8 through 36 Processing helix chain 'f' and resid 47 through 51 Processing helix chain 'f' and resid 54 through 94 removed outlier: 3.925A pdb=" N ILE f 58 " --> pdb=" O GLY f 54 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU f 94 " --> pdb=" O ASN f 90 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 45 removed outlier: 4.308A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 47 No H-bonds generated for 'chain 'g' and resid 46 through 47' Processing helix chain 'g' and resid 48 through 55 removed outlier: 3.610A pdb=" N ILE g 52 " --> pdb=" O PRO g 49 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N MET g 53 " --> pdb=" O GLU g 50 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS g 54 " --> pdb=" O LEU g 51 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER g 55 " --> pdb=" O ILE g 52 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 79 removed outlier: 3.775A pdb=" N VAL g 60 " --> pdb=" O ILE g 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 124 removed outlier: 3.566A pdb=" N LEU g 91 " --> pdb=" O TYR g 87 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 153 removed outlier: 3.510A pdb=" N ILE g 134 " --> pdb=" O GLY g 130 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU g 139 " --> pdb=" O LEU g 135 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY g 145 " --> pdb=" O LEU g 141 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU g 152 " --> pdb=" O VAL g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 45 removed outlier: 4.066A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 52 removed outlier: 3.955A pdb=" N LEU h 51 " --> pdb=" O ARG h 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE h 52 " --> pdb=" O PRO h 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 48 through 52' Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'h' and resid 56 through 78 removed outlier: 3.688A pdb=" N VAL h 60 " --> pdb=" O ILE h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 124 removed outlier: 3.500A pdb=" N LEU h 91 " --> pdb=" O TYR h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 127 through 155 removed outlier: 4.131A pdb=" N ILE h 136 " --> pdb=" O ILE h 132 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR h 154 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 10 No H-bonds generated for 'chain 'i' and resid 8 through 10' Processing helix chain 'i' and resid 11 through 43 removed outlier: 3.718A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 52 through 55 Processing helix chain 'i' and resid 56 through 80 Processing helix chain 'i' and resid 86 through 122 removed outlier: 3.734A pdb=" N PHE i 90 " --> pdb=" O LEU i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 125 No H-bonds generated for 'chain 'i' and resid 123 through 125' Processing helix chain 'i' and resid 126 through 154 removed outlier: 4.663A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU i 133 " --> pdb=" O VAL i 129 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 10 through 46 removed outlier: 3.770A pdb=" N PHE j 14 " --> pdb=" O TYR j 10 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL j 46 " --> pdb=" O ALA j 42 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 through 55 removed outlier: 4.763A pdb=" N MET j 53 " --> pdb=" O GLU j 50 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS j 54 " --> pdb=" O LEU j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 80 removed outlier: 4.151A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE j 67 " --> pdb=" O GLY j 63 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR j 68 " --> pdb=" O ILE j 64 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER j 79 " --> pdb=" O LEU j 75 " (cutoff:3.500A) Processing helix chain 'j' and resid 86 through 124 removed outlier: 3.535A pdb=" N PHE j 90 " --> pdb=" O LEU j 86 " (cutoff:3.500A) Processing helix chain 'j' and resid 126 through 154 removed outlier: 4.812A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE j 132 " --> pdb=" O PHE j 128 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU j 133 " --> pdb=" O VAL j 129 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY j 145 " --> pdb=" O LEU j 141 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 45 removed outlier: 4.064A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 47 No H-bonds generated for 'chain 'k' and resid 46 through 47' Processing helix chain 'k' and resid 48 through 52 Processing helix chain 'k' and resid 56 through 79 removed outlier: 3.507A pdb=" N VAL k 60 " --> pdb=" O ILE k 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 86 through 124 removed outlier: 3.515A pdb=" N PHE k 90 " --> pdb=" O LEU k 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 127 through 154 removed outlier: 4.598A pdb=" N ILE k 136 " --> pdb=" O ILE k 132 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY k 142 " --> pdb=" O ALA k 138 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY k 145 " --> pdb=" O LEU k 141 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU k 146 " --> pdb=" O GLY k 142 " (cutoff:3.500A) Processing helix chain 'l' and resid 10 through 45 removed outlier: 4.295A pdb=" N PHE l 14 " --> pdb=" O TYR l 10 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 52 through 55 Processing helix chain 'l' and resid 56 through 80 Processing helix chain 'l' and resid 86 through 124 removed outlier: 3.808A pdb=" N PHE l 90 " --> pdb=" O LEU l 86 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 127 through 154 removed outlier: 3.540A pdb=" N LEU l 135 " --> pdb=" O MET l 131 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE l 136 " --> pdb=" O ILE l 132 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY l 145 " --> pdb=" O LEU l 141 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 46 removed outlier: 4.424A pdb=" N PHE m 14 " --> pdb=" O TYR m 10 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER m 26 " --> pdb=" O ALA m 22 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL m 46 " --> pdb=" O ALA m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 47 through 55 removed outlier: 6.241A pdb=" N GLU m 50 " --> pdb=" O MET m 47 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET m 53 " --> pdb=" O GLU m 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 56 through 79 removed outlier: 3.789A pdb=" N SER m 79 " --> pdb=" O LEU m 75 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 122 removed outlier: 3.535A pdb=" N ALA m 122 " --> pdb=" O VAL m 118 " (cutoff:3.500A) Processing helix chain 'm' and resid 123 through 125 No H-bonds generated for 'chain 'm' and resid 123 through 125' Processing helix chain 'm' and resid 126 through 154 removed outlier: 4.085A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE m 132 " --> pdb=" O PHE m 128 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU m 133 " --> pdb=" O VAL m 129 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE m 136 " --> pdb=" O ILE m 132 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE m 137 " --> pdb=" O LEU m 133 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA m 138 " --> pdb=" O ILE m 134 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU m 139 " --> pdb=" O LEU m 135 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 45 removed outlier: 4.354A pdb=" N PHE n 14 " --> pdb=" O TYR n 10 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 53 removed outlier: 3.643A pdb=" N ILE n 52 " --> pdb=" O PRO n 49 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET n 53 " --> pdb=" O GLU n 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 49 through 53' Processing helix chain 'n' and resid 56 through 79 Processing helix chain 'n' and resid 87 through 124 removed outlier: 3.521A pdb=" N LEU n 91 " --> pdb=" O TYR n 87 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 127 through 154 removed outlier: 3.522A pdb=" N MET n 131 " --> pdb=" O LEU n 127 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU n 133 " --> pdb=" O VAL n 129 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ILE n 136 " --> pdb=" O ILE n 132 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY n 142 " --> pdb=" O ALA n 138 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 46 removed outlier: 4.334A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER o 26 " --> pdb=" O ALA o 22 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL o 46 " --> pdb=" O ALA o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 47 through 55 removed outlier: 6.691A pdb=" N GLU o 50 " --> pdb=" O MET o 47 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU o 51 " --> pdb=" O ARG o 48 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE o 52 " --> pdb=" O PRO o 49 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N MET o 53 " --> pdb=" O GLU o 50 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS o 54 " --> pdb=" O LEU o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.963A pdb=" N ALA o 66 " --> pdb=" O ALA o 62 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE o 67 " --> pdb=" O GLY o 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR o 68 " --> pdb=" O ILE o 64 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 124 Processing helix chain 'o' and resid 126 through 155 removed outlier: 4.462A pdb=" N GLY o 130 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY o 142 " --> pdb=" O ALA o 138 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR o 144 " --> pdb=" O VAL o 140 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU o 152 " --> pdb=" O VAL o 148 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR o 154 " --> pdb=" O LEU o 150 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS o 155 " --> pdb=" O ILE o 151 " (cutoff:3.500A) Processing helix chain 'p' and resid 302 through 330 removed outlier: 3.721A pdb=" N VAL p 306 " --> pdb=" O GLU p 302 " (cutoff:3.500A) Processing helix chain 'p' and resid 336 through 340 Processing sheet with id=AA1, first strand: chain 'a' and resid 311 through 312 removed outlier: 4.189A pdb=" N LEU a 12 " --> pdb=" O ASN a 353 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 217 through 223 removed outlier: 4.118A pdb=" N ALA a 172 " --> pdb=" O TYR a 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 258 through 260 Processing sheet with id=AA4, first strand: chain 'c' and resid 258 through 260 removed outlier: 6.650A pdb=" N GLU c 372 " --> pdb=" O ASN c 398 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN c 400 " --> pdb=" O HIS c 370 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS c 370 " --> pdb=" O GLN c 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 301 through 302 removed outlier: 5.086A pdb=" N ALA c 319 " --> pdb=" O PRO c 315 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR c 320 " --> pdb=" O SER c 349 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER c 349 " --> pdb=" O THR c 320 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR c 322 " --> pdb=" O ILE c 347 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE c 347 " --> pdb=" O THR c 322 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS c 324 " --> pdb=" O LEU c 345 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU c 345 " --> pdb=" O LYS c 324 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE c 326 " --> pdb=" O GLU c 343 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG c 337 " --> pdb=" O TYR c 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 301 through 302 removed outlier: 5.086A pdb=" N ALA c 319 " --> pdb=" O PRO c 315 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR c 320 " --> pdb=" O SER c 349 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER c 349 " --> pdb=" O THR c 320 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR c 322 " --> pdb=" O ILE c 347 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE c 347 " --> pdb=" O THR c 322 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS c 324 " --> pdb=" O LEU c 345 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU c 345 " --> pdb=" O LYS c 324 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE c 326 " --> pdb=" O GLU c 343 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG c 337 " --> pdb=" O TYR c 332 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU c 343 " --> pdb=" O VAL c 358 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL c 358 " --> pdb=" O GLU c 343 " (cutoff:3.500A) 1796 hydrogen bonds defined for protein. 5292 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: 4.49 Time building geometry restraints manager: 2.93 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: 7114 1.34 - 1.46: 4782 1.46 - 1.58: 11332 1.58 - 1.70: 0 1.70 - 1.82: 267 Bond restraints: 23495 Sorted by residual: bond pdb=" C ALA a 392 " pdb=" N PRO a 393 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.79e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 23490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 31598 2.89 - 5.77: 260 5.77 - 8.66: 30 8.66 - 11.54: 10 11.54 - 14.43: 3 Bond angle restraints: 31901 Sorted by residual: angle pdb=" CB MET b 107 " pdb=" CG MET b 107 " pdb=" SD MET b 107 " ideal model delta sigma weight residual 112.70 126.32 -13.62 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C GLU m 9 " pdb=" CA GLU m 9 " pdb=" CB GLU m 9 " ideal model delta sigma weight residual 116.54 111.36 5.18 1.15e+00 7.56e-01 2.03e+01 angle pdb=" CA LEU f 75 " pdb=" CB LEU f 75 " pdb=" CG LEU f 75 " ideal model delta sigma weight residual 116.30 130.73 -14.43 3.50e+00 8.16e-02 1.70e+01 angle pdb=" CB MET f 28 " pdb=" CG MET f 28 " pdb=" SD MET f 28 " ideal model delta sigma weight residual 112.70 123.59 -10.89 3.00e+00 1.11e-01 1.32e+01 angle pdb=" CB MET i 23 " pdb=" CG MET i 23 " pdb=" SD MET i 23 " ideal model delta sigma weight residual 112.70 123.29 -10.59 3.00e+00 1.11e-01 1.25e+01 ... (remaining 31896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.67: 12076 20.67 - 41.34: 1421 41.34 - 62.01: 250 62.01 - 82.67: 21 82.67 - 103.34: 18 Dihedral angle restraints: 13786 sinusoidal: 5072 harmonic: 8714 Sorted by residual: dihedral pdb=" CA LEU a 402 " pdb=" C LEU a 402 " pdb=" N PHE a 403 " pdb=" CA PHE a 403 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA LEU l 133 " pdb=" C LEU l 133 " pdb=" N ILE l 134 " pdb=" CA ILE l 134 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA GLY a 226 " pdb=" C GLY a 226 " pdb=" N ASP a 227 " pdb=" CA ASP a 227 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 13783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3294 0.060 - 0.119: 492 0.119 - 0.179: 23 0.179 - 0.239: 1 0.239 - 0.298: 1 Chirality restraints: 3811 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN c 273 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE a 723 " pdb=" CA ILE a 723 " pdb=" CG1 ILE a 723 " pdb=" CG2 ILE a 723 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU i 70 " pdb=" CB LEU i 70 " pdb=" CD1 LEU i 70 " pdb=" CD2 LEU i 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 3808 not shown) Planarity restraints: 3972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS a 655 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO a 656 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO a 656 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO a 656 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 743 " -0.007 2.00e-02 2.50e+03 1.46e-02 5.34e+00 pdb=" CG TRP a 743 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP a 743 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP a 743 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP a 743 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP a 743 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP a 743 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 743 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 743 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP a 743 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE b 189 " -0.010 2.00e-02 2.50e+03 1.64e-02 4.70e+00 pdb=" CG PHE b 189 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE b 189 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE b 189 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE b 189 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE b 189 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE b 189 " 0.001 2.00e-02 2.50e+03 ... (remaining 3969 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 441 2.68 - 3.23: 25043 3.23 - 3.79: 38950 3.79 - 4.34: 47797 4.34 - 4.90: 76823 Nonbonded interactions: 189054 Sorted by model distance: nonbonded pdb=" OG1 THR a 385 " pdb=" OE1 GLU a 388 " model vdw 2.123 3.040 nonbonded pdb=" OG1 THR a 250 " pdb=" OE1 GLU a 253 " model vdw 2.173 3.040 nonbonded pdb=" O ALA b 38 " pdb=" OG1 THR b 42 " model vdw 2.190 3.040 nonbonded pdb=" O THR b 42 " pdb=" OH TYR b 131 " model vdw 2.205 3.040 nonbonded pdb=" O LEU b 41 " pdb=" OH TYR b 135 " model vdw 2.210 3.040 ... (remaining 189049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.210 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 0.045 23504 Z= 0.151 Angle : 0.689 14.428 31925 Z= 0.344 Chirality : 0.040 0.298 3811 Planarity : 0.005 0.078 3968 Dihedral : 17.391 103.342 8238 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.42 % Favored : 93.35 % Rotamer: Outliers : 0.47 % Allowed : 34.37 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.16), residues: 3037 helix: 1.34 (0.11), residues: 2081 sheet: -1.18 (0.55), residues: 99 loop : -2.30 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 119 TYR 0.022 0.001 TYR o 68 PHE 0.037 0.001 PHE b 189 TRP 0.035 0.002 TRP a 743 HIS 0.005 0.001 HIS a 807 Details of bonding type rmsd covalent geometry : bond 0.00310 (23495) covalent geometry : angle 0.68702 (31901) hydrogen bonds : bond 0.15127 ( 1772) hydrogen bonds : angle 6.17180 ( 5292) Misc. bond : bond 0.00047 ( 1) link_BETA1-4 : bond 0.00867 ( 4) link_BETA1-4 : angle 1.71308 ( 12) link_NAG-ASN : bond 0.00339 ( 4) link_NAG-ASN : angle 2.56211 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 372 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 402 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7507 (mm) REVERT: a 455 LEU cc_start: 0.9276 (mm) cc_final: 0.8608 (tt) REVERT: b 82 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8391 (mmmm) REVERT: e 59 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: f 70 PHE cc_start: 0.8201 (m-80) cc_final: 0.7888 (m-80) REVERT: f 79 LEU cc_start: 0.9084 (pp) cc_final: 0.8779 (mm) REVERT: g 123 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7697 (tm-30) REVERT: j 47 MET cc_start: 0.6925 (tpt) cc_final: 0.6660 (tpt) REVERT: n 131 MET cc_start: 0.6895 (mmp) cc_final: 0.6408 (mmt) REVERT: p 312 TRP cc_start: 0.8328 (m100) cc_final: 0.7802 (m100) outliers start: 11 outliers final: 3 residues processed: 377 average time/residue: 0.1456 time to fit residues: 91.3236 Evaluate side-chains 355 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 350 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 402 LEU Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 189 TYR Chi-restraints excluded: chain e residue 59 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 528 ASN ** a 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 HIS h 92 GLN ** l 92 GLN ** 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 = 0.099621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.084214 restraints weight = 79085.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.085975 restraints weight = 45122.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087341 restraints weight = 30198.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.088171 restraints weight = 23214.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088678 restraints weight = 19135.027| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23504 Z= 0.178 Angle : 0.656 12.176 31925 Z= 0.336 Chirality : 0.041 0.222 3811 Planarity : 0.004 0.075 3968 Dihedral : 6.237 76.987 3433 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.66 % Favored : 94.11 % Rotamer: Outliers : 4.98 % Allowed : 29.09 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.16), residues: 3037 helix: 1.63 (0.11), residues: 2133 sheet: -1.07 (0.57), residues: 98 loop : -2.10 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 34 TYR 0.023 0.001 TYR i 144 PHE 0.035 0.002 PHE b 150 TRP 0.023 0.001 TRP f 21 HIS 0.004 0.001 HIS c 370 Details of bonding type rmsd covalent geometry : bond 0.00383 (23495) covalent geometry : angle 0.65324 (31901) hydrogen bonds : bond 0.05765 ( 1772) hydrogen bonds : angle 4.64980 ( 5292) Misc. bond : bond 0.00047 ( 1) link_BETA1-4 : bond 0.01006 ( 4) link_BETA1-4 : angle 2.00041 ( 12) link_NAG-ASN : bond 0.00333 ( 4) link_NAG-ASN : angle 2.54700 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 365 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 57 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7930 (tmt170) REVERT: a 256 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: a 257 MET cc_start: 0.5929 (ptp) cc_final: 0.5555 (ptt) REVERT: a 402 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7854 (mm) REVERT: a 757 TRP cc_start: 0.9104 (t-100) cc_final: 0.8799 (t60) REVERT: b 82 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8412 (mmmm) REVERT: d 75 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6928 (mmtt) REVERT: d 138 MET cc_start: 0.4076 (tpp) cc_final: 0.3483 (tpp) REVERT: f 70 PHE cc_start: 0.8335 (m-80) cc_final: 0.8111 (m-80) REVERT: g 123 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7797 (tm-30) REVERT: j 47 MET cc_start: 0.6958 (tpt) cc_final: 0.6716 (tpt) REVERT: j 132 ILE cc_start: 0.8614 (pt) cc_final: 0.8374 (pt) REVERT: j 155 LYS cc_start: 0.6781 (tptp) cc_final: 0.6183 (tptt) REVERT: n 17 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7509 (mtt) REVERT: n 56 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7909 (pp) REVERT: n 131 MET cc_start: 0.7828 (mmp) cc_final: 0.7366 (tpp) outliers start: 117 outliers final: 60 residues processed: 451 average time/residue: 0.1491 time to fit residues: 110.5517 Evaluate side-chains 411 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 345 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 57 ARG Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 314 VAL Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 377 ILE Chi-restraints excluded: chain a residue 389 ILE Chi-restraints excluded: chain a residue 402 LEU Chi-restraints excluded: chain a residue 441 SER Chi-restraints excluded: chain a residue 445 SER Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 612 HIS Chi-restraints excluded: chain a residue 736 THR Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 759 MET Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 102 ILE Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 164 LEU Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 340 PHE Chi-restraints excluded: chain c residue 345 LEU Chi-restraints excluded: chain c residue 372 GLU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 75 LYS Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 178 ILE Chi-restraints excluded: chain d residue 189 TYR Chi-restraints excluded: chain d residue 197 CYS Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 48 ARG Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 136 ILE Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain j residue 139 GLU Chi-restraints excluded: chain j residue 148 VAL Chi-restraints excluded: chain k residue 127 LEU Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 146 LEU Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain n residue 17 MET Chi-restraints excluded: chain n residue 56 ILE Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 141 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain p residue 305 VAL Chi-restraints excluded: chain p residue 321 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 240 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 84 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 131 optimal weight: 0.0670 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.107193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.090030 restraints weight = 85271.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091717 restraints weight = 50525.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092839 restraints weight = 35025.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.093605 restraints weight = 27449.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.093888 restraints weight = 23260.389| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23504 Z= 0.148 Angle : 0.620 11.712 31925 Z= 0.314 Chirality : 0.040 0.217 3811 Planarity : 0.004 0.073 3968 Dihedral : 5.394 55.867 3427 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.37 % Favored : 94.40 % Rotamer: Outliers : 5.40 % Allowed : 29.26 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.16), residues: 3037 helix: 1.82 (0.11), residues: 2116 sheet: -1.13 (0.54), residues: 102 loop : -2.31 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 119 TYR 0.025 0.001 TYR i 144 PHE 0.037 0.001 PHE b 150 TRP 0.021 0.001 TRP f 21 HIS 0.003 0.001 HIS a 807 Details of bonding type rmsd covalent geometry : bond 0.00307 (23495) covalent geometry : angle 0.61746 (31901) hydrogen bonds : bond 0.05230 ( 1772) hydrogen bonds : angle 4.38025 ( 5292) Misc. bond : bond 0.00029 ( 1) link_BETA1-4 : bond 0.00975 ( 4) link_BETA1-4 : angle 2.28658 ( 12) link_NAG-ASN : bond 0.00254 ( 4) link_NAG-ASN : angle 2.30143 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 378 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 257 MET cc_start: 0.6025 (ptp) cc_final: 0.5741 (ptt) REVERT: a 402 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7545 (mm) REVERT: a 472 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7942 (mt) REVERT: a 550 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9018 (mm) REVERT: a 757 TRP cc_start: 0.9054 (t-100) cc_final: 0.8603 (t60) REVERT: b 19 MET cc_start: 0.8116 (tpp) cc_final: 0.7916 (ttt) REVERT: b 82 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8303 (mmmm) REVERT: d 75 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6892 (mmtt) REVERT: d 138 MET cc_start: 0.3975 (tpp) cc_final: 0.3580 (tpp) REVERT: d 170 GLU cc_start: 0.0078 (OUTLIER) cc_final: -0.0371 (pm20) REVERT: f 70 PHE cc_start: 0.8438 (m-80) cc_final: 0.8148 (m-80) REVERT: g 48 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8003 (mmm-85) REVERT: g 61 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7901 (mmm) REVERT: g 123 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7757 (tm-30) REVERT: g 139 GLU cc_start: 0.7762 (tt0) cc_final: 0.7550 (tt0) REVERT: h 131 MET cc_start: 0.7789 (tpp) cc_final: 0.7473 (tpp) REVERT: j 47 MET cc_start: 0.7351 (tpt) cc_final: 0.7017 (tpt) REVERT: j 68 TYR cc_start: 0.8598 (m-80) cc_final: 0.8354 (m-80) REVERT: j 155 LYS cc_start: 0.6997 (tptp) cc_final: 0.6426 (tptt) REVERT: k 128 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6484 (t80) REVERT: l 17 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8151 (mtp) REVERT: n 131 MET cc_start: 0.8028 (mmp) cc_final: 0.7480 (mmm) REVERT: o 136 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8774 (mp) REVERT: p 312 TRP cc_start: 0.8387 (m100) cc_final: 0.7806 (m100) outliers start: 127 outliers final: 67 residues processed: 470 average time/residue: 0.1437 time to fit residues: 111.7167 Evaluate side-chains 428 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 351 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 314 VAL Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 378 VAL Chi-restraints excluded: chain a residue 389 ILE Chi-restraints excluded: chain a residue 401 PHE Chi-restraints excluded: chain a residue 402 LEU Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 614 ILE Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 759 MET Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 164 LEU Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 340 PHE Chi-restraints excluded: chain c residue 345 LEU Chi-restraints excluded: chain c residue 372 GLU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 431 THR Chi-restraints excluded: chain c residue 453 ASP Chi-restraints excluded: chain d residue 75 LYS Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 170 GLU Chi-restraints excluded: chain d residue 178 ILE Chi-restraints excluded: chain d residue 189 TYR Chi-restraints excluded: chain d residue 197 CYS Chi-restraints excluded: chain f residue 21 TRP Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 48 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 86 LEU Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 28 MET Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain j residue 146 LEU Chi-restraints excluded: chain k residue 128 PHE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain k residue 146 LEU Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 152 LEU Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain o residue 28 MET Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain p residue 305 VAL Chi-restraints excluded: chain p residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 27 optimal weight: 7.9990 chunk 267 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 276 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 242 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 230 optimal weight: 0.0030 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 504 ASN ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.102605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.087031 restraints weight = 80570.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088889 restraints weight = 45790.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.090241 restraints weight = 29957.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091006 restraints weight = 22328.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091584 restraints weight = 18627.074| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23504 Z= 0.140 Angle : 0.625 12.616 31925 Z= 0.314 Chirality : 0.040 0.220 3811 Planarity : 0.004 0.070 3968 Dihedral : 5.023 56.236 3427 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.70 % Favored : 94.07 % Rotamer: Outliers : 5.27 % Allowed : 29.82 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.16), residues: 3037 helix: 1.87 (0.11), residues: 2120 sheet: -1.04 (0.54), residues: 101 loop : -2.36 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG k 119 TYR 0.021 0.001 TYR k 144 PHE 0.025 0.001 PHE g 13 TRP 0.023 0.001 TRP f 21 HIS 0.008 0.001 HIS a 612 Details of bonding type rmsd covalent geometry : bond 0.00290 (23495) covalent geometry : angle 0.62210 (31901) hydrogen bonds : bond 0.04929 ( 1772) hydrogen bonds : angle 4.24325 ( 5292) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.00974 ( 4) link_BETA1-4 : angle 2.59320 ( 12) link_NAG-ASN : bond 0.00229 ( 4) link_NAG-ASN : angle 2.19412 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 391 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 57 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8140 (tmt170) REVERT: a 257 MET cc_start: 0.5692 (ptp) cc_final: 0.5357 (ptt) REVERT: a 455 LEU cc_start: 0.9288 (mm) cc_final: 0.8602 (tt) REVERT: a 472 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7913 (mt) REVERT: a 550 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8958 (mm) REVERT: a 757 TRP cc_start: 0.9058 (t-100) cc_final: 0.8690 (t60) REVERT: a 802 HIS cc_start: 0.8055 (m-70) cc_final: 0.7830 (m-70) REVERT: a 804 LEU cc_start: 0.7597 (tt) cc_final: 0.7332 (tt) REVERT: b 82 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8278 (mmmm) REVERT: b 192 ILE cc_start: 0.8072 (mt) cc_final: 0.7821 (mt) REVERT: c 345 LEU cc_start: 0.7297 (tt) cc_final: 0.7061 (tt) REVERT: d 75 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6870 (mmtt) REVERT: d 138 MET cc_start: 0.4117 (tpp) cc_final: 0.3711 (tpp) REVERT: f 70 PHE cc_start: 0.8299 (m-80) cc_final: 0.8015 (m-80) REVERT: g 7 ASN cc_start: 0.8191 (t0) cc_final: 0.7418 (p0) REVERT: g 48 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7756 (mmm-85) REVERT: g 61 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7928 (mmm) REVERT: g 123 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7721 (tm-30) REVERT: g 139 GLU cc_start: 0.7650 (tt0) cc_final: 0.7412 (tt0) REVERT: g 140 VAL cc_start: 0.7897 (t) cc_final: 0.7689 (t) REVERT: h 131 MET cc_start: 0.7678 (tpp) cc_final: 0.7406 (tpp) REVERT: h 133 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8572 (mm) REVERT: j 47 MET cc_start: 0.7160 (tpt) cc_final: 0.6817 (tpt) REVERT: j 68 TYR cc_start: 0.8619 (m-80) cc_final: 0.8330 (m-80) REVERT: j 155 LYS cc_start: 0.7021 (tptp) cc_final: 0.6646 (tptt) REVERT: k 128 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6480 (t80) REVERT: l 17 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8198 (mtp) REVERT: m 28 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7273 (mtt) REVERT: m 140 VAL cc_start: 0.9311 (t) cc_final: 0.9100 (t) REVERT: n 68 TYR cc_start: 0.7848 (m-10) cc_final: 0.7563 (m-80) REVERT: n 131 MET cc_start: 0.8057 (mmp) cc_final: 0.7517 (mmm) REVERT: n 137 PHE cc_start: 0.8439 (m-80) cc_final: 0.7985 (m-80) REVERT: o 136 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8574 (mp) REVERT: p 312 TRP cc_start: 0.8353 (m100) cc_final: 0.7754 (m100) outliers start: 124 outliers final: 75 residues processed: 482 average time/residue: 0.1436 time to fit residues: 114.9936 Evaluate side-chains 445 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 359 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 57 ARG Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 372 HIS Chi-restraints excluded: chain a residue 378 VAL Chi-restraints excluded: chain a residue 389 ILE Chi-restraints excluded: chain a residue 401 PHE Chi-restraints excluded: chain a residue 402 LEU Chi-restraints excluded: chain a residue 445 SER Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 611 ILE Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 759 MET Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 137 MET Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 164 LEU Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 327 LEU Chi-restraints excluded: chain c residue 340 PHE Chi-restraints excluded: chain c residue 372 GLU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 431 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 75 LYS Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 189 TYR Chi-restraints excluded: chain d residue 197 CYS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 48 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 86 LEU Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 28 MET Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 70 LEU Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain k residue 84 ILE Chi-restraints excluded: chain k residue 128 PHE Chi-restraints excluded: chain k residue 146 LEU Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 28 MET Chi-restraints excluded: chain m residue 135 LEU Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain o residue 28 MET Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain p residue 305 VAL Chi-restraints excluded: chain p residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 242 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 99 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.100622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.085377 restraints weight = 77939.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.087281 restraints weight = 44356.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.088532 restraints weight = 29409.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.089380 restraints weight = 22124.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.089811 restraints weight = 18323.531| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23504 Z= 0.152 Angle : 0.639 10.454 31925 Z= 0.321 Chirality : 0.040 0.276 3811 Planarity : 0.004 0.069 3968 Dihedral : 4.871 57.060 3427 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.40 % Favored : 94.37 % Rotamer: Outliers : 6.34 % Allowed : 29.60 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.16), residues: 3037 helix: 1.89 (0.11), residues: 2121 sheet: -0.45 (0.58), residues: 89 loop : -2.34 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG l 48 TYR 0.024 0.001 TYR k 144 PHE 0.027 0.001 PHE g 13 TRP 0.024 0.001 TRP f 21 HIS 0.003 0.001 HIS c 370 Details of bonding type rmsd covalent geometry : bond 0.00331 (23495) covalent geometry : angle 0.63514 (31901) hydrogen bonds : bond 0.04908 ( 1772) hydrogen bonds : angle 4.21822 ( 5292) Misc. bond : bond 0.00026 ( 1) link_BETA1-4 : bond 0.01026 ( 4) link_BETA1-4 : angle 2.76197 ( 12) link_NAG-ASN : bond 0.00285 ( 4) link_NAG-ASN : angle 2.37175 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 369 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 16 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.5155 (m-80) REVERT: a 57 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8104 (tmt170) REVERT: a 79 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.6167 (tp) REVERT: a 472 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7939 (mt) REVERT: a 550 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8961 (mm) REVERT: a 757 TRP cc_start: 0.9115 (t-100) cc_final: 0.8809 (t60) REVERT: a 802 HIS cc_start: 0.8135 (m-70) cc_final: 0.7809 (m-70) REVERT: b 19 MET cc_start: 0.8119 (tpp) cc_final: 0.7853 (ttt) REVERT: b 82 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8288 (mmmm) REVERT: d 75 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6823 (mmtt) REVERT: d 138 MET cc_start: 0.4192 (tpp) cc_final: 0.3978 (tpp) REVERT: f 70 PHE cc_start: 0.8442 (m-80) cc_final: 0.8069 (m-80) REVERT: f 82 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: g 7 ASN cc_start: 0.8288 (t0) cc_final: 0.7565 (p0) REVERT: g 48 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7765 (mmm-85) REVERT: g 61 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7964 (mmm) REVERT: g 123 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7713 (tm-30) REVERT: g 139 GLU cc_start: 0.7744 (tt0) cc_final: 0.7473 (tt0) REVERT: h 131 MET cc_start: 0.7605 (tpp) cc_final: 0.7285 (mmp) REVERT: i 151 ILE cc_start: 0.9130 (tp) cc_final: 0.8823 (tp) REVERT: j 47 MET cc_start: 0.6947 (tpt) cc_final: 0.6659 (tpt) REVERT: j 131 MET cc_start: 0.9174 (mmm) cc_final: 0.8962 (tpt) REVERT: j 155 LYS cc_start: 0.7120 (tptp) cc_final: 0.6759 (tptt) REVERT: k 128 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6639 (t80) REVERT: k 144 TYR cc_start: 0.9133 (m-80) cc_final: 0.8894 (m-80) REVERT: l 17 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8299 (mtp) REVERT: m 28 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7317 (mtt) REVERT: n 131 MET cc_start: 0.8107 (mmp) cc_final: 0.7629 (tpp) REVERT: n 137 PHE cc_start: 0.8475 (m-80) cc_final: 0.8012 (m-80) REVERT: o 136 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8610 (mp) REVERT: p 312 TRP cc_start: 0.8380 (m100) cc_final: 0.7764 (m100) REVERT: p 340 TYR cc_start: 0.4159 (OUTLIER) cc_final: 0.3797 (t80) outliers start: 149 outliers final: 89 residues processed: 480 average time/residue: 0.1451 time to fit residues: 116.1976 Evaluate side-chains 456 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 353 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 16 PHE Chi-restraints excluded: chain a residue 57 ARG Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 85 ASN Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 372 HIS Chi-restraints excluded: chain a residue 378 VAL Chi-restraints excluded: chain a residue 389 ILE Chi-restraints excluded: chain a residue 401 PHE Chi-restraints excluded: chain a residue 402 LEU Chi-restraints excluded: chain a residue 445 SER Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 591 ILE Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 611 ILE Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 759 MET Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 164 LEU Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain c residue 255 HIS Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 327 LEU Chi-restraints excluded: chain c residue 340 PHE Chi-restraints excluded: chain c residue 372 GLU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 431 THR Chi-restraints excluded: chain c residue 453 ASP Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 75 LYS Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 178 ILE Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 189 TYR Chi-restraints excluded: chain d residue 197 CYS Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 37 SER Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 48 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 86 LEU Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 154 THR Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 28 MET Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 137 PHE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain j residue 70 LEU Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain k residue 84 ILE Chi-restraints excluded: chain k residue 128 PHE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 28 MET Chi-restraints excluded: chain m residue 152 LEU Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain p residue 305 VAL Chi-restraints excluded: chain p residue 321 VAL Chi-restraints excluded: chain p residue 340 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 228 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 chunk 299 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 166 optimal weight: 5.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 225 GLN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.101602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.086012 restraints weight = 80603.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.087941 restraints weight = 45301.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089141 restraints weight = 29816.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.089870 restraints weight = 22327.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.090553 restraints weight = 18523.829| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23504 Z= 0.157 Angle : 0.654 13.405 31925 Z= 0.326 Chirality : 0.040 0.258 3811 Planarity : 0.004 0.068 3968 Dihedral : 4.856 56.187 3427 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.70 % Favored : 94.11 % Rotamer: Outliers : 6.47 % Allowed : 29.77 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.16), residues: 3037 helix: 1.91 (0.11), residues: 2114 sheet: -0.52 (0.58), residues: 91 loop : -2.30 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG k 119 TYR 0.021 0.001 TYR b 70 PHE 0.026 0.001 PHE g 13 TRP 0.025 0.001 TRP f 21 HIS 0.003 0.001 HIS c 370 Details of bonding type rmsd covalent geometry : bond 0.00346 (23495) covalent geometry : angle 0.65027 (31901) hydrogen bonds : bond 0.04925 ( 1772) hydrogen bonds : angle 4.20280 ( 5292) Misc. bond : bond 0.00030 ( 1) link_BETA1-4 : bond 0.01099 ( 4) link_BETA1-4 : angle 2.92910 ( 12) link_NAG-ASN : bond 0.00290 ( 4) link_NAG-ASN : angle 2.43934 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 366 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 16 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.5196 (m-80) REVERT: a 57 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8152 (tmt170) REVERT: a 257 MET cc_start: 0.5957 (ptt) cc_final: 0.5636 (ptt) REVERT: a 402 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7531 (mm) REVERT: a 472 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7931 (mt) REVERT: a 550 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8962 (mm) REVERT: a 757 TRP cc_start: 0.9103 (t-100) cc_final: 0.8900 (t60) REVERT: b 82 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8305 (mmmm) REVERT: d 75 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6845 (mmtt) REVERT: d 138 MET cc_start: 0.4408 (tpp) cc_final: 0.4201 (tpp) REVERT: d 168 ILE cc_start: 0.7409 (mm) cc_final: 0.7099 (mm) REVERT: f 24 ILE cc_start: 0.9238 (pt) cc_final: 0.8915 (mt) REVERT: f 70 PHE cc_start: 0.8277 (m-80) cc_final: 0.7945 (m-80) REVERT: f 79 LEU cc_start: 0.9088 (pp) cc_final: 0.8814 (mm) REVERT: f 82 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: g 7 ASN cc_start: 0.8272 (t0) cc_final: 0.7537 (p0) REVERT: g 48 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7742 (mmm-85) REVERT: g 61 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7974 (mmm) REVERT: g 123 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7698 (tm-30) REVERT: g 139 GLU cc_start: 0.7760 (tt0) cc_final: 0.7530 (tt0) REVERT: g 140 VAL cc_start: 0.7855 (t) cc_final: 0.7622 (t) REVERT: h 131 MET cc_start: 0.7539 (tpp) cc_final: 0.7207 (mmp) REVERT: i 151 ILE cc_start: 0.9165 (tp) cc_final: 0.8840 (tp) REVERT: j 47 MET cc_start: 0.7022 (tpt) cc_final: 0.6756 (tpt) REVERT: j 155 LYS cc_start: 0.7223 (tptp) cc_final: 0.6869 (tptt) REVERT: k 36 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8486 (ttmm) REVERT: k 128 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.6817 (t80) REVERT: k 144 TYR cc_start: 0.9139 (m-80) cc_final: 0.8903 (m-80) REVERT: l 17 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8314 (mtp) REVERT: l 119 ARG cc_start: 0.8243 (mmt180) cc_final: 0.7679 (mmt180) REVERT: m 131 MET cc_start: 0.8442 (mmp) cc_final: 0.7996 (mmm) REVERT: n 68 TYR cc_start: 0.7788 (m-80) cc_final: 0.7465 (m-80) REVERT: n 131 MET cc_start: 0.8068 (mmp) cc_final: 0.7821 (mmm) REVERT: o 133 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7829 (mm) REVERT: o 136 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8638 (mp) REVERT: p 312 TRP cc_start: 0.8420 (m100) cc_final: 0.7812 (m100) REVERT: p 340 TYR cc_start: 0.4162 (OUTLIER) cc_final: 0.3805 (t80) outliers start: 152 outliers final: 91 residues processed: 479 average time/residue: 0.1447 time to fit residues: 115.2473 Evaluate side-chains 460 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 355 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 10 MET Chi-restraints excluded: chain a residue 16 PHE Chi-restraints excluded: chain a residue 57 ARG Chi-restraints excluded: chain a residue 85 ASN Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 372 HIS Chi-restraints excluded: chain a residue 378 VAL Chi-restraints excluded: chain a residue 389 ILE Chi-restraints excluded: chain a residue 401 PHE Chi-restraints excluded: chain a residue 402 LEU Chi-restraints excluded: chain a residue 445 SER Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 571 PHE Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 759 MET Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 164 LEU Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain c residue 255 HIS Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 327 LEU Chi-restraints excluded: chain c residue 340 PHE Chi-restraints excluded: chain c residue 372 GLU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 431 THR Chi-restraints excluded: chain c residue 453 ASP Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 75 LYS Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 178 ILE Chi-restraints excluded: chain d residue 189 TYR Chi-restraints excluded: chain d residue 197 CYS Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 21 TRP Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain f residue 37 SER Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 48 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 86 LEU Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 154 THR Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 115 ASP Chi-restraints excluded: chain i residue 28 MET Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain k residue 84 ILE Chi-restraints excluded: chain k residue 128 PHE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 93 LEU Chi-restraints excluded: chain m residue 135 LEU Chi-restraints excluded: chain m residue 152 LEU Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain p residue 305 VAL Chi-restraints excluded: chain p residue 309 LEU Chi-restraints excluded: chain p residue 321 VAL Chi-restraints excluded: chain p residue 325 SER Chi-restraints excluded: chain p residue 340 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 291 optimal weight: 2.9990 chunk 268 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 152 optimal weight: 0.4980 chunk 174 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 140 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 286 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.102474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.087012 restraints weight = 79707.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088945 restraints weight = 44382.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.090187 restraints weight = 29151.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.090645 restraints weight = 21719.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.091432 restraints weight = 18740.342| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23504 Z= 0.144 Angle : 0.667 13.243 31925 Z= 0.329 Chirality : 0.041 0.285 3811 Planarity : 0.004 0.067 3968 Dihedral : 4.839 58.303 3427 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.43 % Favored : 94.37 % Rotamer: Outliers : 5.61 % Allowed : 30.84 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.16), residues: 3037 helix: 1.91 (0.11), residues: 2114 sheet: -0.52 (0.58), residues: 91 loop : -2.31 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG k 119 TYR 0.022 0.001 TYR k 144 PHE 0.024 0.001 PHE g 13 TRP 0.023 0.001 TRP f 21 HIS 0.022 0.001 HIS a 802 Details of bonding type rmsd covalent geometry : bond 0.00309 (23495) covalent geometry : angle 0.66281 (31901) hydrogen bonds : bond 0.04832 ( 1772) hydrogen bonds : angle 4.16011 ( 5292) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.01109 ( 4) link_BETA1-4 : angle 3.00914 ( 12) link_NAG-ASN : bond 0.00240 ( 4) link_NAG-ASN : angle 2.25577 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 377 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 16 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.5179 (m-80) REVERT: a 57 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8091 (tmt170) REVERT: a 257 MET cc_start: 0.6000 (ptt) cc_final: 0.5692 (ptt) REVERT: a 550 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8947 (mm) REVERT: a 757 TRP cc_start: 0.9089 (t-100) cc_final: 0.8875 (t60) REVERT: a 804 LEU cc_start: 0.7311 (tt) cc_final: 0.7105 (tt) REVERT: b 19 MET cc_start: 0.8124 (tpp) cc_final: 0.7814 (tpt) REVERT: b 82 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8311 (mmmm) REVERT: d 75 LYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6801 (mmtt) REVERT: d 168 ILE cc_start: 0.7438 (mm) cc_final: 0.7135 (mm) REVERT: f 24 ILE cc_start: 0.9241 (pt) cc_final: 0.8910 (mt) REVERT: f 62 TYR cc_start: 0.8890 (m-80) cc_final: 0.8551 (m-10) REVERT: f 70 PHE cc_start: 0.8384 (m-80) cc_final: 0.8044 (m-80) REVERT: f 79 LEU cc_start: 0.9068 (pp) cc_final: 0.8803 (mm) REVERT: f 82 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: g 7 ASN cc_start: 0.8257 (t0) cc_final: 0.7564 (p0) REVERT: g 48 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7744 (mmm-85) REVERT: g 61 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7567 (mmm) REVERT: g 139 GLU cc_start: 0.7618 (tt0) cc_final: 0.7119 (tt0) REVERT: i 151 ILE cc_start: 0.9200 (tp) cc_final: 0.8868 (tp) REVERT: j 47 MET cc_start: 0.6935 (tpt) cc_final: 0.6656 (tpt) REVERT: j 155 LYS cc_start: 0.7199 (tptp) cc_final: 0.6866 (tptt) REVERT: k 36 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8486 (ttmm) REVERT: k 128 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6658 (t80) REVERT: k 144 TYR cc_start: 0.9157 (m-80) cc_final: 0.8814 (m-80) REVERT: l 17 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8345 (mtp) REVERT: m 28 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7319 (mtt) REVERT: m 131 MET cc_start: 0.8432 (mmp) cc_final: 0.8021 (mmm) REVERT: n 68 TYR cc_start: 0.7792 (m-80) cc_final: 0.7296 (m-80) REVERT: n 131 MET cc_start: 0.8063 (mmp) cc_final: 0.7853 (mmm) REVERT: n 137 PHE cc_start: 0.8454 (m-80) cc_final: 0.8131 (m-80) REVERT: o 133 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7844 (mm) REVERT: o 136 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8614 (mp) REVERT: p 312 TRP cc_start: 0.8318 (m100) cc_final: 0.7725 (m100) REVERT: p 340 TYR cc_start: 0.4261 (OUTLIER) cc_final: 0.3926 (t80) outliers start: 132 outliers final: 93 residues processed: 473 average time/residue: 0.1472 time to fit residues: 115.4530 Evaluate side-chains 465 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 359 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 16 PHE Chi-restraints excluded: chain a residue 57 ARG Chi-restraints excluded: chain a residue 228 GLN Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 372 HIS Chi-restraints excluded: chain a residue 378 VAL Chi-restraints excluded: chain a residue 389 ILE Chi-restraints excluded: chain a residue 401 PHE Chi-restraints excluded: chain a residue 402 LEU Chi-restraints excluded: chain a residue 445 SER Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 571 PHE Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 759 MET Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 164 LEU Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 255 HIS Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 327 LEU Chi-restraints excluded: chain c residue 340 PHE Chi-restraints excluded: chain c residue 355 HIS Chi-restraints excluded: chain c residue 372 GLU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 431 THR Chi-restraints excluded: chain c residue 453 ASP Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 75 LYS Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 178 ILE Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 189 TYR Chi-restraints excluded: chain d residue 197 CYS Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain f residue 37 SER Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 48 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 61 MET Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 86 LEU Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 28 MET Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 137 PHE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain k residue 84 ILE Chi-restraints excluded: chain k residue 128 PHE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 28 MET Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain m residue 135 LEU Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain p residue 305 VAL Chi-restraints excluded: chain p residue 309 LEU Chi-restraints excluded: chain p residue 317 LEU Chi-restraints excluded: chain p residue 321 VAL Chi-restraints excluded: chain p residue 325 SER Chi-restraints excluded: chain p residue 340 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 140 optimal weight: 5.9990 chunk 282 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 177 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.103341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.088603 restraints weight = 78107.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.090481 restraints weight = 43669.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.091602 restraints weight = 28721.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.092491 restraints weight = 21807.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.093080 restraints weight = 17782.411| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23504 Z= 0.145 Angle : 0.676 12.783 31925 Z= 0.332 Chirality : 0.040 0.296 3811 Planarity : 0.004 0.066 3968 Dihedral : 4.810 59.596 3427 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.60 % Favored : 94.20 % Rotamer: Outliers : 5.53 % Allowed : 31.09 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.16), residues: 3037 helix: 1.92 (0.11), residues: 2114 sheet: -0.47 (0.59), residues: 91 loop : -2.32 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG k 119 TYR 0.025 0.001 TYR k 144 PHE 0.031 0.001 PHE m 90 TRP 0.028 0.001 TRP f 21 HIS 0.013 0.001 HIS a 802 Details of bonding type rmsd covalent geometry : bond 0.00312 (23495) covalent geometry : angle 0.67184 (31901) hydrogen bonds : bond 0.04774 ( 1772) hydrogen bonds : angle 4.14830 ( 5292) Misc. bond : bond 0.00030 ( 1) link_BETA1-4 : bond 0.01036 ( 4) link_BETA1-4 : angle 3.08334 ( 12) link_NAG-ASN : bond 0.00231 ( 4) link_NAG-ASN : angle 2.23495 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 374 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 16 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.5065 (m-80) REVERT: a 57 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8108 (tmt170) REVERT: a 257 MET cc_start: 0.6023 (ptt) cc_final: 0.5757 (ptt) REVERT: a 455 LEU cc_start: 0.9256 (mm) cc_final: 0.8568 (tt) REVERT: a 550 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8957 (mm) REVERT: a 718 MET cc_start: 0.7095 (ptt) cc_final: 0.6471 (mmt) REVERT: a 804 LEU cc_start: 0.7588 (tt) cc_final: 0.7362 (tt) REVERT: b 19 MET cc_start: 0.8040 (tpp) cc_final: 0.7679 (tpt) REVERT: b 82 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8314 (mmmm) REVERT: b 192 ILE cc_start: 0.8156 (mt) cc_final: 0.7905 (mt) REVERT: c 420 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.6210 (p90) REVERT: d 138 MET cc_start: 0.4616 (tpp) cc_final: 0.3641 (tpp) REVERT: d 168 ILE cc_start: 0.7359 (mm) cc_final: 0.7056 (mm) REVERT: f 24 ILE cc_start: 0.9234 (pt) cc_final: 0.8884 (mt) REVERT: f 62 TYR cc_start: 0.8835 (m-80) cc_final: 0.8460 (m-10) REVERT: f 70 PHE cc_start: 0.8346 (m-80) cc_final: 0.8047 (m-80) REVERT: f 79 LEU cc_start: 0.9033 (pp) cc_final: 0.8810 (mm) REVERT: f 82 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: g 7 ASN cc_start: 0.8182 (t0) cc_final: 0.7500 (p0) REVERT: g 48 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7778 (mmm-85) REVERT: g 139 GLU cc_start: 0.7500 (tt0) cc_final: 0.7145 (tt0) REVERT: g 144 TYR cc_start: 0.8783 (m-80) cc_final: 0.8242 (m-80) REVERT: h 144 TYR cc_start: 0.5972 (m-10) cc_final: 0.5525 (m-10) REVERT: j 47 MET cc_start: 0.6839 (tpt) cc_final: 0.6577 (tpt) REVERT: j 131 MET cc_start: 0.9065 (mmm) cc_final: 0.8758 (mmm) REVERT: j 155 LYS cc_start: 0.7186 (tptp) cc_final: 0.6849 (tptt) REVERT: k 36 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8463 (ttmm) REVERT: k 128 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6887 (t80) REVERT: k 144 TYR cc_start: 0.9089 (m-80) cc_final: 0.8662 (m-80) REVERT: l 17 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8255 (mtp) REVERT: l 119 ARG cc_start: 0.8313 (mmt180) cc_final: 0.7663 (mmt180) REVERT: m 28 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7208 (mtt) REVERT: n 68 TYR cc_start: 0.7714 (m-80) cc_final: 0.7192 (m-80) REVERT: n 137 PHE cc_start: 0.8397 (m-80) cc_final: 0.8092 (m-80) REVERT: n 139 GLU cc_start: 0.8549 (tp30) cc_final: 0.8020 (tm-30) REVERT: o 133 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7871 (mm) REVERT: o 136 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8639 (mp) REVERT: p 312 TRP cc_start: 0.8285 (m100) cc_final: 0.7683 (m100) REVERT: p 340 TYR cc_start: 0.4290 (OUTLIER) cc_final: 0.3927 (t80) outliers start: 130 outliers final: 95 residues processed: 471 average time/residue: 0.1498 time to fit residues: 116.3820 Evaluate side-chains 471 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 364 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 10 MET Chi-restraints excluded: chain a residue 16 PHE Chi-restraints excluded: chain a residue 57 ARG Chi-restraints excluded: chain a residue 228 GLN Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 372 HIS Chi-restraints excluded: chain a residue 378 VAL Chi-restraints excluded: chain a residue 389 ILE Chi-restraints excluded: chain a residue 401 PHE Chi-restraints excluded: chain a residue 402 LEU Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 445 SER Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 571 PHE Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 759 MET Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 164 LEU Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 255 HIS Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 327 LEU Chi-restraints excluded: chain c residue 340 PHE Chi-restraints excluded: chain c residue 355 HIS Chi-restraints excluded: chain c residue 372 GLU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 420 PHE Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 431 THR Chi-restraints excluded: chain c residue 453 ASP Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 178 ILE Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 197 CYS Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain f residue 37 SER Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 48 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 28 MET Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 137 PHE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain j residue 70 LEU Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain k residue 84 ILE Chi-restraints excluded: chain k residue 128 PHE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 28 MET Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain p residue 305 VAL Chi-restraints excluded: chain p residue 309 LEU Chi-restraints excluded: chain p residue 317 LEU Chi-restraints excluded: chain p residue 321 VAL Chi-restraints excluded: chain p residue 325 SER Chi-restraints excluded: chain p residue 340 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 49 optimal weight: 0.5980 chunk 199 optimal weight: 0.3980 chunk 164 optimal weight: 10.0000 chunk 234 optimal weight: 0.7980 chunk 273 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 279 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 281 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.104105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.089146 restraints weight = 79028.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.091056 restraints weight = 44301.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.092226 restraints weight = 28924.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.093113 restraints weight = 21714.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.093706 restraints weight = 17811.984| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23504 Z= 0.145 Angle : 0.685 12.289 31925 Z= 0.335 Chirality : 0.041 0.254 3811 Planarity : 0.004 0.065 3968 Dihedral : 4.729 57.750 3425 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.66 % Favored : 94.14 % Rotamer: Outliers : 5.23 % Allowed : 31.52 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.16), residues: 3037 helix: 1.89 (0.11), residues: 2127 sheet: -0.47 (0.59), residues: 91 loop : -2.33 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG k 119 TYR 0.023 0.001 TYR k 144 PHE 0.031 0.001 PHE m 90 TRP 0.032 0.001 TRP a 757 HIS 0.023 0.001 HIS a 802 Details of bonding type rmsd covalent geometry : bond 0.00315 (23495) covalent geometry : angle 0.68083 (31901) hydrogen bonds : bond 0.04743 ( 1772) hydrogen bonds : angle 4.13454 ( 5292) Misc. bond : bond 0.00030 ( 1) link_BETA1-4 : bond 0.01110 ( 4) link_BETA1-4 : angle 3.13850 ( 12) link_NAG-ASN : bond 0.00235 ( 4) link_NAG-ASN : angle 2.22120 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 370 time to evaluate : 0.969 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: a 16 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.5114 (m-80) REVERT: a 57 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8220 (tmt170) REVERT: a 455 LEU cc_start: 0.9247 (mm) cc_final: 0.8549 (tt) REVERT: a 550 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8959 (mm) REVERT: b 19 MET cc_start: 0.8044 (tpp) cc_final: 0.7684 (tpt) REVERT: b 82 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8322 (mmmm) REVERT: b 192 ILE cc_start: 0.8142 (mt) cc_final: 0.7874 (mt) REVERT: c 420 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.6201 (p90) REVERT: d 138 MET cc_start: 0.4611 (tpp) cc_final: 0.3730 (tpp) REVERT: d 168 ILE cc_start: 0.7407 (mm) cc_final: 0.7111 (mm) REVERT: f 24 ILE cc_start: 0.9233 (pt) cc_final: 0.8897 (mt) REVERT: f 62 TYR cc_start: 0.8847 (m-80) cc_final: 0.8466 (m-10) REVERT: f 70 PHE cc_start: 0.8352 (m-80) cc_final: 0.8042 (m-80) REVERT: f 82 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: g 7 ASN cc_start: 0.8229 (t0) cc_final: 0.7500 (p0) REVERT: g 48 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7757 (mmm-85) REVERT: g 139 GLU cc_start: 0.7617 (tt0) cc_final: 0.7351 (tt0) REVERT: g 144 TYR cc_start: 0.8765 (m-80) cc_final: 0.8187 (m-80) REVERT: h 144 TYR cc_start: 0.6117 (m-10) cc_final: 0.5674 (m-10) REVERT: j 47 MET cc_start: 0.6852 (tpt) cc_final: 0.6578 (tpt) REVERT: j 131 MET cc_start: 0.9138 (mmm) cc_final: 0.8889 (mmm) REVERT: j 155 LYS cc_start: 0.7173 (tptp) cc_final: 0.6820 (tptt) REVERT: k 36 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8480 (ttmm) REVERT: k 144 TYR cc_start: 0.9055 (m-80) cc_final: 0.8605 (m-80) REVERT: l 17 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8250 (mtp) REVERT: l 47 MET cc_start: 0.8245 (pmm) cc_final: 0.7871 (tmm) REVERT: m 28 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7212 (mtt) REVERT: m 131 MET cc_start: 0.8220 (mmp) cc_final: 0.7888 (tpp) REVERT: n 68 TYR cc_start: 0.7741 (m-80) cc_final: 0.7236 (m-80) REVERT: n 139 GLU cc_start: 0.8504 (tp30) cc_final: 0.8172 (tm-30) REVERT: o 136 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8512 (mp) REVERT: p 312 TRP cc_start: 0.8286 (m100) cc_final: 0.7697 (m100) REVERT: p 314 MET cc_start: 0.8166 (mmm) cc_final: 0.7936 (mmm) REVERT: p 340 TYR cc_start: 0.4301 (OUTLIER) cc_final: 0.3931 (t80) outliers start: 123 outliers final: 96 residues processed: 464 average time/residue: 0.1432 time to fit residues: 110.4923 Evaluate side-chains 466 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 360 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 16 PHE Chi-restraints excluded: chain a residue 57 ARG Chi-restraints excluded: chain a residue 228 GLN Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 372 HIS Chi-restraints excluded: chain a residue 378 VAL Chi-restraints excluded: chain a residue 389 ILE Chi-restraints excluded: chain a residue 401 PHE Chi-restraints excluded: chain a residue 402 LEU Chi-restraints excluded: chain a residue 421 VAL Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 571 PHE Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 759 MET Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 164 LEU Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 255 HIS Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 327 LEU Chi-restraints excluded: chain c residue 340 PHE Chi-restraints excluded: chain c residue 355 HIS Chi-restraints excluded: chain c residue 372 GLU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 420 PHE Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 431 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 178 ILE Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 189 TYR Chi-restraints excluded: chain d residue 197 CYS Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain f residue 37 SER Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 48 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 28 MET Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 137 PHE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain j residue 70 LEU Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain k residue 84 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 28 MET Chi-restraints excluded: chain m residue 123 GLN Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain p residue 305 VAL Chi-restraints excluded: chain p residue 309 LEU Chi-restraints excluded: chain p residue 317 LEU Chi-restraints excluded: chain p residue 321 VAL Chi-restraints excluded: chain p residue 325 SER Chi-restraints excluded: chain p residue 340 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 chunk 246 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 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 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.103432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.088621 restraints weight = 79045.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.090460 restraints weight = 44281.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091667 restraints weight = 29606.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.092443 restraints weight = 22094.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.093001 restraints weight = 18279.741| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23504 Z= 0.151 Angle : 0.705 14.529 31925 Z= 0.344 Chirality : 0.041 0.262 3811 Planarity : 0.004 0.064 3968 Dihedral : 4.718 56.577 3425 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.70 % Favored : 94.11 % Rotamer: Outliers : 4.64 % Allowed : 32.20 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.16), residues: 3037 helix: 1.89 (0.11), residues: 2128 sheet: -0.49 (0.58), residues: 91 loop : -2.32 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG k 119 TYR 0.039 0.001 TYR l 144 PHE 0.035 0.001 PHE g 13 TRP 0.034 0.001 TRP f 21 HIS 0.017 0.001 HIS a 802 Details of bonding type rmsd covalent geometry : bond 0.00330 (23495) covalent geometry : angle 0.70153 (31901) hydrogen bonds : bond 0.04757 ( 1772) hydrogen bonds : angle 4.13589 ( 5292) Misc. bond : bond 0.00028 ( 1) link_BETA1-4 : bond 0.01068 ( 4) link_BETA1-4 : angle 3.19893 ( 12) link_NAG-ASN : bond 0.00246 ( 4) link_NAG-ASN : angle 2.25086 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6074 Ramachandran restraints generated. 3037 Oldfield, 0 Emsley, 3037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 366 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 16 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.5086 (m-80) REVERT: a 57 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8202 (tmt170) REVERT: a 455 LEU cc_start: 0.9256 (mm) cc_final: 0.8548 (tt) REVERT: a 550 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8950 (mm) REVERT: b 19 MET cc_start: 0.8041 (tpp) cc_final: 0.7675 (tpt) REVERT: b 82 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8329 (mmmm) REVERT: b 192 ILE cc_start: 0.8159 (mt) cc_final: 0.7903 (mt) REVERT: c 420 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.6190 (p90) REVERT: d 138 MET cc_start: 0.4699 (tpp) cc_final: 0.3826 (tpp) REVERT: f 24 ILE cc_start: 0.9164 (pt) cc_final: 0.8819 (mt) REVERT: f 62 TYR cc_start: 0.8850 (m-80) cc_final: 0.8476 (m-10) REVERT: f 70 PHE cc_start: 0.8380 (m-80) cc_final: 0.8063 (m-80) REVERT: f 79 LEU cc_start: 0.9154 (mm) cc_final: 0.8879 (pp) REVERT: f 82 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: g 7 ASN cc_start: 0.8238 (t0) cc_final: 0.7508 (p0) REVERT: g 48 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7794 (mmm-85) REVERT: g 144 TYR cc_start: 0.8762 (m-80) cc_final: 0.8233 (m-80) REVERT: h 144 TYR cc_start: 0.6109 (m-10) cc_final: 0.5637 (m-10) REVERT: j 47 MET cc_start: 0.6880 (tpt) cc_final: 0.6580 (tpt) REVERT: j 131 MET cc_start: 0.9134 (mmm) cc_final: 0.8911 (mmm) REVERT: j 155 LYS cc_start: 0.7161 (tptp) cc_final: 0.6799 (tptt) REVERT: k 36 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8487 (ttmm) REVERT: k 144 TYR cc_start: 0.9063 (m-80) cc_final: 0.8740 (m-80) REVERT: l 17 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8256 (mtp) REVERT: l 47 MET cc_start: 0.8346 (pmm) cc_final: 0.7762 (tmm) REVERT: l 119 ARG cc_start: 0.8285 (mmt180) cc_final: 0.7626 (mmt180) REVERT: m 28 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7229 (mtt) REVERT: m 131 MET cc_start: 0.8226 (mmp) cc_final: 0.7882 (tpp) REVERT: n 68 TYR cc_start: 0.7742 (m-80) cc_final: 0.7120 (m-80) REVERT: n 136 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8754 (mt) REVERT: n 139 GLU cc_start: 0.8492 (tp30) cc_final: 0.7999 (tm-30) REVERT: o 133 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7778 (mm) REVERT: o 136 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8516 (mp) REVERT: p 312 TRP cc_start: 0.8281 (m100) cc_final: 0.7677 (m100) REVERT: p 314 MET cc_start: 0.8228 (mmm) cc_final: 0.8015 (mmm) REVERT: p 340 TYR cc_start: 0.4308 (OUTLIER) cc_final: 0.3948 (t80) outliers start: 109 outliers final: 94 residues processed: 448 average time/residue: 0.1465 time to fit residues: 109.1325 Evaluate side-chains 467 residues out of total 2477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 361 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 16 PHE Chi-restraints excluded: chain a residue 57 ARG Chi-restraints excluded: chain a residue 228 GLN Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 331 ASP Chi-restraints excluded: chain a residue 371 THR Chi-restraints excluded: chain a residue 372 HIS Chi-restraints excluded: chain a residue 378 VAL Chi-restraints excluded: chain a residue 389 ILE Chi-restraints excluded: chain a residue 401 PHE Chi-restraints excluded: chain a residue 402 LEU Chi-restraints excluded: chain a residue 453 MET Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 530 LEU Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 571 PHE Chi-restraints excluded: chain a residue 595 TRP Chi-restraints excluded: chain a residue 652 LEU Chi-restraints excluded: chain a residue 740 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 759 MET Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 76 ILE Chi-restraints excluded: chain b residue 100 VAL Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain b residue 149 LEU Chi-restraints excluded: chain b residue 154 CYS Chi-restraints excluded: chain b residue 164 LEU Chi-restraints excluded: chain b residue 178 ILE Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 255 HIS Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain c residue 292 VAL Chi-restraints excluded: chain c residue 327 LEU Chi-restraints excluded: chain c residue 340 PHE Chi-restraints excluded: chain c residue 355 HIS Chi-restraints excluded: chain c residue 372 GLU Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 420 PHE Chi-restraints excluded: chain c residue 430 LEU Chi-restraints excluded: chain c residue 431 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 84 HIS Chi-restraints excluded: chain d residue 178 ILE Chi-restraints excluded: chain d residue 181 ILE Chi-restraints excluded: chain d residue 189 TYR Chi-restraints excluded: chain d residue 197 CYS Chi-restraints excluded: chain e residue 41 LEU Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain f residue 37 SER Chi-restraints excluded: chain f residue 82 PHE Chi-restraints excluded: chain g residue 48 ARG Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 81 THR Chi-restraints excluded: chain g residue 115 ASP Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 136 ILE Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 75 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 28 MET Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 84 ILE Chi-restraints excluded: chain i residue 104 LEU Chi-restraints excluded: chain i residue 135 LEU Chi-restraints excluded: chain i residue 137 PHE Chi-restraints excluded: chain i residue 152 LEU Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 51 LEU Chi-restraints excluded: chain j residue 70 LEU Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 135 LEU Chi-restraints excluded: chain k residue 84 ILE Chi-restraints excluded: chain k residue 143 LEU Chi-restraints excluded: chain l residue 17 MET Chi-restraints excluded: chain l residue 71 VAL Chi-restraints excluded: chain l residue 136 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 17 MET Chi-restraints excluded: chain m residue 28 MET Chi-restraints excluded: chain m residue 86 LEU Chi-restraints excluded: chain n residue 67 ILE Chi-restraints excluded: chain n residue 126 ARG Chi-restraints excluded: chain n residue 136 ILE Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 72 VAL Chi-restraints excluded: chain o residue 133 LEU Chi-restraints excluded: chain o residue 136 ILE Chi-restraints excluded: chain o residue 140 VAL Chi-restraints excluded: chain o residue 143 LEU Chi-restraints excluded: chain o residue 148 VAL Chi-restraints excluded: chain p residue 305 VAL Chi-restraints excluded: chain p residue 309 LEU Chi-restraints excluded: chain p residue 317 LEU Chi-restraints excluded: chain p residue 321 VAL Chi-restraints excluded: chain p residue 325 SER Chi-restraints excluded: chain p residue 340 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 4 optimal weight: 0.0030 chunk 88 optimal weight: 0.8980 chunk 284 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 chunk 288 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 0.0010 chunk 167 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 807 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.105623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090888 restraints weight = 78492.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092824 restraints weight = 43673.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.093934 restraints weight = 28598.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094834 restraints weight = 21597.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.095329 restraints weight = 17727.770| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23504 Z= 0.139 Angle : 0.695 14.629 31925 Z= 0.338 Chirality : 0.041 0.262 3811 Planarity : 0.004 0.063 3968 Dihedral : 4.677 54.541 3425 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.30 % Favored : 94.50 % Rotamer: Outliers : 4.34 % Allowed : 32.62 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.16), residues: 3037 helix: 1.92 (0.11), residues: 2126 sheet: -0.52 (0.58), residues: 91 loop : -2.32 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG k 119 TYR 0.023 0.001 TYR k 144 PHE 0.040 0.001 PHE n 13 TRP 0.033 0.001 TRP f 21 HIS 0.019 0.001 HIS a 802 Details of bonding type rmsd covalent geometry : bond 0.00295 (23495) covalent geometry : angle 0.69178 (31901) hydrogen bonds : bond 0.04623 ( 1772) hydrogen bonds : angle 4.08008 ( 5292) Misc. bond : bond 0.00033 ( 1) link_BETA1-4 : bond 0.01047 ( 4) link_BETA1-4 : angle 3.22948 ( 12) link_NAG-ASN : bond 0.00226 ( 4) link_NAG-ASN : angle 2.00689 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3803.47 seconds wall clock time: 67 minutes 1.56 seconds (4021.56 seconds total)