Starting phenix.real_space_refine on Tue Jun 17 07:59:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh1_19165/06_2025/8rh1_19165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh1_19165/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rh1_19165/06_2025/8rh1_19165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh1_19165/06_2025/8rh1_19165.map" model { file = "/net/cci-nas-00/data/ceres_data/8rh1_19165/06_2025/8rh1_19165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh1_19165/06_2025/8rh1_19165.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.22, per 1000 atoms: 0.62 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: 5.30 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 3.05 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: 8.87 Time building geometry restraints manager: 6.20 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: 0.01 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 50.080 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.530 ------------------------------------------------------------------------------- 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 : 10.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), 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 TRP 0.050 0.008 TRP C 348 HIS 0.035 0.005 HIS B 300 PHE 0.066 0.007 PHE C 286 TYR 0.059 0.007 TYR A 504 ARG 0.033 0.002 ARG C 499 Details of bonding type rmsd hydrogen bonds : bond 0.16164 ( 734) hydrogen bonds : angle 8.00916 ( 2202) SS BOND : bond 0.03334 ( 21) SS BOND : angle 2.39578 ( 42) covalent geometry : bond 0.00759 (20064) covalent geometry : angle 0.85383 (27273) *********************** 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 : 2.138 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: 0.7288 (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: 0.6448 (m-80) REVERT: D 51 SER cc_start: 0.7652 (m) cc_final: 0.6993 (t) REVERT: D 57 TRP cc_start: 0.8623 (m100) cc_final: 0.8263 (m100) REVERT: D 78 LYS cc_start: 0.7460 (mtmm) cc_final: 0.6806 (mtmm) REVERT: D 97 ASN cc_start: 0.4708 (t0) cc_final: 0.4276 (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: 0.5789 (mmp) REVERT: E 46 GLN cc_start: 0.6290 (mt0) cc_final: 0.5732 (tt0) REVERT: E 64 PRO cc_start: 0.6062 (Cg_exo) cc_final: 0.5805 (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: 0.6851 (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: 0.6180 (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: 0.6781 (mtp85) REVERT: G 63 LYS cc_start: 0.7466 (mttp) cc_final: 0.7222 (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: 0.4793 (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: 0.7374 (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: 0.7086 (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: 0.7259 (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: 0.3711 time to fit residues: 228.9407 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 : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 240 HIS A 393 GLN A 506 HIS ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN E 62 GLN H 105 ASN B 506 HIS B 508 GLN ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102817 restraints weight = 33690.764| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.48 r_work: 0.3281 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20085 Z= 0.168 Angle : 0.589 14.131 27315 Z= 0.315 Chirality : 0.043 0.175 2970 Planarity : 0.004 0.042 3513 Dihedral : 4.455 25.000 2736 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.99 % Allowed : 9.44 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2418 helix: -0.03 (0.27), residues: 345 sheet: -0.19 (0.18), residues: 816 loop : 0.01 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 533 HIS 0.018 0.001 HIS C 528 PHE 0.025 0.002 PHE B 635 TYR 0.020 0.002 TYR C 647 ARG 0.007 0.001 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 734) hydrogen bonds : angle 5.84851 ( 2202) SS BOND : bond 0.00559 ( 21) SS BOND : angle 3.52397 ( 42) covalent geometry : bond 0.00380 (20064) covalent geometry : angle 0.57291 (27273) *********************** 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 315 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 294 time to evaluate : 2.147 Fit side-chains revert: symmetry clash REVERT: A 668 ASN cc_start: 0.7566 (m-40) cc_final: 0.7108 (t0) REVERT: D 78 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7543 (mttp) REVERT: D 103 MET cc_start: 0.8106 (ttt) cc_final: 0.7864 (ttm) REVERT: D 106 MET cc_start: 0.6287 (tpt) cc_final: 0.6009 (mmp) REVERT: D 136 LEU cc_start: 0.8076 (tt) cc_final: 0.7669 (mp) REVERT: E 46 GLN cc_start: 0.7485 (mt0) cc_final: 0.6999 (tt0) REVERT: E 64 PRO cc_start: 0.6046 (Cg_exo) cc_final: 0.5751 (Cg_endo) REVERT: E 94 ASP cc_start: 0.7048 (p0) cc_final: 0.5998 (t70) REVERT: H 91 SER cc_start: 0.8692 (t) cc_final: 0.8362 (m) REVERT: F 32 LYS cc_start: 0.7538 (mtpp) cc_final: 0.7247 (mptt) REVERT: F 106 MET cc_start: 0.7243 (mmp) cc_final: 0.7020 (mmt) REVERT: F 111 THR cc_start: 0.9001 (m) cc_final: 0.8789 (p) REVERT: L 23 MET cc_start: 0.8659 (mmm) cc_final: 0.8448 (mmm) REVERT: L 48 ILE cc_start: 0.8979 (mm) cc_final: 0.8696 (mm) REVERT: B 217 ARG cc_start: 0.6729 (mmm160) cc_final: 0.6478 (ttm-80) REVERT: B 227 LYS cc_start: 0.7675 (pttp) cc_final: 0.7471 (mtmm) REVERT: B 554 SER cc_start: 0.8662 (t) cc_final: 0.8424 (p) REVERT: C 210 MET cc_start: 0.8887 (ttp) cc_final: 0.8599 (ttp) REVERT: C 532 LEU cc_start: 0.8750 (mt) cc_final: 0.8540 (mt) REVERT: C 556 ARG cc_start: 0.7427 (ttp-110) cc_final: 0.7145 (ptm160) REVERT: C 645 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7153 (mm-30) REVERT: C 661 VAL cc_start: 0.9094 (m) cc_final: 0.8811 (p) outliers start: 21 outliers final: 14 residues processed: 306 average time/residue: 0.3474 time to fit residues: 157.7175 Evaluate side-chains 247 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 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 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 63 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN C 194 ASN C 240 HIS C 262 ASN ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.120833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100918 restraints weight = 33640.809| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.41 r_work: 0.3248 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 20085 Z= 0.227 Angle : 0.600 11.005 27315 Z= 0.318 Chirality : 0.044 0.158 2970 Planarity : 0.005 0.045 3513 Dihedral : 4.540 20.024 2736 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.39 % Allowed : 11.03 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2418 helix: 0.22 (0.27), residues: 345 sheet: -0.24 (0.17), residues: 846 loop : -0.07 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 533 HIS 0.014 0.002 HIS C 528 PHE 0.020 0.002 PHE B 151 TYR 0.021 0.002 TYR B 649 ARG 0.006 0.001 ARG F 59 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 734) hydrogen bonds : angle 5.65020 ( 2202) SS BOND : bond 0.00427 ( 21) SS BOND : angle 2.52294 ( 42) covalent geometry : bond 0.00538 (20064) covalent geometry : angle 0.59226 (27273) *********************** 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 288 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 668 ASN cc_start: 0.7725 (m-40) cc_final: 0.7258 (t0) REVERT: D 103 MET cc_start: 0.8257 (ttt) cc_final: 0.8008 (ttm) REVERT: D 136 LEU cc_start: 0.8084 (tt) cc_final: 0.7602 (mp) REVERT: E 46 GLN cc_start: 0.7618 (mt0) cc_final: 0.7109 (tt0) REVERT: E 94 ASP cc_start: 0.7427 (p0) cc_final: 0.6366 (t70) REVERT: F 32 LYS cc_start: 0.7503 (mtpp) cc_final: 0.7108 (mptt) REVERT: F 106 MET cc_start: 0.7564 (mmp) cc_final: 0.7237 (mmt) REVERT: F 124 ARG cc_start: 0.8440 (mmm160) cc_final: 0.8121 (mmt90) REVERT: G 84 ASP cc_start: 0.7845 (t0) cc_final: 0.7548 (t0) REVERT: B 217 ARG cc_start: 0.6926 (mmm160) cc_final: 0.6687 (ttm-80) REVERT: B 554 SER cc_start: 0.8738 (t) cc_final: 0.8449 (p) REVERT: C 119 PHE cc_start: 0.7842 (m-10) cc_final: 0.7621 (m-10) REVERT: C 532 LEU cc_start: 0.8955 (mt) cc_final: 0.8728 (mt) REVERT: C 556 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.7139 (ptm160) REVERT: C 562 MET cc_start: 0.7732 (pmm) cc_final: 0.7161 (ptp) REVERT: C 578 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6087 (mt0) REVERT: C 661 VAL cc_start: 0.9110 (m) cc_final: 0.8862 (p) outliers start: 51 outliers final: 33 residues processed: 276 average time/residue: 0.3581 time to fit residues: 146.8536 Evaluate side-chains 249 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 L residue 22 VAL 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 213 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 392 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 168 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 218 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 H 105 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 HIS ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101903 restraints weight = 33778.610| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.44 r_work: 0.3278 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20085 Z= 0.144 Angle : 0.529 8.848 27315 Z= 0.282 Chirality : 0.042 0.150 2970 Planarity : 0.004 0.038 3513 Dihedral : 4.383 20.038 2736 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.25 % Allowed : 12.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2418 helix: 0.38 (0.27), residues: 345 sheet: -0.12 (0.18), residues: 807 loop : -0.03 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 533 HIS 0.012 0.001 HIS C 528 PHE 0.019 0.002 PHE C 292 TYR 0.025 0.001 TYR B 647 ARG 0.005 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 734) hydrogen bonds : angle 5.41682 ( 2202) SS BOND : bond 0.00312 ( 21) SS BOND : angle 1.84312 ( 42) covalent geometry : bond 0.00333 (20064) covalent geometry : angle 0.52446 (27273) *********************** 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 276 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.6507 (mmm-85) cc_final: 0.6204 (mmm-85) REVERT: A 668 ASN cc_start: 0.7735 (m-40) cc_final: 0.7382 (t0) REVERT: D 136 LEU cc_start: 0.8043 (tt) cc_final: 0.7633 (mp) REVERT: E 46 GLN cc_start: 0.7541 (mt0) cc_final: 0.7028 (tt0) REVERT: E 94 ASP cc_start: 0.7388 (p0) cc_final: 0.5886 (t70) REVERT: F 24 LYS cc_start: 0.8465 (tppt) cc_final: 0.8258 (tppt) REVERT: F 32 LYS cc_start: 0.7679 (mtpp) cc_final: 0.7444 (mptt) REVERT: F 121 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.7570 (m-80) REVERT: F 124 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8126 (mmt90) REVERT: L 109 VAL cc_start: 0.8562 (t) cc_final: 0.8210 (m) REVERT: G 84 ASP cc_start: 0.8012 (t0) cc_final: 0.7659 (t0) REVERT: B 106 TYR cc_start: 0.7245 (m-80) cc_final: 0.6888 (m-80) REVERT: B 217 ARG cc_start: 0.6991 (mmm160) cc_final: 0.6562 (ttm-80) REVERT: B 554 SER cc_start: 0.8713 (t) cc_final: 0.8450 (p) REVERT: B 562 MET cc_start: 0.7788 (pmm) cc_final: 0.7259 (ptp) REVERT: B 578 GLN cc_start: 0.7098 (tm-30) cc_final: 0.6608 (tm-30) REVERT: C 210 MET cc_start: 0.8918 (ttp) cc_final: 0.8701 (ttp) REVERT: C 262 ASN cc_start: 0.8554 (t0) cc_final: 0.8185 (t0) REVERT: C 404 CYS cc_start: 0.5640 (m) cc_final: 0.5081 (m) REVERT: C 532 LEU cc_start: 0.8960 (mt) cc_final: 0.8717 (mt) REVERT: C 556 ARG cc_start: 0.7515 (ttp-110) cc_final: 0.7041 (ptm160) REVERT: C 562 MET cc_start: 0.7711 (pmm) cc_final: 0.7107 (ptp) REVERT: C 661 VAL cc_start: 0.9078 (m) cc_final: 0.8858 (p) outliers start: 48 outliers final: 34 residues processed: 266 average time/residue: 0.3550 time to fit residues: 140.6118 Evaluate side-chains 244 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 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 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 121 TYR 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 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 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 44 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 183 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 445 GLN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN L 62 GLN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN C 631 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.118946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098823 restraints weight = 34536.401| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.45 r_work: 0.3219 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 20085 Z= 0.285 Angle : 0.642 8.546 27315 Z= 0.339 Chirality : 0.045 0.158 2970 Planarity : 0.005 0.051 3513 Dihedral : 4.729 19.612 2736 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.19 % Allowed : 12.58 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2418 helix: 0.23 (0.27), residues: 342 sheet: -0.35 (0.18), residues: 831 loop : -0.14 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 68 HIS 0.010 0.002 HIS C 510 PHE 0.022 0.003 PHE A 174 TYR 0.031 0.002 TYR B 647 ARG 0.007 0.001 ARG A 701 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 734) hydrogen bonds : angle 5.56896 ( 2202) SS BOND : bond 0.00457 ( 21) SS BOND : angle 2.51894 ( 42) covalent geometry : bond 0.00674 (20064) covalent geometry : angle 0.63492 (27273) *********************** 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 291 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 223 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ARG cc_start: 0.6657 (mmm-85) cc_final: 0.5956 (mtm180) REVERT: A 601 GLU cc_start: 0.6682 (mp0) cc_final: 0.6449 (pm20) REVERT: A 668 ASN cc_start: 0.7953 (m-40) cc_final: 0.7561 (t0) REVERT: D 106 MET cc_start: 0.6559 (tpp) cc_final: 0.6315 (tpp) REVERT: D 136 LEU cc_start: 0.7997 (tt) cc_final: 0.7771 (mp) REVERT: E 43 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7848 (ttm170) REVERT: E 46 GLN cc_start: 0.7688 (mt0) cc_final: 0.7190 (tt0) REVERT: E 94 ASP cc_start: 0.7469 (p0) cc_final: 0.7153 (p0) REVERT: F 32 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7306 (mptt) REVERT: F 43 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: F 121 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.7672 (m-10) REVERT: L 23 MET cc_start: 0.8714 (mmm) cc_final: 0.8447 (mmm) REVERT: L 89 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8374 (m) REVERT: L 109 VAL cc_start: 0.8631 (t) cc_final: 0.8193 (m) REVERT: G 84 ASP cc_start: 0.8051 (t0) cc_final: 0.7672 (t0) REVERT: B 217 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6738 (ttm-80) REVERT: B 554 SER cc_start: 0.8939 (t) cc_final: 0.8616 (p) REVERT: B 562 MET cc_start: 0.7813 (pmm) cc_final: 0.7478 (ptp) REVERT: B 578 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6476 (tm-30) REVERT: C 556 ARG cc_start: 0.7395 (ttp-110) cc_final: 0.6882 (ptm160) REVERT: C 562 MET cc_start: 0.7748 (pmm) cc_final: 0.7161 (ptp) REVERT: C 573 ASP cc_start: 0.7470 (p0) cc_final: 0.7147 (t0) REVERT: C 578 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6241 (mt0) REVERT: C 661 VAL cc_start: 0.9043 (m) cc_final: 0.8797 (p) outliers start: 68 outliers final: 52 residues processed: 275 average time/residue: 0.3349 time to fit residues: 139.0237 Evaluate side-chains 266 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 2.192 ------------------------------------------------------------------------------- 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 332 THR 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 574 ASN 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 100 VAL Chi-restraints excluded: chain D residue 104 THR 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 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 24 THR 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 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 392 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 116 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 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 = 0.3664 r_free = 0.3664 target = 0.120350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.100495 restraints weight = 34004.523| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.43 r_work: 0.3255 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20085 Z= 0.176 Angle : 0.559 9.659 27315 Z= 0.295 Chirality : 0.042 0.148 2970 Planarity : 0.004 0.041 3513 Dihedral : 4.552 19.350 2736 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.15 % Allowed : 13.52 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2418 helix: 0.40 (0.27), residues: 342 sheet: -0.32 (0.18), residues: 801 loop : -0.19 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 68 HIS 0.009 0.001 HIS C 510 PHE 0.043 0.002 PHE B 635 TYR 0.021 0.001 TYR B 156 ARG 0.007 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 734) hydrogen bonds : angle 5.35474 ( 2202) SS BOND : bond 0.00495 ( 21) SS BOND : angle 1.96885 ( 42) covalent geometry : bond 0.00415 (20064) covalent geometry : angle 0.55421 (27273) *********************** 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 287 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 220 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 GLU cc_start: 0.6632 (mp0) cc_final: 0.6374 (pm20) REVERT: D 78 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7187 (mttt) REVERT: D 124 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6713 (mtm110) REVERT: E 43 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7844 (ttm170) REVERT: E 46 GLN cc_start: 0.7578 (mt0) cc_final: 0.7044 (tt0) REVERT: E 94 ASP cc_start: 0.7300 (p0) cc_final: 0.7069 (p0) REVERT: F 24 LYS cc_start: 0.8574 (tppt) cc_final: 0.8303 (tttt) REVERT: F 32 LYS cc_start: 0.7771 (mtpp) cc_final: 0.7351 (mptt) REVERT: F 121 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: F 124 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8072 (mtp180) REVERT: L 23 MET cc_start: 0.8549 (mmm) cc_final: 0.8278 (mmm) REVERT: L 89 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8406 (m) REVERT: L 109 VAL cc_start: 0.8548 (t) cc_final: 0.8118 (m) REVERT: G 98 LYS cc_start: 0.7578 (mmtm) cc_final: 0.7373 (mmtm) REVERT: B 217 ARG cc_start: 0.7052 (mmm160) cc_final: 0.6704 (ttm-80) REVERT: B 554 SER cc_start: 0.8799 (t) cc_final: 0.8484 (p) REVERT: B 557 MET cc_start: 0.7246 (mmt) cc_final: 0.7004 (tpt) REVERT: B 562 MET cc_start: 0.7869 (pmm) cc_final: 0.7658 (ptp) REVERT: B 578 GLN cc_start: 0.6977 (tm-30) cc_final: 0.6448 (tm-30) REVERT: C 262 ASN cc_start: 0.8587 (t0) cc_final: 0.8182 (t0) REVERT: C 404 CYS cc_start: 0.6078 (m) cc_final: 0.5635 (m) REVERT: C 556 ARG cc_start: 0.7527 (ttp-110) cc_final: 0.6994 (ptm160) REVERT: C 562 MET cc_start: 0.7616 (pmm) cc_final: 0.7197 (ptp) REVERT: C 578 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6196 (mt0) REVERT: C 661 VAL cc_start: 0.9055 (m) cc_final: 0.8813 (p) outliers start: 67 outliers final: 46 residues processed: 273 average time/residue: 0.3360 time to fit residues: 138.9029 Evaluate side-chains 256 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 2.347 ------------------------------------------------------------------------------- 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 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 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 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 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 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 392 THR 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 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 78 optimal weight: 0.0970 chunk 149 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.0170 chunk 8 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 GLN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.121740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102459 restraints weight = 33562.991| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.42 r_work: 0.3275 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20085 Z= 0.122 Angle : 0.524 9.639 27315 Z= 0.276 Chirality : 0.041 0.150 2970 Planarity : 0.004 0.040 3513 Dihedral : 4.376 19.471 2736 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.82 % Allowed : 14.13 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2418 helix: 0.56 (0.28), residues: 342 sheet: -0.15 (0.18), residues: 795 loop : -0.17 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 68 HIS 0.009 0.001 HIS C 510 PHE 0.019 0.002 PHE C 292 TYR 0.018 0.001 TYR C 372 ARG 0.008 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 734) hydrogen bonds : angle 5.19800 ( 2202) SS BOND : bond 0.00396 ( 21) SS BOND : angle 1.67230 ( 42) covalent geometry : bond 0.00285 (20064) covalent geometry : angle 0.52014 (27273) *********************** 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 272 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 212 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 78 LYS cc_start: 0.7875 (mtmt) cc_final: 0.7149 (mttt) REVERT: D 124 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6741 (mtm110) REVERT: E 43 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7838 (ttm170) REVERT: E 46 GLN cc_start: 0.7559 (mt0) cc_final: 0.7021 (tt0) REVERT: E 70 LEU cc_start: 0.8523 (tt) cc_final: 0.8118 (tp) REVERT: F 24 LYS cc_start: 0.8543 (tppt) cc_final: 0.8234 (tttt) REVERT: F 32 LYS cc_start: 0.7729 (mtpp) cc_final: 0.7429 (mptt) REVERT: F 121 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: F 124 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.8091 (mtp180) REVERT: L 89 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8296 (m) REVERT: L 109 VAL cc_start: 0.8556 (t) cc_final: 0.8126 (m) REVERT: B 217 ARG cc_start: 0.7108 (mmm160) cc_final: 0.6656 (ttm-80) REVERT: B 554 SER cc_start: 0.8703 (t) cc_final: 0.8444 (p) REVERT: B 557 MET cc_start: 0.7180 (mmt) cc_final: 0.6970 (tpt) REVERT: C 262 ASN cc_start: 0.8539 (t0) cc_final: 0.8189 (t0) REVERT: C 404 CYS cc_start: 0.6116 (m) cc_final: 0.5735 (m) REVERT: C 556 ARG cc_start: 0.7476 (ttp-110) cc_final: 0.6964 (ptm160) REVERT: C 562 MET cc_start: 0.7637 (pmm) cc_final: 0.7225 (ptp) REVERT: C 661 VAL cc_start: 0.9035 (m) cc_final: 0.8807 (p) outliers start: 60 outliers final: 40 residues processed: 258 average time/residue: 0.3350 time to fit residues: 129.7356 Evaluate side-chains 246 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 2.117 ------------------------------------------------------------------------------- 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 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 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 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 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 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 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 392 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 81 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 157 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 247 ASN A 528 HIS ** 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** ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.118980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099200 restraints weight = 34279.339| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.43 r_work: 0.3232 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 20085 Z= 0.264 Angle : 0.620 13.211 27315 Z= 0.327 Chirality : 0.045 0.163 2970 Planarity : 0.005 0.042 3513 Dihedral : 4.672 23.060 2736 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.24 % Allowed : 14.23 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.17), residues: 2418 helix: 0.31 (0.27), residues: 345 sheet: -0.38 (0.17), residues: 885 loop : -0.22 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 533 HIS 0.013 0.002 HIS B 528 PHE 0.021 0.002 PHE A 151 TYR 0.035 0.002 TYR B 647 ARG 0.007 0.001 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 734) hydrogen bonds : angle 5.41768 ( 2202) SS BOND : bond 0.00492 ( 21) SS BOND : angle 2.85107 ( 42) covalent geometry : bond 0.00631 (20064) covalent geometry : angle 0.61076 (27273) *********************** 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 281 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 212 time to evaluate : 2.467 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.6845 (tp-100) cc_final: 0.6598 (tp-100) REVERT: A 717 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.7728 (mp) REVERT: D 78 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7368 (mtmt) REVERT: D 124 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6796 (mtm110) REVERT: D 136 LEU cc_start: 0.7986 (tt) cc_final: 0.7766 (mp) REVERT: E 43 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7822 (ttm170) REVERT: E 46 GLN cc_start: 0.7615 (mt0) cc_final: 0.7052 (tt0) REVERT: E 70 LEU cc_start: 0.8550 (tt) cc_final: 0.8145 (tp) REVERT: F 24 LYS cc_start: 0.8553 (tppt) cc_final: 0.8319 (tttt) REVERT: F 32 LYS cc_start: 0.7744 (mtpp) cc_final: 0.7351 (mptt) REVERT: F 43 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.6787 (m-80) REVERT: F 93 ASP cc_start: 0.7636 (t0) cc_final: 0.7421 (t70) REVERT: F 121 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: F 124 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8121 (mtp180) REVERT: L 89 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8323 (m) REVERT: B 217 ARG cc_start: 0.7131 (mmm160) cc_final: 0.6756 (ttm-80) REVERT: B 554 SER cc_start: 0.8856 (t) cc_final: 0.8550 (p) REVERT: B 598 PHE cc_start: 0.6363 (p90) cc_final: 0.6004 (p90) REVERT: C 556 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7051 (ptm160) REVERT: C 562 MET cc_start: 0.7660 (pmm) cc_final: 0.7333 (ptp) REVERT: C 661 VAL cc_start: 0.9035 (m) cc_final: 0.8792 (p) outliers start: 69 outliers final: 53 residues processed: 266 average time/residue: 0.3510 time to fit residues: 140.7520 Evaluate side-chains 257 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 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 A residue 717 ILE Chi-restraints excluded: chain D residue 43 PHE 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 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 46 GLN Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 126 THR 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 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 309 ASP Chi-restraints excluded: chain B residue 392 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101470 restraints weight = 33782.365| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.43 r_work: 0.3266 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20085 Z= 0.144 Angle : 0.550 9.999 27315 Z= 0.289 Chirality : 0.042 0.159 2970 Planarity : 0.004 0.041 3513 Dihedral : 4.503 23.337 2736 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.00 % Allowed : 14.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2418 helix: 0.36 (0.27), residues: 345 sheet: -0.26 (0.18), residues: 819 loop : -0.24 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 533 HIS 0.015 0.001 HIS A 528 PHE 0.017 0.002 PHE C 292 TYR 0.021 0.001 TYR B 647 ARG 0.004 0.000 ARG G 43 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 734) hydrogen bonds : angle 5.25608 ( 2202) SS BOND : bond 0.00419 ( 21) SS BOND : angle 2.49647 ( 42) covalent geometry : bond 0.00336 (20064) covalent geometry : angle 0.54122 (27273) *********************** 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 268 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 2.244 Fit side-chains revert: symmetry clash REVERT: A 717 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7595 (mp) REVERT: D 78 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7312 (mtmt) REVERT: D 124 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6826 (mtm110) REVERT: E 43 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7750 (ttm170) REVERT: E 46 GLN cc_start: 0.7579 (mt0) cc_final: 0.7010 (tt0) REVERT: E 70 LEU cc_start: 0.8464 (tt) cc_final: 0.7992 (tp) REVERT: F 24 LYS cc_start: 0.8488 (tppt) cc_final: 0.8250 (tttt) REVERT: F 32 LYS cc_start: 0.7778 (mtpp) cc_final: 0.7446 (mptt) REVERT: F 93 ASP cc_start: 0.7591 (t0) cc_final: 0.7365 (t70) REVERT: F 121 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: F 124 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8157 (mtp180) REVERT: L 89 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8375 (m) REVERT: L 109 VAL cc_start: 0.8745 (t) cc_final: 0.8254 (m) REVERT: G 33 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7557 (p) REVERT: B 217 ARG cc_start: 0.7213 (mmm160) cc_final: 0.6745 (ttm-80) REVERT: B 554 SER cc_start: 0.8834 (t) cc_final: 0.8570 (p) REVERT: C 262 ASN cc_start: 0.8563 (t0) cc_final: 0.8184 (t0) REVERT: C 556 ARG cc_start: 0.7571 (ttp-110) cc_final: 0.6996 (ptm160) REVERT: C 562 MET cc_start: 0.7580 (pmm) cc_final: 0.7251 (ptp) REVERT: C 661 VAL cc_start: 0.9028 (m) cc_final: 0.8797 (p) outliers start: 64 outliers final: 49 residues processed: 256 average time/residue: 0.3475 time to fit residues: 133.6451 Evaluate side-chains 257 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 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 A residue 717 ILE Chi-restraints excluded: chain D residue 43 PHE 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 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 121 TYR 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 126 THR 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 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 309 ASP Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain C residue 125 CYS 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 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 125 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 528 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.100313 restraints weight = 33926.813| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.43 r_work: 0.3257 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20085 Z= 0.197 Angle : 0.577 8.443 27315 Z= 0.303 Chirality : 0.043 0.158 2970 Planarity : 0.004 0.043 3513 Dihedral : 4.579 23.704 2736 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.96 % Allowed : 15.07 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2418 helix: 0.35 (0.27), residues: 345 sheet: -0.30 (0.17), residues: 879 loop : -0.24 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 131 HIS 0.014 0.001 HIS B 528 PHE 0.018 0.002 PHE A 151 TYR 0.034 0.002 TYR B 647 ARG 0.006 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 734) hydrogen bonds : angle 5.29468 ( 2202) SS BOND : bond 0.00425 ( 21) SS BOND : angle 2.38859 ( 42) covalent geometry : bond 0.00468 (20064) covalent geometry : angle 0.56989 (27273) ********************** 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 266 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 203 time to evaluate : 2.182 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.6814 (tp-100) cc_final: 0.6602 (tp-100) REVERT: A 717 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7703 (mp) REVERT: D 124 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6781 (mtm110) REVERT: E 43 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7715 (ttm170) REVERT: E 46 GLN cc_start: 0.7589 (mt0) cc_final: 0.7036 (tt0) REVERT: E 70 LEU cc_start: 0.8455 (tt) cc_final: 0.7983 (tp) REVERT: H 64 LYS cc_start: 0.8090 (mmtp) cc_final: 0.7360 (mttp) REVERT: F 24 LYS cc_start: 0.8535 (tppt) cc_final: 0.8302 (tttt) REVERT: F 32 LYS cc_start: 0.7779 (mtpp) cc_final: 0.7485 (mptt) REVERT: F 121 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: F 124 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8146 (mtp180) REVERT: L 89 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8327 (m) REVERT: L 109 VAL cc_start: 0.8767 (t) cc_final: 0.8247 (m) REVERT: G 131 LYS cc_start: 0.3732 (mmmt) cc_final: 0.2909 (pttp) REVERT: B 217 ARG cc_start: 0.7121 (mmm160) cc_final: 0.6759 (ttm-80) REVERT: B 554 SER cc_start: 0.8854 (t) cc_final: 0.8588 (p) REVERT: C 262 ASN cc_start: 0.8591 (t0) cc_final: 0.8188 (t0) REVERT: C 404 CYS cc_start: 0.5976 (m) cc_final: 0.5503 (m) REVERT: C 556 ARG cc_start: 0.7606 (ttp-110) cc_final: 0.7022 (ptm160) REVERT: C 562 MET cc_start: 0.7600 (pmm) cc_final: 0.7264 (ptp) REVERT: C 661 VAL cc_start: 0.9029 (m) cc_final: 0.8795 (p) outliers start: 63 outliers final: 54 residues processed: 255 average time/residue: 0.3325 time to fit residues: 128.3609 Evaluate side-chains 252 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 333 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 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 84 LEU Chi-restraints excluded: chain D residue 86 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 121 TYR 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 109 VAL 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 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 309 ASP Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain C residue 125 CYS 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 336 LEU 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 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 60 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 186 optimal weight: 0.4980 chunk 210 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 0.0770 chunk 226 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.120384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100824 restraints weight = 34077.055| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.42 r_work: 0.3261 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20085 Z= 0.175 Angle : 0.568 11.204 27315 Z= 0.297 Chirality : 0.043 0.156 2970 Planarity : 0.004 0.052 3513 Dihedral : 4.539 23.912 2736 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.00 % Allowed : 15.12 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2418 helix: 0.39 (0.27), residues: 345 sheet: -0.26 (0.18), residues: 849 loop : -0.28 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 68 HIS 0.014 0.001 HIS A 528 PHE 0.040 0.002 PHE B 635 TYR 0.020 0.002 TYR B 647 ARG 0.008 0.000 ARG A 582 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 734) hydrogen bonds : angle 5.25603 ( 2202) SS BOND : bond 0.00435 ( 21) SS BOND : angle 2.26664 ( 42) covalent geometry : bond 0.00412 (20064) covalent geometry : angle 0.56153 (27273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11058.65 seconds wall clock time: 189 minutes 49.60 seconds (11389.60 seconds total)