Starting phenix.real_space_refine on Thu Sep 18 19:51:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh1_19165/09_2025/8rh1_19165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh1_19165/09_2025/8rh1_19165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rh1_19165/09_2025/8rh1_19165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh1_19165/09_2025/8rh1_19165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rh1_19165/09_2025/8rh1_19165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh1_19165/09_2025/8rh1_19165.map" } resolution = 3.45 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= 0.002 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 96 5.16 5 C 12402 2.51 5 N 3387 2.21 5 O 3675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 19560 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4710 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "E" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 102} Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "L" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 102} Chain: "G" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4710 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Chain: "C" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4710 Classifications: {'peptide': 583} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 555} Chain breaks: 1 Time building chain proxies: 5.27, per 1000 atoms: 0.27 Number of scatterers: 19560 At special positions: 0 Unit cell: (189.441, 164.955, 159.801, 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 96 16.00 O 3675 8.00 N 3387 7.00 C 12402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 567 " distance=2.04 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 523 " distance=2.07 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 263 " distance=2.10 Simple disulfide: pdb=" SG CYS A 356 " - pdb=" SG CYS A 404 " distance=2.06 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 627 " distance=2.07 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 116 " distance=2.04 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 112 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 116 " distance=2.06 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 112 " distance=2.08 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 567 " distance=2.05 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 523 " distance=2.07 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 263 " distance=2.09 Simple disulfide: pdb=" SG CYS B 356 " - pdb=" SG CYS B 404 " distance=2.04 Simple disulfide: pdb=" SG CYS B 590 " - pdb=" SG CYS B 627 " distance=2.06 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 567 " distance=2.05 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 523 " distance=2.05 Simple disulfide: pdb=" SG CYS C 199 " - pdb=" SG CYS C 263 " distance=2.10 Simple disulfide: pdb=" SG CYS C 356 " - pdb=" SG CYS C 404 " distance=2.06 Simple disulfide: pdb=" SG CYS C 590 " - pdb=" SG CYS C 627 " distance=2.05 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=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 892.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 50 sheets defined 16.9% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.534A pdb=" N ASP A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 402 through 421 removed outlier: 4.699A pdb=" N GLY A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 540 removed outlier: 4.379A pdb=" N GLY A 516 " --> pdb=" O ASN A 512 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.523A pdb=" N GLY A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 684 through 692 removed outlier: 3.940A pdb=" N GLY A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 705 removed outlier: 3.627A pdb=" N LEU A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 711 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.543A pdb=" N VAL E 107 " --> pdb=" O ALA E 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.584A pdb=" N VAL G 107 " --> pdb=" O ALA G 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 402 through 421 removed outlier: 4.693A pdb=" N GLY B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 540 removed outlier: 3.800A pdb=" N GLY B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 532 " --> pdb=" O HIS B 528 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 550 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 654 through 658 Processing helix chain 'B' and resid 684 through 691 Processing helix chain 'B' and resid 695 through 704 Processing helix chain 'B' and resid 705 through 711 Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.515A pdb=" N ASP C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 403 through 420 removed outlier: 4.336A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 540 removed outlier: 3.866A pdb=" N GLY C 516 " --> pdb=" O ASN C 512 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 532 " --> pdb=" O HIS C 528 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU C 535 " --> pdb=" O THR C 531 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS C 538 " --> pdb=" O ASN C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 550 removed outlier: 3.512A pdb=" N ILE C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 654 through 658 Processing helix chain 'C' and resid 684 through 692 removed outlier: 3.948A pdb=" N GLY C 692 " --> pdb=" O ILE C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 705 removed outlier: 3.561A pdb=" N LEU C 705 " --> pdb=" O ARG C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 711 Processing sheet with id=AA1, first strand: chain 'A' and resid 568 through 570 removed outlier: 7.494A pdb=" N TYR A 106 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 553 through 557 removed outlier: 3.686A pdb=" N MET A 562 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 116 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL C 661 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN A 118 " --> pdb=" O VAL C 661 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 358 through 364 removed outlier: 5.424A pdb=" N LYS A 360 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS A 143 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 364 removed outlier: 5.424A pdb=" N LYS A 360 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS A 143 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 183 removed outlier: 5.955A pdb=" N GLN A 164 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 177 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 162 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 179 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 160 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 181 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS A 158 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TYR A 156 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 228 removed outlier: 7.556A pdb=" N LYS A 152 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP A 347 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG A 334 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP A 315 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A 336 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN A 313 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N THR A 338 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE A 311 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AA8, first strand: chain 'A' and resid 202 through 207 Processing sheet with id=AA9, first strand: chain 'A' and resid 367 through 372 Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB2, first strand: chain 'A' and resid 632 through 637 removed outlier: 5.201A pdb=" N GLU A 645 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N TYR A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 659 through 661 removed outlier: 3.884A pdb=" N THR A 659 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET B 562 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.616A pdb=" N SER D 54 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL D 55 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N HIS D 71 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP D 57 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 37 through 38 Processing sheet with id=AB6, first strand: chain 'D' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'E' and resid 23 through 26 Processing sheet with id=AB8, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.565A pdb=" N LEU E 30 " --> pdb=" O LYS E 127 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU E 129 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY E 108 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU E 57 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR E 73 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.565A pdb=" N LEU E 30 " --> pdb=" O LYS E 127 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU E 129 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY E 108 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 114 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER E 121 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 24 through 26 Processing sheet with id=AC2, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.603A pdb=" N SER H 54 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL H 55 " --> pdb=" O HIS H 71 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N HIS H 71 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP H 57 " --> pdb=" O LEU H 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.884A pdb=" N SER F 54 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL F 55 " --> pdb=" O HIS F 71 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N HIS F 71 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP F 57 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC5, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC6, first strand: chain 'L' and resid 23 through 26 Processing sheet with id=AC7, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.979A pdb=" N GLY L 108 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU L 57 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR L 73 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.979A pdb=" N GLY L 108 " --> pdb=" O LEU L 128 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER L 121 " --> pdb=" O GLN L 114 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 23 through 26 Processing sheet with id=AD1, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.749A pdb=" N LEU G 57 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N TYR G 73 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.930A pdb=" N SER G 121 " --> pdb=" O GLN G 114 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 568 through 570 removed outlier: 7.833A pdb=" N TYR B 106 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 358 through 364 removed outlier: 6.556A pdb=" N VAL B 141 " --> pdb=" O TRP B 361 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU B 363 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA B 139 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 358 through 364 removed outlier: 6.556A pdb=" N VAL B 141 " --> pdb=" O TRP B 361 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU B 363 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA B 139 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 172 through 183 removed outlier: 5.978A pdb=" N GLN B 164 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B 177 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL B 162 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU B 179 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 160 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG B 181 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS B 158 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N TYR B 156 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 227 through 228 removed outlier: 7.353A pdb=" N LYS B 152 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP B 347 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG B 334 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ASP B 315 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU B 336 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLN B 313 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N THR B 338 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE B 311 " --> pdb=" O THR B 338 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 198 through 200 Processing sheet with id=AD9, first strand: chain 'B' and resid 202 through 206 Processing sheet with id=AE1, first strand: chain 'B' and resid 367 through 372 Processing sheet with id=AE2, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AE3, first strand: chain 'B' and resid 632 through 637 removed outlier: 5.113A pdb=" N GLU B 645 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 659 through 661 removed outlier: 6.401A pdb=" N THR B 659 " --> pdb=" O GLN C 118 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 117 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET C 562 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 568 through 570 removed outlier: 7.808A pdb=" N TYR C 106 " --> pdb=" O LEU C 617 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 358 through 364 removed outlier: 6.517A pdb=" N VAL C 141 " --> pdb=" O TRP C 361 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU C 363 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA C 139 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 358 through 364 removed outlier: 6.517A pdb=" N VAL C 141 " --> pdb=" O TRP C 361 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU C 363 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA C 139 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 172 through 183 removed outlier: 6.035A pdb=" N GLN C 164 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE C 177 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 162 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU C 179 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 160 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG C 181 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS C 158 " --> pdb=" O ARG C 181 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N TYR C 156 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 227 through 228 removed outlier: 7.340A pdb=" N LYS C 152 " --> pdb=" O ASP C 347 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP C 347 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG C 334 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP C 315 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C 336 " --> pdb=" O GLN C 313 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLN C 313 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N THR C 338 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE C 311 " --> pdb=" O THR C 338 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AF2, first strand: chain 'C' and resid 202 through 206 Processing sheet with id=AF3, first strand: chain 'C' and resid 367 through 372 Processing sheet with id=AF4, first strand: chain 'C' and resid 589 through 591 Processing sheet with id=AF5, first strand: chain 'C' and resid 632 through 637 removed outlier: 5.212A pdb=" N GLU C 645 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TYR C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2202 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: 4.61 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4668 1.33 - 1.46: 6837 1.46 - 1.59: 8409 1.59 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 20064 Sorted by residual: bond pdb=" C PRO A 587 " pdb=" N GLY A 588 " ideal model delta sigma weight residual 1.331 1.435 -0.104 1.46e-02 4.69e+03 5.12e+01 bond pdb=" CE1 HIS G 117 " pdb=" NE2 HIS G 117 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.11e+01 bond pdb=" CE1 HIS B 506 " pdb=" NE2 HIS B 506 " ideal model delta sigma weight residual 1.321 1.376 -0.055 1.00e-02 1.00e+04 2.99e+01 bond pdb=" CE1 HIS B 425 " pdb=" NE2 HIS B 425 " ideal model delta sigma weight residual 1.321 1.376 -0.055 1.00e-02 1.00e+04 2.99e+01 bond pdb=" CE1 HIS B 510 " pdb=" NE2 HIS B 510 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.94e+01 ... (remaining 20059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 25657 1.62 - 3.24: 1492 3.24 - 4.86: 105 4.86 - 6.47: 14 6.47 - 8.09: 5 Bond angle restraints: 27273 Sorted by residual: angle pdb=" N LYS F 96 " pdb=" CA LYS F 96 " pdb=" C LYS F 96 " ideal model delta sigma weight residual 113.28 107.98 5.30 1.22e+00 6.72e-01 1.89e+01 angle pdb=" C PRO A 587 " pdb=" N GLY A 588 " pdb=" CA GLY A 588 " ideal model delta sigma weight residual 121.41 113.64 7.77 1.96e+00 2.60e-01 1.57e+01 angle pdb=" N GLU A 297 " pdb=" CA GLU A 297 " pdb=" C GLU A 297 " ideal model delta sigma weight residual 111.28 116.10 -4.82 1.35e+00 5.49e-01 1.27e+01 angle pdb=" NE ARG B 499 " pdb=" CZ ARG B 499 " pdb=" NH1 ARG B 499 " ideal model delta sigma weight residual 121.50 118.14 3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" N SER A 585 " pdb=" CA SER A 585 " pdb=" C SER A 585 " ideal model delta sigma weight residual 113.23 109.11 4.12 1.24e+00 6.50e-01 1.11e+01 ... (remaining 27268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 10886 17.55 - 35.10: 854 35.10 - 52.65: 150 52.65 - 70.20: 39 70.20 - 87.75: 26 Dihedral angle restraints: 11955 sinusoidal: 4803 harmonic: 7152 Sorted by residual: dihedral pdb=" CB CYS C 590 " pdb=" SG CYS C 590 " pdb=" SG CYS C 627 " pdb=" CB CYS C 627 " ideal model delta sinusoidal sigma weight residual -86.00 -173.75 87.75 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 590 " pdb=" SG CYS A 590 " pdb=" SG CYS A 627 " pdb=" CB CYS A 627 " ideal model delta sinusoidal sigma weight residual 93.00 179.62 -86.62 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS B 590 " pdb=" SG CYS B 590 " pdb=" SG CYS B 627 " pdb=" CB CYS B 627 " ideal model delta sinusoidal sigma weight residual 93.00 176.03 -83.03 1 1.00e+01 1.00e-02 8.44e+01 ... (remaining 11952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1508 0.042 - 0.085: 1002 0.085 - 0.127: 397 0.127 - 0.170: 53 0.170 - 0.212: 10 Chirality restraints: 2970 Sorted by residual: chirality pdb=" CA PRO F 125 " pdb=" N PRO F 125 " pdb=" C PRO F 125 " pdb=" CB PRO F 125 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA SER L 116 " pdb=" N SER L 116 " pdb=" C SER L 116 " pdb=" CB SER L 116 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA CYS G 42 " pdb=" N CYS G 42 " pdb=" C CYS G 42 " pdb=" CB CYS G 42 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 2967 not shown) Planarity restraints: 3513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 286 " 0.047 2.00e-02 2.50e+03 4.30e-02 3.24e+01 pdb=" CG PHE C 286 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE C 286 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE C 286 " -0.066 2.00e-02 2.50e+03 pdb=" CE1 PHE C 286 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 286 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 286 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 286 " 0.054 2.00e-02 2.50e+03 4.04e-02 2.86e+01 pdb=" CG PHE A 286 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 PHE A 286 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE A 286 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 PHE A 286 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 286 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 286 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 504 " -0.059 2.00e-02 2.50e+03 3.65e-02 2.66e+01 pdb=" CG TYR A 504 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 504 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR A 504 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 504 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 504 " 0.042 2.00e-02 2.50e+03 pdb=" CZ TYR A 504 " -0.040 2.00e-02 2.50e+03 pdb=" OH TYR A 504 " -0.023 2.00e-02 2.50e+03 ... (remaining 3510 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3135 2.76 - 3.30: 18484 3.30 - 3.83: 33059 3.83 - 4.37: 39644 4.37 - 4.90: 68712 Nonbonded interactions: 163034 Sorted by model distance: nonbonded pdb=" OH TYR D 121 " pdb=" OE2 GLU E 58 " model vdw 2.230 3.040 nonbonded pdb=" O ALA F 127 " pdb=" OH TYR G 60 " model vdw 2.236 3.040 nonbonded pdb=" NE2 GLN C 104 " pdb=" O PHE C 105 " model vdw 2.248 3.120 nonbonded pdb=" OD2 ASP A 712 " pdb=" OG1 THR A 715 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP B 712 " pdb=" OG1 THR B 715 " model vdw 2.252 3.040 ... (remaining 163029 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.030 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 20085 Z= 0.506 Angle : 0.858 8.092 27315 Z= 0.541 Chirality : 0.059 0.212 2970 Planarity : 0.009 0.120 3513 Dihedral : 13.620 86.383 7308 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.79 (0.16), residues: 2418 helix: -1.58 (0.25), residues: 342 sheet: -0.33 (0.18), residues: 804 loop : -0.19 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG C 499 TYR 0.059 0.007 TYR A 504 PHE 0.066 0.007 PHE C 286 TRP 0.050 0.008 TRP C 348 HIS 0.035 0.005 HIS B 300 Details of bonding type rmsd covalent geometry : bond 0.00759 (20064) covalent geometry : angle 0.85383 (27273) SS BOND : bond 0.03334 ( 21) SS BOND : angle 2.39578 ( 42) hydrogen bonds : bond 0.16164 ( 734) hydrogen bonds : angle 8.00916 ( 2202) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7709 (tp-100) cc_final: 0.7506 (tp40) REVERT: A 169 HIS cc_start: 0.8185 (t-90) cc_final: 0.7287 (p90) REVERT: A 179 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8234 (pt0) REVERT: A 616 GLU cc_start: 0.7905 (pp20) cc_final: 0.7615 (tp30) REVERT: A 668 ASN cc_start: 0.7563 (m-40) cc_final: 0.6687 (t0) REVERT: A 718 ARG cc_start: 0.7236 (tpt170) cc_final: 0.6988 (mmm-85) REVERT: D 43 PHE cc_start: 0.7197 (m-80) cc_final: 0.6510 (m-80) REVERT: D 51 SER cc_start: 0.7652 (m) cc_final: 0.6992 (t) REVERT: D 57 TRP cc_start: 0.8623 (m100) cc_final: 0.8266 (m100) REVERT: D 78 LYS cc_start: 0.7460 (mtmm) cc_final: 0.6817 (mttm) REVERT: D 97 ASN cc_start: 0.4708 (t0) cc_final: 0.4362 (t0) REVERT: D 103 MET cc_start: 0.7092 (ttt) cc_final: 0.6532 (ttm) REVERT: D 106 MET cc_start: 0.6098 (tpt) cc_final: 0.5788 (mmp) REVERT: E 46 GLN cc_start: 0.6290 (mt0) cc_final: 0.5733 (tt0) REVERT: E 64 PRO cc_start: 0.6062 (Cg_exo) cc_final: 0.5806 (Cg_endo) REVERT: E 94 ASP cc_start: 0.6537 (p0) cc_final: 0.5554 (t70) REVERT: E 101 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.6852 (mtp85) REVERT: H 87 ARG cc_start: 0.7550 (mtp180) cc_final: 0.7290 (ptp-170) REVERT: H 91 SER cc_start: 0.8288 (t) cc_final: 0.7853 (m) REVERT: H 106 MET cc_start: 0.7466 (mmm) cc_final: 0.7010 (mmp) REVERT: H 133 GLN cc_start: 0.7685 (pm20) cc_final: 0.7421 (mm-40) REVERT: F 32 LYS cc_start: 0.7480 (mtpp) cc_final: 0.6904 (mptt) REVERT: F 93 ASP cc_start: 0.5809 (t0) cc_final: 0.5535 (t70) REVERT: F 97 ASN cc_start: 0.6461 (t0) cc_final: 0.6179 (t0) REVERT: F 111 THR cc_start: 0.8807 (m) cc_final: 0.8577 (p) REVERT: L 46 GLN cc_start: 0.7419 (mt0) cc_final: 0.7122 (tt0) REVERT: L 48 ILE cc_start: 0.8811 (mm) cc_final: 0.8567 (mm) REVERT: L 103 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6605 (tt0) REVERT: L 129 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6373 (tp30) REVERT: G 43 ARG cc_start: 0.7363 (ttm110) cc_final: 0.6780 (mtp85) REVERT: G 48 ILE cc_start: 0.7906 (mt) cc_final: 0.7705 (mp) REVERT: G 63 LYS cc_start: 0.7466 (mttp) cc_final: 0.7223 (mmtt) REVERT: B 128 ARG cc_start: 0.5948 (mtt90) cc_final: 0.5663 (mtt180) REVERT: B 170 ARG cc_start: 0.7839 (tmm160) cc_final: 0.7625 (mtt90) REVERT: B 179 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7950 (pt0) REVERT: B 211 GLU cc_start: 0.7754 (tp30) cc_final: 0.7551 (tt0) REVERT: B 217 ARG cc_start: 0.7008 (mmm160) cc_final: 0.6370 (ttm-80) REVERT: B 220 HIS cc_start: 0.8289 (m-70) cc_final: 0.8075 (m-70) REVERT: B 221 GLU cc_start: 0.7888 (tt0) cc_final: 0.7349 (tm-30) REVERT: B 224 MET cc_start: 0.8252 (mtt) cc_final: 0.7979 (mtm) REVERT: B 227 LYS cc_start: 0.8105 (pttp) cc_final: 0.7765 (mtmm) REVERT: B 234 ARG cc_start: 0.5189 (mtm180) cc_final: 0.4794 (mtp-110) REVERT: B 299 SER cc_start: 0.8768 (m) cc_final: 0.8530 (p) REVERT: B 358 MET cc_start: 0.8970 (mmt) cc_final: 0.8728 (mmt) REVERT: B 371 GLU cc_start: 0.7097 (pm20) cc_final: 0.6836 (tt0) REVERT: B 417 PHE cc_start: 0.7219 (t80) cc_final: 0.7017 (t80) REVERT: B 509 ARG cc_start: 0.7060 (ttp80) cc_final: 0.6768 (ttm170) REVERT: B 540 ASN cc_start: 0.8513 (t0) cc_final: 0.7784 (t0) REVERT: B 554 SER cc_start: 0.8195 (t) cc_final: 0.7777 (p) REVERT: B 698 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7942 (tt0) REVERT: B 713 ILE cc_start: 0.7583 (mm) cc_final: 0.7375 (mt) REVERT: C 170 ARG cc_start: 0.7731 (tpp80) cc_final: 0.7103 (tmm160) REVERT: C 210 MET cc_start: 0.9010 (ttp) cc_final: 0.8362 (ttp) REVERT: C 227 LYS cc_start: 0.8364 (pttp) cc_final: 0.7746 (mttp) REVERT: C 233 THR cc_start: 0.7097 (m) cc_final: 0.6605 (p) REVERT: C 289 MET cc_start: 0.8784 (ttm) cc_final: 0.8572 (ttp) REVERT: C 372 TYR cc_start: 0.7435 (t80) cc_final: 0.7095 (t80) REVERT: C 411 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7097 (tm-30) REVERT: C 556 ARG cc_start: 0.7709 (ttp-110) cc_final: 0.7228 (ptm160) REVERT: C 641 TYR cc_start: 0.5842 (m-80) cc_final: 0.5508 (m-80) REVERT: C 645 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7206 (mm-30) REVERT: C 646 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7255 (tp30) REVERT: C 698 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7465 (tp30) REVERT: C 718 ARG cc_start: 0.5427 (mtt180) cc_final: 0.5048 (mtm180) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.1899 time to fit residues: 117.1254 Evaluate side-chains 276 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0980 chunk 235 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 121 GLN A 240 HIS A 393 GLN A 506 HIS A 615 ASN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN H 105 ASN B 506 HIS B 508 GLN ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 651 HIS C 118 GLN C 247 ASN C 262 ASN ** C 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 GLN C 610 GLN ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101847 restraints weight = 33805.653| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.46 r_work: 0.3282 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 20085 Z= 0.199 Angle : 0.605 14.018 27315 Z= 0.323 Chirality : 0.044 0.174 2970 Planarity : 0.004 0.043 3513 Dihedral : 4.536 25.624 2736 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.22 % Allowed : 9.53 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.26 (0.16), residues: 2418 helix: -0.10 (0.26), residues: 345 sheet: -0.16 (0.18), residues: 801 loop : -0.06 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 124 TYR 0.022 0.002 TYR C 647 PHE 0.027 0.002 PHE B 635 TRP 0.021 0.002 TRP B 533 HIS 0.018 0.002 HIS C 528 Details of bonding type rmsd covalent geometry : bond 0.00466 (20064) covalent geometry : angle 0.58988 (27273) SS BOND : bond 0.00612 ( 21) SS BOND : angle 3.52580 ( 42) hydrogen bonds : bond 0.04348 ( 734) hydrogen bonds : angle 5.88065 ( 2202) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 668 ASN cc_start: 0.7623 (m-40) cc_final: 0.7149 (t0) REVERT: D 78 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7611 (mttm) REVERT: D 106 MET cc_start: 0.6339 (tpt) cc_final: 0.5907 (tpt) REVERT: D 136 LEU cc_start: 0.8082 (tt) cc_final: 0.7660 (mp) REVERT: E 46 GLN cc_start: 0.7552 (mt0) cc_final: 0.7061 (tt0) REVERT: E 64 PRO cc_start: 0.6049 (Cg_exo) cc_final: 0.5748 (Cg_endo) REVERT: E 94 ASP cc_start: 0.7010 (p0) cc_final: 0.6018 (t70) REVERT: H 91 SER cc_start: 0.8692 (t) cc_final: 0.8354 (m) REVERT: F 32 LYS cc_start: 0.7543 (mtpp) cc_final: 0.7144 (mptt) REVERT: F 106 MET cc_start: 0.7287 (mmp) cc_final: 0.7080 (mmt) REVERT: F 111 THR cc_start: 0.9006 (m) cc_final: 0.8787 (p) REVERT: B 106 TYR cc_start: 0.7402 (m-80) cc_final: 0.7126 (m-80) REVERT: B 217 ARG cc_start: 0.6765 (mmm160) cc_final: 0.6534 (ttm-80) REVERT: B 227 LYS cc_start: 0.7695 (pttp) cc_final: 0.7488 (mtmm) REVERT: B 554 SER cc_start: 0.8701 (t) cc_final: 0.8447 (p) REVERT: B 635 PHE cc_start: 0.8395 (m-80) cc_final: 0.8101 (m-10) REVERT: C 532 LEU cc_start: 0.8775 (mt) cc_final: 0.8543 (mt) REVERT: C 556 ARG cc_start: 0.7446 (ttp-110) cc_final: 0.7144 (ptm160) REVERT: C 645 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7085 (mm-30) REVERT: C 661 VAL cc_start: 0.9102 (m) cc_final: 0.8831 (p) outliers start: 26 outliers final: 18 residues processed: 304 average time/residue: 0.1707 time to fit residues: 76.9156 Evaluate side-chains 242 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 669 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN H 105 ASN B 121 GLN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 240 HIS C 528 HIS ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101180 restraints weight = 33955.991| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.44 r_work: 0.3259 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 20085 Z= 0.198 Angle : 0.576 9.665 27315 Z= 0.305 Chirality : 0.043 0.161 2970 Planarity : 0.004 0.043 3513 Dihedral : 4.486 19.945 2736 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.30 % Allowed : 11.41 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.22 (0.16), residues: 2418 helix: 0.27 (0.27), residues: 345 sheet: -0.21 (0.18), residues: 813 loop : -0.07 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 701 TYR 0.023 0.002 TYR B 649 PHE 0.018 0.002 PHE B 151 TRP 0.015 0.001 TRP B 533 HIS 0.015 0.002 HIS C 528 Details of bonding type rmsd covalent geometry : bond 0.00468 (20064) covalent geometry : angle 0.56945 (27273) SS BOND : bond 0.00564 ( 21) SS BOND : angle 2.26399 ( 42) hydrogen bonds : bond 0.04024 ( 734) hydrogen bonds : angle 5.58923 ( 2202) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 668 ASN cc_start: 0.7774 (m-40) cc_final: 0.7385 (t0) REVERT: D 106 MET cc_start: 0.6627 (tpt) cc_final: 0.6179 (tpt) REVERT: D 136 LEU cc_start: 0.8026 (tt) cc_final: 0.7573 (mp) REVERT: E 46 GLN cc_start: 0.7589 (mt0) cc_final: 0.7090 (tt0) REVERT: E 64 PRO cc_start: 0.5981 (Cg_exo) cc_final: 0.5650 (Cg_endo) REVERT: E 94 ASP cc_start: 0.7358 (p0) cc_final: 0.6334 (t70) REVERT: H 93 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6253 (m-30) REVERT: F 32 LYS cc_start: 0.7671 (mtpp) cc_final: 0.7289 (mptt) REVERT: F 106 MET cc_start: 0.7511 (mmp) cc_final: 0.7211 (mmt) REVERT: F 124 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8134 (mmt90) REVERT: L 23 MET cc_start: 0.8727 (mmm) cc_final: 0.8314 (mmm) REVERT: G 84 ASP cc_start: 0.7783 (t0) cc_final: 0.7504 (t0) REVERT: B 217 ARG cc_start: 0.6940 (mmm160) cc_final: 0.6636 (ttm-80) REVERT: B 227 LYS cc_start: 0.7805 (pttp) cc_final: 0.7600 (mtmm) REVERT: B 554 SER cc_start: 0.8709 (t) cc_final: 0.8431 (p) REVERT: B 635 PHE cc_start: 0.8603 (m-80) cc_final: 0.8341 (m-10) REVERT: C 119 PHE cc_start: 0.7846 (m-10) cc_final: 0.7615 (m-10) REVERT: C 210 MET cc_start: 0.8952 (ttp) cc_final: 0.8749 (ttp) REVERT: C 532 LEU cc_start: 0.8951 (mt) cc_final: 0.8731 (mt) REVERT: C 556 ARG cc_start: 0.7542 (ttp-110) cc_final: 0.7111 (ptm160) REVERT: C 562 MET cc_start: 0.7682 (pmm) cc_final: 0.7087 (ptp) REVERT: C 578 GLN cc_start: 0.6719 (OUTLIER) cc_final: 0.6030 (mt0) REVERT: C 645 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7127 (mm-30) REVERT: C 661 VAL cc_start: 0.9113 (m) cc_final: 0.8876 (p) outliers start: 49 outliers final: 32 residues processed: 269 average time/residue: 0.1591 time to fit residues: 64.0166 Evaluate side-chains 244 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 235 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN E 77 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 631 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.121753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102792 restraints weight = 33852.502| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.50 r_work: 0.3258 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20085 Z= 0.149 Angle : 0.526 8.486 27315 Z= 0.280 Chirality : 0.042 0.147 2970 Planarity : 0.004 0.038 3513 Dihedral : 4.361 19.936 2736 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.30 % Allowed : 12.54 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.11 (0.16), residues: 2418 helix: 0.40 (0.27), residues: 345 sheet: -0.11 (0.18), residues: 807 loop : -0.05 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.023 0.001 TYR B 647 PHE 0.018 0.002 PHE C 292 TRP 0.011 0.001 TRP B 533 HIS 0.010 0.001 HIS C 510 Details of bonding type rmsd covalent geometry : bond 0.00349 (20064) covalent geometry : angle 0.52156 (27273) SS BOND : bond 0.00476 ( 21) SS BOND : angle 1.78665 ( 42) hydrogen bonds : bond 0.03682 ( 734) hydrogen bonds : angle 5.39868 ( 2202) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.6569 (mmm-85) cc_final: 0.6230 (mmm-85) REVERT: A 668 ASN cc_start: 0.7778 (m-40) cc_final: 0.7396 (t0) REVERT: D 25 GLU cc_start: 0.8006 (mp0) cc_final: 0.7451 (mp0) REVERT: D 78 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7974 (mtmt) REVERT: D 136 LEU cc_start: 0.8024 (tt) cc_final: 0.7604 (mp) REVERT: E 46 GLN cc_start: 0.7552 (mt0) cc_final: 0.7037 (tt0) REVERT: E 94 ASP cc_start: 0.7466 (p0) cc_final: 0.5854 (t70) REVERT: H 91 SER cc_start: 0.8650 (t) cc_final: 0.8350 (m) REVERT: F 24 LYS cc_start: 0.8517 (tppt) cc_final: 0.8299 (tppt) REVERT: F 32 LYS cc_start: 0.7703 (mtpp) cc_final: 0.7445 (mptt) REVERT: F 121 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: F 124 ARG cc_start: 0.8546 (mmm160) cc_final: 0.8202 (mmt90) REVERT: L 23 MET cc_start: 0.8579 (mmm) cc_final: 0.8185 (mmm) REVERT: L 109 VAL cc_start: 0.8550 (t) cc_final: 0.8195 (m) REVERT: G 84 ASP cc_start: 0.8020 (t0) cc_final: 0.7680 (t0) REVERT: B 217 ARG cc_start: 0.7017 (mmm160) cc_final: 0.6585 (ttm-80) REVERT: B 554 SER cc_start: 0.8698 (t) cc_final: 0.8449 (p) REVERT: B 562 MET cc_start: 0.7769 (pmm) cc_final: 0.7273 (ptp) REVERT: B 578 GLN cc_start: 0.7073 (tm-30) cc_final: 0.6587 (tm-30) REVERT: C 404 CYS cc_start: 0.5852 (m) cc_final: 0.5300 (m) REVERT: C 556 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7085 (ptm160) REVERT: C 562 MET cc_start: 0.7724 (pmm) cc_final: 0.7098 (ptp) REVERT: C 578 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6144 (mt0) REVERT: C 661 VAL cc_start: 0.9078 (m) cc_final: 0.8856 (p) outliers start: 49 outliers final: 35 residues processed: 270 average time/residue: 0.1614 time to fit residues: 64.4906 Evaluate side-chains 250 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 224 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 184 optimal weight: 0.4980 chunk 149 optimal weight: 0.0020 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 ASN ** 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 = 0.3696 r_free = 0.3696 target = 0.122444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103253 restraints weight = 33770.123| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.50 r_work: 0.3267 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20085 Z= 0.128 Angle : 0.513 7.084 27315 Z= 0.274 Chirality : 0.041 0.146 2970 Planarity : 0.004 0.037 3513 Dihedral : 4.282 20.448 2736 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.77 % Allowed : 13.10 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.01 (0.16), residues: 2418 helix: 0.50 (0.27), residues: 345 sheet: 0.02 (0.18), residues: 780 loop : -0.04 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 43 TYR 0.033 0.001 TYR B 647 PHE 0.020 0.002 PHE C 292 TRP 0.009 0.001 TRP F 68 HIS 0.009 0.001 HIS C 510 Details of bonding type rmsd covalent geometry : bond 0.00297 (20064) covalent geometry : angle 0.50814 (27273) SS BOND : bond 0.00520 ( 21) SS BOND : angle 1.85441 ( 42) hydrogen bonds : bond 0.03534 ( 734) hydrogen bonds : angle 5.19529 ( 2202) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 222 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.6339 (mmm-85) cc_final: 0.5683 (mtm180) REVERT: A 668 ASN cc_start: 0.7841 (m-40) cc_final: 0.7467 (t0) REVERT: D 25 GLU cc_start: 0.8032 (mp0) cc_final: 0.7550 (mp0) REVERT: E 46 GLN cc_start: 0.7608 (mt0) cc_final: 0.7099 (tt0) REVERT: E 94 ASP cc_start: 0.7522 (p0) cc_final: 0.5870 (t70) REVERT: F 32 LYS cc_start: 0.7711 (mtpp) cc_final: 0.7441 (mptt) REVERT: F 121 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.7615 (m-10) REVERT: F 124 ARG cc_start: 0.8564 (mmm160) cc_final: 0.8201 (mmt90) REVERT: L 89 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8254 (m) REVERT: L 109 VAL cc_start: 0.8570 (t) cc_final: 0.8211 (m) REVERT: G 23 MET cc_start: 0.8173 (mmm) cc_final: 0.7956 (mmm) REVERT: G 84 ASP cc_start: 0.8049 (t0) cc_final: 0.7698 (t0) REVERT: G 131 LYS cc_start: 0.2889 (mmmt) cc_final: 0.2455 (pttp) REVERT: B 106 TYR cc_start: 0.7331 (m-80) cc_final: 0.6947 (m-80) REVERT: B 217 ARG cc_start: 0.7113 (mmm160) cc_final: 0.6656 (ttm-80) REVERT: B 554 SER cc_start: 0.8708 (t) cc_final: 0.8488 (p) REVERT: B 562 MET cc_start: 0.7857 (pmm) cc_final: 0.7487 (ptp) REVERT: B 578 GLN cc_start: 0.7052 (tm-30) cc_final: 0.6572 (tm-30) REVERT: C 262 ASN cc_start: 0.8537 (t0) cc_final: 0.8211 (t0) REVERT: C 404 CYS cc_start: 0.5945 (m) cc_final: 0.5479 (m) REVERT: C 556 ARG cc_start: 0.7358 (ttp-110) cc_final: 0.7008 (ptm160) REVERT: C 562 MET cc_start: 0.7700 (pmm) cc_final: 0.7039 (ptp) REVERT: C 573 ASP cc_start: 0.7376 (p0) cc_final: 0.7043 (t0) REVERT: C 661 VAL cc_start: 0.9019 (m) cc_final: 0.8789 (p) outliers start: 59 outliers final: 44 residues processed: 269 average time/residue: 0.1674 time to fit residues: 67.6778 Evaluate side-chains 256 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 225 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 335 ASN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN L 46 GLN L 62 GLN G 52 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.119423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099245 restraints weight = 34052.695| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.46 r_work: 0.3232 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 20085 Z= 0.256 Angle : 0.603 7.851 27315 Z= 0.319 Chirality : 0.044 0.147 2970 Planarity : 0.005 0.041 3513 Dihedral : 4.564 19.131 2736 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.52 % Allowed : 13.19 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.25 (0.17), residues: 2418 helix: 0.41 (0.27), residues: 342 sheet: -0.25 (0.18), residues: 855 loop : -0.12 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 124 TYR 0.024 0.002 TYR B 156 PHE 0.021 0.002 PHE A 151 TRP 0.010 0.002 TRP A 346 HIS 0.009 0.002 HIS C 510 Details of bonding type rmsd covalent geometry : bond 0.00604 (20064) covalent geometry : angle 0.59730 (27273) SS BOND : bond 0.00418 ( 21) SS BOND : angle 2.20157 ( 42) hydrogen bonds : bond 0.03995 ( 734) hydrogen bonds : angle 5.39968 ( 2202) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.6584 (mmm-85) cc_final: 0.6359 (mpp80) REVERT: A 601 GLU cc_start: 0.6653 (mp0) cc_final: 0.6398 (pm20) REVERT: A 668 ASN cc_start: 0.7916 (m-40) cc_final: 0.7525 (t0) REVERT: D 124 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6667 (mtm110) REVERT: D 136 LEU cc_start: 0.8111 (tt) cc_final: 0.7746 (mp) REVERT: E 46 GLN cc_start: 0.7615 (mt0) cc_final: 0.7090 (tt0) REVERT: E 94 ASP cc_start: 0.7522 (p0) cc_final: 0.7218 (p0) REVERT: F 32 LYS cc_start: 0.7732 (mtpp) cc_final: 0.7353 (mptt) REVERT: F 43 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: F 120 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7879 (t80) REVERT: F 121 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.7739 (m-10) REVERT: F 124 ARG cc_start: 0.8459 (mmm160) cc_final: 0.8130 (mtp180) REVERT: L 89 SER cc_start: 0.8671 (OUTLIER) cc_final: 0.8347 (m) REVERT: L 109 VAL cc_start: 0.8628 (t) cc_final: 0.8232 (m) REVERT: G 131 LYS cc_start: 0.3411 (mmmt) cc_final: 0.3196 (mmmt) REVERT: B 217 ARG cc_start: 0.7134 (mmm160) cc_final: 0.6693 (ttm-80) REVERT: B 554 SER cc_start: 0.8908 (t) cc_final: 0.8619 (p) REVERT: B 562 MET cc_start: 0.7865 (pmm) cc_final: 0.7628 (ptp) REVERT: B 578 GLN cc_start: 0.7137 (tm-30) cc_final: 0.6607 (tm-30) REVERT: C 556 ARG cc_start: 0.7328 (ttp-110) cc_final: 0.6812 (ptm160) REVERT: C 562 MET cc_start: 0.7713 (pmm) cc_final: 0.7267 (ptp) REVERT: C 578 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6246 (mt0) REVERT: C 661 VAL cc_start: 0.9031 (m) cc_final: 0.8793 (p) outliers start: 75 outliers final: 53 residues processed: 278 average time/residue: 0.1605 time to fit residues: 66.5579 Evaluate side-chains 263 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 100 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 237 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.121125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101486 restraints weight = 33977.588| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.43 r_work: 0.3271 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20085 Z= 0.148 Angle : 0.534 9.894 27315 Z= 0.281 Chirality : 0.042 0.145 2970 Planarity : 0.004 0.039 3513 Dihedral : 4.402 19.239 2736 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.96 % Allowed : 14.23 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.18 (0.16), residues: 2418 helix: 0.55 (0.28), residues: 342 sheet: -0.11 (0.18), residues: 792 loop : -0.20 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 124 TYR 0.034 0.001 TYR B 647 PHE 0.017 0.002 PHE C 292 TRP 0.011 0.001 TRP D 68 HIS 0.009 0.001 HIS C 510 Details of bonding type rmsd covalent geometry : bond 0.00346 (20064) covalent geometry : angle 0.53025 (27273) SS BOND : bond 0.00388 ( 21) SS BOND : angle 1.76601 ( 42) hydrogen bonds : bond 0.03577 ( 734) hydrogen bonds : angle 5.22488 ( 2202) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 216 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 599 ARG cc_start: 0.6351 (mmm-85) cc_final: 0.5715 (mtm180) REVERT: A 601 GLU cc_start: 0.6575 (mp0) cc_final: 0.6369 (pm20) REVERT: A 668 ASN cc_start: 0.7792 (m-40) cc_final: 0.7411 (t0) REVERT: D 78 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7167 (mttt) REVERT: D 124 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6801 (mtm110) REVERT: E 46 GLN cc_start: 0.7532 (mt0) cc_final: 0.6980 (tt0) REVERT: E 94 ASP cc_start: 0.7471 (p0) cc_final: 0.7267 (p0) REVERT: F 32 LYS cc_start: 0.7745 (mtpp) cc_final: 0.7417 (mptt) REVERT: F 120 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7826 (t80) REVERT: F 121 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: F 124 ARG cc_start: 0.8482 (mmm160) cc_final: 0.8135 (mtp180) REVERT: L 89 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8353 (m) REVERT: L 109 VAL cc_start: 0.8570 (t) cc_final: 0.8172 (m) REVERT: G 33 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7404 (p) REVERT: G 131 LYS cc_start: 0.3098 (mmmt) cc_final: 0.2813 (pttp) REVERT: B 217 ARG cc_start: 0.7068 (mmm160) cc_final: 0.6663 (ttm-80) REVERT: B 554 SER cc_start: 0.8708 (t) cc_final: 0.8487 (p) REVERT: B 562 MET cc_start: 0.7815 (pmm) cc_final: 0.7603 (ptp) REVERT: C 262 ASN cc_start: 0.8549 (t0) cc_final: 0.8202 (t0) REVERT: C 404 CYS cc_start: 0.6035 (m) cc_final: 0.5613 (m) REVERT: C 556 ARG cc_start: 0.7454 (ttp-110) cc_final: 0.6910 (ptm160) REVERT: C 562 MET cc_start: 0.7634 (pmm) cc_final: 0.7204 (ptp) REVERT: C 661 VAL cc_start: 0.9015 (m) cc_final: 0.8770 (p) outliers start: 63 outliers final: 48 residues processed: 268 average time/residue: 0.1520 time to fit residues: 61.6198 Evaluate side-chains 259 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 528 HIS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 172 optimal weight: 4.9990 chunk 198 optimal weight: 0.0970 chunk 166 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN L 46 GLN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.121882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102233 restraints weight = 33911.391| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.43 r_work: 0.3278 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20085 Z= 0.129 Angle : 0.521 9.642 27315 Z= 0.274 Chirality : 0.041 0.147 2970 Planarity : 0.004 0.040 3513 Dihedral : 4.268 18.946 2736 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.10 % Allowed : 14.60 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.10 (0.17), residues: 2418 helix: 0.61 (0.28), residues: 342 sheet: -0.05 (0.18), residues: 816 loop : -0.15 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 124 TYR 0.022 0.001 TYR B 643 PHE 0.017 0.002 PHE B 635 TRP 0.010 0.001 TRP B 533 HIS 0.009 0.001 HIS C 510 Details of bonding type rmsd covalent geometry : bond 0.00300 (20064) covalent geometry : angle 0.51793 (27273) SS BOND : bond 0.00367 ( 21) SS BOND : angle 1.56186 ( 42) hydrogen bonds : bond 0.03432 ( 734) hydrogen bonds : angle 5.11364 ( 2202) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.6811 (tp40) cc_final: 0.6523 (tp-100) REVERT: A 601 GLU cc_start: 0.6468 (mp0) cc_final: 0.6216 (pm20) REVERT: A 668 ASN cc_start: 0.7790 (m-40) cc_final: 0.7406 (t0) REVERT: D 78 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7124 (mttt) REVERT: D 124 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6764 (mtm110) REVERT: E 46 GLN cc_start: 0.7523 (mt0) cc_final: 0.7000 (tt0) REVERT: E 70 LEU cc_start: 0.8564 (tt) cc_final: 0.8133 (tp) REVERT: F 24 LYS cc_start: 0.8444 (tppt) cc_final: 0.8242 (tttt) REVERT: F 32 LYS cc_start: 0.7700 (mtpp) cc_final: 0.7384 (mptt) REVERT: F 120 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7804 (t80) REVERT: F 121 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: F 124 ARG cc_start: 0.8496 (mmm160) cc_final: 0.8151 (mtp180) REVERT: L 89 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8326 (m) REVERT: L 109 VAL cc_start: 0.8571 (t) cc_final: 0.8189 (m) REVERT: G 131 LYS cc_start: 0.3252 (mmmt) cc_final: 0.2948 (pttp) REVERT: B 106 TYR cc_start: 0.7317 (m-80) cc_final: 0.6862 (m-80) REVERT: B 217 ARG cc_start: 0.7092 (mmm160) cc_final: 0.6647 (ttm-80) REVERT: B 289 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8366 (ttp) REVERT: B 554 SER cc_start: 0.8711 (t) cc_final: 0.8504 (p) REVERT: B 613 GLU cc_start: 0.7738 (mp0) cc_final: 0.7538 (mp0) REVERT: C 262 ASN cc_start: 0.8546 (t0) cc_final: 0.8182 (t0) REVERT: C 404 CYS cc_start: 0.6160 (m) cc_final: 0.5767 (m) REVERT: C 556 ARG cc_start: 0.7408 (ttp-110) cc_final: 0.6942 (ptm160) REVERT: C 562 MET cc_start: 0.7635 (pmm) cc_final: 0.7225 (ptp) REVERT: C 578 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6050 (mt0) REVERT: C 661 VAL cc_start: 0.9017 (m) cc_final: 0.8787 (p) outliers start: 66 outliers final: 49 residues processed: 274 average time/residue: 0.1447 time to fit residues: 60.0940 Evaluate side-chains 264 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 528 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 528 HIS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 167 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 226 optimal weight: 0.0770 chunk 106 optimal weight: 0.0170 chunk 125 optimal weight: 3.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 ASN ** 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 = 0.3699 r_free = 0.3699 target = 0.122661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103355 restraints weight = 33430.180| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.39 r_work: 0.3305 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20085 Z= 0.115 Angle : 0.520 9.990 27315 Z= 0.272 Chirality : 0.041 0.142 2970 Planarity : 0.004 0.043 3513 Dihedral : 4.248 24.029 2736 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.77 % Allowed : 14.51 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.06 (0.17), residues: 2418 helix: 0.59 (0.28), residues: 342 sheet: 0.02 (0.18), residues: 816 loop : -0.13 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 124 TYR 0.030 0.001 TYR B 647 PHE 0.019 0.001 PHE C 292 TRP 0.010 0.001 TRP F 68 HIS 0.012 0.001 HIS B 528 Details of bonding type rmsd covalent geometry : bond 0.00268 (20064) covalent geometry : angle 0.51374 (27273) SS BOND : bond 0.00387 ( 21) SS BOND : angle 2.13928 ( 42) hydrogen bonds : bond 0.03336 ( 734) hydrogen bonds : angle 5.04201 ( 2202) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 221 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 601 GLU cc_start: 0.6526 (mp0) cc_final: 0.6177 (pm20) REVERT: A 668 ASN cc_start: 0.7778 (m-40) cc_final: 0.7409 (t0) REVERT: A 717 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7524 (mp) REVERT: D 78 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7129 (mttt) REVERT: D 124 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6735 (mtm110) REVERT: E 46 GLN cc_start: 0.7495 (mt0) cc_final: 0.6967 (tt0) REVERT: E 70 LEU cc_start: 0.8509 (tt) cc_final: 0.8095 (tp) REVERT: E 94 ASP cc_start: 0.7055 (p0) cc_final: 0.5996 (t70) REVERT: F 32 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7414 (mptt) REVERT: F 120 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7822 (t80) REVERT: F 121 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: L 48 ILE cc_start: 0.9153 (mm) cc_final: 0.8947 (mm) REVERT: L 89 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8288 (m) REVERT: L 109 VAL cc_start: 0.8578 (t) cc_final: 0.8199 (m) REVERT: B 106 TYR cc_start: 0.7357 (m-80) cc_final: 0.6914 (m-80) REVERT: B 217 ARG cc_start: 0.7055 (mmm160) cc_final: 0.6617 (ttm-80) REVERT: B 289 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8313 (ttp) REVERT: B 613 GLU cc_start: 0.7721 (mp0) cc_final: 0.7514 (mp0) REVERT: C 262 ASN cc_start: 0.8522 (t0) cc_final: 0.8186 (t0) REVERT: C 404 CYS cc_start: 0.6131 (m) cc_final: 0.5750 (m) REVERT: C 556 ARG cc_start: 0.7408 (ttp-110) cc_final: 0.6929 (ptm160) REVERT: C 562 MET cc_start: 0.7588 (pmm) cc_final: 0.7184 (ptp) REVERT: C 661 VAL cc_start: 0.9021 (m) cc_final: 0.8779 (p) outliers start: 59 outliers final: 46 residues processed: 269 average time/residue: 0.1503 time to fit residues: 60.5931 Evaluate side-chains 261 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 528 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 528 HIS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 170 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 76 optimal weight: 0.2980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN C 578 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.120382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.100689 restraints weight = 34023.494| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.44 r_work: 0.3260 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20085 Z= 0.204 Angle : 0.581 10.841 27315 Z= 0.303 Chirality : 0.043 0.142 2970 Planarity : 0.004 0.045 3513 Dihedral : 4.456 25.818 2736 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.86 % Allowed : 15.07 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.18 (0.17), residues: 2418 helix: 0.49 (0.28), residues: 342 sheet: -0.11 (0.18), residues: 849 loop : -0.18 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 582 TYR 0.022 0.002 TYR B 647 PHE 0.018 0.002 PHE B 635 TRP 0.009 0.001 TRP C 361 HIS 0.014 0.001 HIS B 528 Details of bonding type rmsd covalent geometry : bond 0.00484 (20064) covalent geometry : angle 0.57261 (27273) SS BOND : bond 0.00470 ( 21) SS BOND : angle 2.54761 ( 42) hydrogen bonds : bond 0.03664 ( 734) hydrogen bonds : angle 5.18723 ( 2202) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4836 Ramachandran restraints generated. 2418 Oldfield, 0 Emsley, 2418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 203 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7273 (tm-30) cc_final: 0.6918 (tp40) REVERT: A 717 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7526 (mp) REVERT: D 78 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7178 (mttt) REVERT: D 124 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6736 (mtm110) REVERT: D 136 LEU cc_start: 0.8052 (tt) cc_final: 0.7755 (mp) REVERT: E 46 GLN cc_start: 0.7564 (mt0) cc_final: 0.7014 (tt0) REVERT: E 70 LEU cc_start: 0.8546 (tt) cc_final: 0.8113 (tp) REVERT: F 32 LYS cc_start: 0.7748 (mtpp) cc_final: 0.7475 (mptt) REVERT: F 120 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7970 (t80) REVERT: F 121 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: F 124 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.7975 (mtp180) REVERT: L 89 SER cc_start: 0.8688 (OUTLIER) cc_final: 0.8365 (m) REVERT: L 103 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: L 109 VAL cc_start: 0.8591 (t) cc_final: 0.8204 (m) REVERT: G 40 ILE cc_start: 0.8117 (mt) cc_final: 0.7724 (tp) REVERT: B 217 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6708 (ttm-80) REVERT: B 289 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8363 (ttp) REVERT: C 262 ASN cc_start: 0.8591 (t0) cc_final: 0.8185 (t0) REVERT: C 404 CYS cc_start: 0.6222 (m) cc_final: 0.5810 (m) REVERT: C 556 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7006 (ptm160) REVERT: C 562 MET cc_start: 0.7626 (pmm) cc_final: 0.7263 (ptp) REVERT: C 661 VAL cc_start: 0.9022 (m) cc_final: 0.8763 (p) outliers start: 61 outliers final: 50 residues processed: 252 average time/residue: 0.1524 time to fit residues: 57.7529 Evaluate side-chains 254 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 197 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 528 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 198 optimal weight: 0.0470 chunk 121 optimal weight: 0.3980 chunk 197 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 ASN ** 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 = 0.3697 r_free = 0.3697 target = 0.122463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102882 restraints weight = 33659.600| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.42 r_work: 0.3304 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20085 Z= 0.113 Angle : 0.524 9.324 27315 Z= 0.275 Chirality : 0.041 0.145 2970 Planarity : 0.004 0.045 3513 Dihedral : 4.303 26.838 2736 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.39 % Allowed : 15.40 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.09 (0.17), residues: 2418 helix: 0.53 (0.28), residues: 342 sheet: -0.01 (0.18), residues: 816 loop : -0.14 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 582 TYR 0.028 0.001 TYR B 647 PHE 0.020 0.001 PHE C 292 TRP 0.020 0.001 TRP C 533 HIS 0.025 0.001 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00260 (20064) covalent geometry : angle 0.51806 (27273) SS BOND : bond 0.00364 ( 21) SS BOND : angle 2.04784 ( 42) hydrogen bonds : bond 0.03350 ( 734) hydrogen bonds : angle 5.03513 ( 2202) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5180.86 seconds wall clock time: 89 minutes 24.29 seconds (5364.29 seconds total)