Starting phenix.real_space_refine on Sat Jun 29 22:48:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh1_19165/06_2024/8rh1_19165.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh1_19165/06_2024/8rh1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh1_19165/06_2024/8rh1_19165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh1_19165/06_2024/8rh1_19165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh1_19165/06_2024/8rh1_19165.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rh1_19165/06_2024/8rh1_19165.pdb" } 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 Residue "E GLU 105": "OE1" <-> "OE2" Residue "L ARG 43": "NH1" <-> "NH2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 712": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 9.55, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.04 Conformation dependent library (CDL) restraints added in 3.0 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: 2.24 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: 7.74 Time building geometry restraints manager: 7.87 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: 97.54 - 104.94: 419 104.94 - 112.34: 9902 112.34 - 119.74: 6707 119.74 - 127.14: 10041 127.14 - 134.53: 204 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 2.440 nonbonded pdb=" O ALA F 127 " pdb=" OH TYR G 60 " model vdw 2.236 2.440 nonbonded pdb=" NE2 GLN C 104 " pdb=" O PHE C 105 " model vdw 2.248 2.520 nonbonded pdb=" OD2 ASP A 712 " pdb=" OG1 THR A 715 " model vdw 2.249 2.440 nonbonded pdb=" OD2 ASP B 712 " pdb=" OG1 THR B 715 " model vdw 2.252 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 5.940 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 50.870 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.790 ------------------------------------------------------------------------------- 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 20064 Z= 0.501 Angle : 0.854 8.092 27273 Z= 0.539 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 2.252 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: 0.3596 time to fit residues: 222.7742 Evaluate side-chains 276 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.123 ------------------------------------------------------------------------------- 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: 0.6980 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN B 506 HIS ** B 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 651 HIS C 118 GLN C 247 ASN C 262 ASN C 528 HIS C 578 GLN C 610 GLN ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 20064 Z= 0.240 Angle : 0.553 9.786 27273 Z= 0.294 Chirality : 0.043 0.179 2970 Planarity : 0.004 0.040 3513 Dihedral : 4.411 25.619 2736 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.31 % Allowed : 9.01 % Favored : 89.67 % 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 (0.17), residues: 2418 helix: -0.01 (0.27), residues: 345 sheet: -0.22 (0.18), residues: 825 loop : -0.01 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 533 HIS 0.018 0.001 HIS C 528 PHE 0.027 0.002 PHE B 635 TYR 0.020 0.001 TYR C 647 ARG 0.009 0.000 ARG A 123 *********************** 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 314 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 286 time to evaluate : 2.273 Fit side-chains revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7412 (tp40) REVERT: A 169 HIS cc_start: 0.8168 (t-90) cc_final: 0.7266 (p90) REVERT: A 225 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8333 (mp0) REVERT: A 524 GLU cc_start: 0.8032 (tp30) cc_final: 0.7619 (mt-10) REVERT: A 574 ASN cc_start: 0.7220 (m110) cc_final: 0.6993 (t0) REVERT: A 668 ASN cc_start: 0.7434 (m-40) cc_final: 0.6586 (t0) REVERT: A 718 ARG cc_start: 0.7250 (tpt170) cc_final: 0.6955 (mmm-85) REVERT: D 51 SER cc_start: 0.7465 (m) cc_final: 0.6908 (t) REVERT: D 78 LYS cc_start: 0.7469 (mtmm) cc_final: 0.6761 (mtmm) REVERT: D 103 MET cc_start: 0.7810 (ttt) cc_final: 0.7275 (ttm) REVERT: D 106 MET cc_start: 0.6649 (tpt) cc_final: 0.6339 (mmp) REVERT: D 136 LEU cc_start: 0.7874 (tt) cc_final: 0.7486 (mp) REVERT: E 46 GLN cc_start: 0.6891 (mt0) cc_final: 0.6098 (tt0) REVERT: E 64 PRO cc_start: 0.6116 (Cg_exo) cc_final: 0.5831 (Cg_endo) REVERT: E 94 ASP cc_start: 0.6691 (p0) cc_final: 0.5646 (t70) REVERT: E 101 ARG cc_start: 0.7518 (mtm-85) cc_final: 0.6817 (mtp85) REVERT: H 133 GLN cc_start: 0.7831 (pm20) cc_final: 0.7535 (mm-40) REVERT: F 32 LYS cc_start: 0.7569 (mtpp) cc_final: 0.6975 (mptt) REVERT: F 106 MET cc_start: 0.7123 (mmp) cc_final: 0.6681 (mmt) REVERT: L 23 MET cc_start: 0.8451 (mmm) cc_final: 0.8155 (mmm) REVERT: L 46 GLN cc_start: 0.7702 (mt0) cc_final: 0.7228 (tt0) REVERT: L 48 ILE cc_start: 0.8716 (mm) cc_final: 0.8463 (mm) REVERT: L 129 GLU cc_start: 0.5760 (mm-30) cc_final: 0.5513 (tp30) REVERT: G 43 ARG cc_start: 0.7457 (ttm110) cc_final: 0.6923 (mtp85) REVERT: G 63 LYS cc_start: 0.7480 (mttp) cc_final: 0.7237 (mmtt) REVERT: B 106 TYR cc_start: 0.6676 (m-80) cc_final: 0.6363 (m-80) REVERT: B 128 ARG cc_start: 0.5711 (mtt90) cc_final: 0.5281 (mtt180) REVERT: B 179 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7858 (pt0) REVERT: B 217 ARG cc_start: 0.7000 (mmm160) cc_final: 0.6359 (ttm-80) REVERT: B 220 HIS cc_start: 0.8274 (m-70) cc_final: 0.8072 (m-70) REVERT: B 221 GLU cc_start: 0.7925 (tt0) cc_final: 0.7348 (tm-30) REVERT: B 224 MET cc_start: 0.8165 (mtt) cc_final: 0.7958 (mtm) REVERT: B 227 LYS cc_start: 0.7660 (pttp) cc_final: 0.7322 (mtmm) REVERT: B 299 SER cc_start: 0.8767 (m) cc_final: 0.8547 (p) REVERT: B 371 GLU cc_start: 0.7137 (pm20) cc_final: 0.6825 (tt0) REVERT: B 509 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7155 (ttm170) REVERT: B 554 SER cc_start: 0.8137 (t) cc_final: 0.7715 (p) REVERT: B 654 SER cc_start: 0.7063 (t) cc_final: 0.6738 (p) REVERT: B 698 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7935 (mm-30) REVERT: C 170 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7138 (tmm160) REVERT: C 227 LYS cc_start: 0.8010 (pttp) cc_final: 0.7531 (mtpp) REVERT: C 411 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7144 (tm-30) REVERT: C 513 ASP cc_start: 0.7098 (m-30) cc_final: 0.6779 (t0) REVERT: C 556 ARG cc_start: 0.7849 (ttp-110) cc_final: 0.7313 (ptm160) REVERT: C 661 VAL cc_start: 0.8861 (m) cc_final: 0.8596 (p) REVERT: C 698 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7496 (tp30) REVERT: C 718 ARG cc_start: 0.5653 (mtt180) cc_final: 0.5211 (mtm180) outliers start: 28 outliers final: 19 residues processed: 302 average time/residue: 0.3430 time to fit residues: 153.4759 Evaluate side-chains 261 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain B residue 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 122 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 54 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 20064 Z= 0.353 Angle : 0.581 7.711 27273 Z= 0.308 Chirality : 0.044 0.152 2970 Planarity : 0.004 0.044 3513 Dihedral : 4.511 20.422 2736 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.63 % Allowed : 11.36 % Favored : 86.01 % 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 (0.17), residues: 2418 helix: 0.30 (0.27), residues: 345 sheet: -0.23 (0.17), residues: 849 loop : -0.06 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 533 HIS 0.012 0.002 HIS C 510 PHE 0.020 0.002 PHE A 286 TYR 0.018 0.002 TYR B 649 ARG 0.005 0.001 ARG F 59 *********************** 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 301 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 245 time to evaluate : 2.247 Fit side-chains revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7909 (t-90) cc_final: 0.7148 (p90) REVERT: A 225 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8235 (mp0) REVERT: A 509 ARG cc_start: 0.7230 (ttp80) cc_final: 0.6873 (ttt180) REVERT: A 524 GLU cc_start: 0.7998 (tp30) cc_final: 0.7617 (mt-10) REVERT: A 574 ASN cc_start: 0.7293 (m110) cc_final: 0.7042 (t0) REVERT: A 668 ASN cc_start: 0.7603 (m-40) cc_final: 0.6798 (t0) REVERT: A 718 ARG cc_start: 0.7109 (tpt170) cc_final: 0.6688 (mmm-85) REVERT: D 51 SER cc_start: 0.7653 (m) cc_final: 0.7062 (t) REVERT: D 78 LYS cc_start: 0.7554 (mtmm) cc_final: 0.7041 (mtmt) REVERT: D 103 MET cc_start: 0.7895 (ttt) cc_final: 0.7648 (ttp) REVERT: D 136 LEU cc_start: 0.7838 (tt) cc_final: 0.7401 (mp) REVERT: E 46 GLN cc_start: 0.7066 (mt0) cc_final: 0.6216 (tt0) REVERT: E 94 ASP cc_start: 0.6471 (p0) cc_final: 0.5478 (t70) REVERT: E 101 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.6810 (mtp85) REVERT: H 129 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: H 133 GLN cc_start: 0.7735 (pm20) cc_final: 0.7363 (mm-40) REVERT: F 32 LYS cc_start: 0.7588 (mtpp) cc_final: 0.6941 (mptt) REVERT: F 106 MET cc_start: 0.7456 (mmp) cc_final: 0.6980 (mmt) REVERT: L 46 GLN cc_start: 0.7710 (mt0) cc_final: 0.7259 (tt0) REVERT: L 103 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6722 (tt0) REVERT: L 129 GLU cc_start: 0.6248 (mm-30) cc_final: 0.5979 (tp30) REVERT: G 43 ARG cc_start: 0.7501 (ttm110) cc_final: 0.6942 (mtp85) REVERT: B 128 ARG cc_start: 0.5840 (mtt90) cc_final: 0.5303 (mtt180) REVERT: B 217 ARG cc_start: 0.7276 (mmm160) cc_final: 0.6723 (ttm-80) REVERT: B 220 HIS cc_start: 0.8287 (m-70) cc_final: 0.8061 (m-70) REVERT: B 221 GLU cc_start: 0.8049 (tt0) cc_final: 0.7474 (tm-30) REVERT: B 224 MET cc_start: 0.8242 (mtt) cc_final: 0.8041 (mtm) REVERT: B 227 LYS cc_start: 0.7717 (pttp) cc_final: 0.7383 (mtmm) REVERT: B 299 SER cc_start: 0.8804 (m) cc_final: 0.8581 (p) REVERT: B 371 GLU cc_start: 0.7055 (pm20) cc_final: 0.6780 (tt0) REVERT: B 509 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7194 (mtt-85) REVERT: B 554 SER cc_start: 0.8226 (t) cc_final: 0.7731 (p) REVERT: B 635 PHE cc_start: 0.8295 (m-80) cc_final: 0.8069 (m-80) REVERT: B 654 SER cc_start: 0.6953 (t) cc_final: 0.6615 (p) REVERT: B 698 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8044 (mm-30) REVERT: C 170 ARG cc_start: 0.7875 (tpp80) cc_final: 0.6973 (tmm160) REVERT: C 210 MET cc_start: 0.9192 (ttp) cc_final: 0.8939 (ttp) REVERT: C 227 LYS cc_start: 0.7926 (pttp) cc_final: 0.7441 (mttp) REVERT: C 411 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7133 (tm-30) REVERT: C 513 ASP cc_start: 0.7437 (m-30) cc_final: 0.7022 (t0) REVERT: C 556 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7147 (ptm160) REVERT: C 578 GLN cc_start: 0.6062 (OUTLIER) cc_final: 0.5730 (mt0) REVERT: C 661 VAL cc_start: 0.8856 (m) cc_final: 0.8624 (p) REVERT: C 698 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7599 (tp30) REVERT: C 718 ARG cc_start: 0.5835 (mtt180) cc_final: 0.5076 (mtm180) outliers start: 56 outliers final: 40 residues processed: 286 average time/residue: 0.3312 time to fit residues: 140.7187 Evaluate side-chains 273 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 231 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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 523 CYS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 579 ASN 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 E residue 118 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 129 ASP 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 F residue 129 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 234 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 506 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN H 98 GLN B 104 GLN ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20064 Z= 0.221 Angle : 0.513 8.885 27273 Z= 0.271 Chirality : 0.042 0.150 2970 Planarity : 0.004 0.040 3513 Dihedral : 4.353 19.999 2736 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.39 % Allowed : 12.11 % Favored : 85.49 % 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: -0.13 (0.17), residues: 2418 helix: 0.47 (0.27), residues: 345 sheet: -0.14 (0.18), residues: 816 loop : -0.06 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 533 HIS 0.010 0.001 HIS C 510 PHE 0.017 0.002 PHE C 292 TYR 0.025 0.001 TYR C 647 ARG 0.004 0.000 ARG F 118 *********************** 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 293 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 242 time to evaluate : 2.333 Fit side-chains revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7884 (t-90) cc_final: 0.7137 (p90) REVERT: A 225 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8252 (mp0) REVERT: A 509 ARG cc_start: 0.7236 (ttp80) cc_final: 0.6893 (ttt180) REVERT: A 524 GLU cc_start: 0.8047 (tp30) cc_final: 0.7682 (mt-10) REVERT: A 574 ASN cc_start: 0.7252 (m110) cc_final: 0.7044 (t0) REVERT: A 582 ARG cc_start: 0.6425 (mmt180) cc_final: 0.6220 (mmm-85) REVERT: A 668 ASN cc_start: 0.7540 (m-40) cc_final: 0.6678 (t0) REVERT: A 718 ARG cc_start: 0.7098 (tpt170) cc_final: 0.6668 (mmm-85) REVERT: D 78 LYS cc_start: 0.7548 (mtmm) cc_final: 0.7056 (mtmt) REVERT: E 46 GLN cc_start: 0.6993 (mt0) cc_final: 0.6167 (tt0) REVERT: E 94 ASP cc_start: 0.6456 (p0) cc_final: 0.5507 (t70) REVERT: E 101 ARG cc_start: 0.7533 (mtm-85) cc_final: 0.6836 (mtp85) REVERT: H 133 GLN cc_start: 0.7773 (pm20) cc_final: 0.7420 (mm-40) REVERT: F 32 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7158 (mptt) REVERT: L 23 MET cc_start: 0.8782 (mmm) cc_final: 0.8555 (mmm) REVERT: L 46 GLN cc_start: 0.7725 (mt0) cc_final: 0.7224 (tt0) REVERT: L 103 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6808 (tt0) REVERT: L 109 VAL cc_start: 0.7941 (t) cc_final: 0.7633 (m) REVERT: L 129 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5825 (tp30) REVERT: G 43 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7004 (mtp85) REVERT: B 128 ARG cc_start: 0.5732 (mtt90) cc_final: 0.5306 (mtt180) REVERT: B 217 ARG cc_start: 0.7284 (mmm160) cc_final: 0.6592 (ttm-80) REVERT: B 222 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7274 (p) REVERT: B 227 LYS cc_start: 0.7650 (pttp) cc_final: 0.7312 (mtmm) REVERT: B 299 SER cc_start: 0.8788 (m) cc_final: 0.8573 (p) REVERT: B 364 VAL cc_start: 0.8634 (t) cc_final: 0.8332 (m) REVERT: B 371 GLU cc_start: 0.7064 (pm20) cc_final: 0.6755 (tt0) REVERT: B 509 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7022 (mtt-85) REVERT: B 554 SER cc_start: 0.8134 (t) cc_final: 0.7719 (p) REVERT: B 654 SER cc_start: 0.7097 (t) cc_final: 0.6747 (p) REVERT: B 698 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7905 (mm-30) REVERT: C 170 ARG cc_start: 0.7855 (tpp80) cc_final: 0.6916 (tmm160) REVERT: C 210 MET cc_start: 0.9153 (ttp) cc_final: 0.8845 (ttm) REVERT: C 227 LYS cc_start: 0.7889 (pttp) cc_final: 0.7425 (mttp) REVERT: C 262 ASN cc_start: 0.8481 (t0) cc_final: 0.8214 (t0) REVERT: C 404 CYS cc_start: 0.6784 (m) cc_final: 0.6374 (m) REVERT: C 411 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7122 (tm-30) REVERT: C 513 ASP cc_start: 0.7505 (m-30) cc_final: 0.7043 (t0) REVERT: C 556 ARG cc_start: 0.7734 (ttp-110) cc_final: 0.7108 (ptm160) REVERT: C 578 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.5805 (mt0) REVERT: C 661 VAL cc_start: 0.8827 (m) cc_final: 0.8606 (p) REVERT: C 698 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7593 (tp30) REVERT: C 718 ARG cc_start: 0.5875 (mtt180) cc_final: 0.5088 (mtm180) outliers start: 51 outliers final: 37 residues processed: 280 average time/residue: 0.3459 time to fit residues: 143.9051 Evaluate side-chains 267 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 228 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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 575 VAL Chi-restraints excluded: chain A residue 579 ASN 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 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 120 TYR Chi-restraints excluded: chain L residue 52 ASN Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 52 ASN ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20064 Z= 0.264 Angle : 0.525 7.724 27273 Z= 0.277 Chirality : 0.042 0.151 2970 Planarity : 0.004 0.038 3513 Dihedral : 4.335 19.527 2736 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.00 % Allowed : 12.30 % Favored : 84.69 % 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: -0.15 (0.17), residues: 2418 helix: 0.55 (0.27), residues: 345 sheet: -0.17 (0.18), residues: 843 loop : -0.09 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 533 HIS 0.010 0.001 HIS C 510 PHE 0.024 0.002 PHE B 635 TYR 0.019 0.001 TYR B 156 ARG 0.006 0.000 ARG A 124 *********************** 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 297 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 233 time to evaluate : 2.208 Fit side-chains revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7896 (t-90) cc_final: 0.7153 (p90) REVERT: A 225 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8259 (mp0) REVERT: A 509 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6896 (ttt180) REVERT: A 524 GLU cc_start: 0.8010 (tp30) cc_final: 0.7674 (mt-10) REVERT: A 574 ASN cc_start: 0.6996 (m110) cc_final: 0.6789 (t0) REVERT: A 582 ARG cc_start: 0.6363 (mmt180) cc_final: 0.6055 (mmm-85) REVERT: A 668 ASN cc_start: 0.7650 (m-40) cc_final: 0.6817 (t0) REVERT: A 718 ARG cc_start: 0.7136 (tpt170) cc_final: 0.6605 (mmm-85) REVERT: D 78 LYS cc_start: 0.7573 (mtmm) cc_final: 0.7067 (mtmt) REVERT: E 46 GLN cc_start: 0.7000 (mt0) cc_final: 0.6219 (tt0) REVERT: E 94 ASP cc_start: 0.6555 (p0) cc_final: 0.5421 (t70) REVERT: E 101 ARG cc_start: 0.7548 (mtm-85) cc_final: 0.6845 (mtp85) REVERT: H 129 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8158 (m-30) REVERT: H 133 GLN cc_start: 0.7815 (pm20) cc_final: 0.7443 (mm-40) REVERT: F 32 LYS cc_start: 0.7735 (mtpp) cc_final: 0.7166 (mptt) REVERT: L 46 GLN cc_start: 0.7630 (mt0) cc_final: 0.7162 (tt0) REVERT: L 103 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6843 (tt0) REVERT: L 109 VAL cc_start: 0.7904 (t) cc_final: 0.7554 (m) REVERT: L 129 GLU cc_start: 0.6244 (mm-30) cc_final: 0.5873 (tp30) REVERT: G 40 ILE cc_start: 0.8092 (mt) cc_final: 0.7700 (mm) REVERT: G 43 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7006 (mtp85) REVERT: B 128 ARG cc_start: 0.5775 (mtt90) cc_final: 0.5289 (mtt180) REVERT: B 217 ARG cc_start: 0.7305 (mmm160) cc_final: 0.6630 (ttm-80) REVERT: B 221 GLU cc_start: 0.8048 (tt0) cc_final: 0.7263 (tm-30) REVERT: B 227 LYS cc_start: 0.7669 (pttp) cc_final: 0.7327 (mtmm) REVERT: B 299 SER cc_start: 0.8741 (m) cc_final: 0.8496 (p) REVERT: B 364 VAL cc_start: 0.8642 (t) cc_final: 0.8384 (m) REVERT: B 371 GLU cc_start: 0.6960 (pm20) cc_final: 0.6694 (tt0) REVERT: B 509 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7024 (mtt-85) REVERT: B 554 SER cc_start: 0.8179 (t) cc_final: 0.7755 (p) REVERT: B 654 SER cc_start: 0.7086 (t) cc_final: 0.6726 (p) REVERT: B 698 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7812 (mm-30) REVERT: C 170 ARG cc_start: 0.7861 (tpp80) cc_final: 0.6908 (tmm160) REVERT: C 227 LYS cc_start: 0.7877 (pttp) cc_final: 0.7400 (mttp) REVERT: C 262 ASN cc_start: 0.8496 (t0) cc_final: 0.8221 (t0) REVERT: C 404 CYS cc_start: 0.6871 (m) cc_final: 0.6494 (m) REVERT: C 411 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7137 (tm-30) REVERT: C 556 ARG cc_start: 0.7624 (ttp-110) cc_final: 0.7003 (ptm160) REVERT: C 578 GLN cc_start: 0.6184 (OUTLIER) cc_final: 0.5888 (mt0) REVERT: C 661 VAL cc_start: 0.8824 (m) cc_final: 0.8609 (p) REVERT: C 698 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7582 (tp30) REVERT: C 718 ARG cc_start: 0.5865 (mtt180) cc_final: 0.5224 (mtm180) outliers start: 64 outliers final: 49 residues processed: 284 average time/residue: 0.3366 time to fit residues: 142.4687 Evaluate side-chains 280 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 229 time to evaluate : 2.150 ------------------------------------------------------------------------------- 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 575 VAL Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain 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 93 ASP Chi-restraints excluded: chain H residue 129 ASP 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 L residue 52 ASN Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 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 79 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 235 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN C 432 GLN ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20064 Z= 0.209 Angle : 0.502 7.071 27273 Z= 0.265 Chirality : 0.041 0.144 2970 Planarity : 0.004 0.038 3513 Dihedral : 4.268 18.620 2736 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.15 % Allowed : 12.68 % Favored : 84.18 % 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: -0.04 (0.17), residues: 2418 helix: 0.66 (0.28), residues: 342 sheet: -0.04 (0.18), residues: 831 loop : -0.08 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 533 HIS 0.009 0.001 HIS C 510 PHE 0.018 0.002 PHE B 635 TYR 0.020 0.001 TYR B 156 ARG 0.007 0.000 ARG A 124 *********************** 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 312 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 245 time to evaluate : 2.067 Fit side-chains revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7882 (t-90) cc_final: 0.7144 (p90) REVERT: A 225 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8274 (mp0) REVERT: A 509 ARG cc_start: 0.7258 (ttp80) cc_final: 0.6914 (ttt180) REVERT: A 524 GLU cc_start: 0.7999 (tp30) cc_final: 0.7658 (mt-10) REVERT: A 574 ASN cc_start: 0.6987 (m110) cc_final: 0.6783 (t0) REVERT: A 582 ARG cc_start: 0.6433 (mmt180) cc_final: 0.6115 (mmm-85) REVERT: D 78 LYS cc_start: 0.7562 (mtmm) cc_final: 0.7045 (mtmt) REVERT: D 124 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6695 (mtm110) REVERT: E 46 GLN cc_start: 0.6957 (mt0) cc_final: 0.6177 (tt0) REVERT: E 101 ARG cc_start: 0.7529 (mtm-85) cc_final: 0.6828 (mtp85) REVERT: H 133 GLN cc_start: 0.7863 (pm20) cc_final: 0.7487 (mm-40) REVERT: F 32 LYS cc_start: 0.7663 (mtpp) cc_final: 0.7174 (mptt) REVERT: F 124 ARG cc_start: 0.8234 (mmm160) cc_final: 0.8011 (mmt90) REVERT: L 46 GLN cc_start: 0.7629 (mt0) cc_final: 0.7150 (tt0) REVERT: L 103 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6812 (tt0) REVERT: L 109 VAL cc_start: 0.7903 (t) cc_final: 0.7566 (m) REVERT: L 129 GLU cc_start: 0.6097 (mm-30) cc_final: 0.5666 (tp30) REVERT: G 40 ILE cc_start: 0.8116 (mt) cc_final: 0.7705 (mm) REVERT: G 43 ARG cc_start: 0.7624 (ttm110) cc_final: 0.6964 (mtp85) REVERT: B 105 PHE cc_start: 0.6402 (m-10) cc_final: 0.6155 (m-10) REVERT: B 128 ARG cc_start: 0.5770 (mtt90) cc_final: 0.5364 (mtp180) REVERT: B 217 ARG cc_start: 0.7341 (mmm160) cc_final: 0.6669 (ttm-80) REVERT: B 222 THR cc_start: 0.7465 (OUTLIER) cc_final: 0.7078 (p) REVERT: B 227 LYS cc_start: 0.7514 (pttp) cc_final: 0.7261 (mmtm) REVERT: B 299 SER cc_start: 0.8734 (m) cc_final: 0.8490 (p) REVERT: B 371 GLU cc_start: 0.6973 (pm20) cc_final: 0.6730 (tt0) REVERT: B 509 ARG cc_start: 0.7555 (ttp80) cc_final: 0.7020 (mtt-85) REVERT: B 528 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7553 (t70) REVERT: B 533 TRP cc_start: 0.7994 (m100) cc_final: 0.7684 (m100) REVERT: B 554 SER cc_start: 0.8199 (t) cc_final: 0.7821 (p) REVERT: B 654 SER cc_start: 0.7087 (t) cc_final: 0.6726 (p) REVERT: B 698 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7652 (mm-30) REVERT: C 170 ARG cc_start: 0.7905 (tpp80) cc_final: 0.6946 (tmm160) REVERT: C 210 MET cc_start: 0.9147 (ttp) cc_final: 0.8852 (ttm) REVERT: C 227 LYS cc_start: 0.7863 (pttp) cc_final: 0.7406 (mttp) REVERT: C 262 ASN cc_start: 0.8462 (t0) cc_final: 0.8210 (t0) REVERT: C 404 CYS cc_start: 0.6892 (m) cc_final: 0.6528 (m) REVERT: C 411 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7126 (tm-30) REVERT: C 416 MET cc_start: 0.7015 (mtp) cc_final: 0.6676 (ttm) REVERT: C 556 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.6979 (ptm160) REVERT: C 578 GLN cc_start: 0.6177 (OUTLIER) cc_final: 0.5878 (mt0) REVERT: C 616 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6461 (tm-30) REVERT: C 661 VAL cc_start: 0.8704 (m) cc_final: 0.8440 (p) REVERT: C 698 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7667 (tp30) REVERT: C 718 ARG cc_start: 0.6159 (mtt180) cc_final: 0.5666 (mtm180) outliers start: 67 outliers final: 50 residues processed: 296 average time/residue: 0.3301 time to fit residues: 145.0489 Evaluate side-chains 280 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 226 time to evaluate : 2.009 ------------------------------------------------------------------------------- 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 A residue 579 ASN Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 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 100 VAL Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain F residue 31 VAL 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 L residue 22 VAL Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 528 HIS Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 171 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 234 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 506 HIS ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20064 Z= 0.291 Angle : 0.540 7.380 27273 Z= 0.283 Chirality : 0.042 0.145 2970 Planarity : 0.004 0.040 3513 Dihedral : 4.342 19.242 2736 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.57 % Allowed : 12.58 % Favored : 83.85 % 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: -0.13 (0.17), residues: 2418 helix: 0.70 (0.28), residues: 342 sheet: -0.13 (0.18), residues: 843 loop : -0.15 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 533 HIS 0.010 0.001 HIS C 510 PHE 0.018 0.002 PHE A 151 TYR 0.022 0.002 TYR B 647 ARG 0.006 0.000 ARG A 124 *********************** 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 305 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 229 time to evaluate : 1.767 Fit side-chains revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7855 (t-90) cc_final: 0.7095 (p-80) REVERT: A 225 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8272 (mp0) REVERT: A 509 ARG cc_start: 0.7314 (ttp80) cc_final: 0.6932 (ttt180) REVERT: A 524 GLU cc_start: 0.8013 (tp30) cc_final: 0.7709 (mt-10) REVERT: A 582 ARG cc_start: 0.6440 (mmt180) cc_final: 0.6199 (mmm-85) REVERT: D 78 LYS cc_start: 0.7570 (mtmm) cc_final: 0.7049 (mtmt) REVERT: D 124 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6676 (mtm110) REVERT: E 46 GLN cc_start: 0.6959 (mt0) cc_final: 0.6174 (tt0) REVERT: E 101 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.6943 (mtp85) REVERT: H 133 GLN cc_start: 0.7838 (pm20) cc_final: 0.7447 (mm-40) REVERT: F 32 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7182 (mptt) REVERT: F 43 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.6820 (m-80) REVERT: F 124 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7995 (mmt90) REVERT: L 46 GLN cc_start: 0.7602 (mt0) cc_final: 0.7096 (tt0) REVERT: L 103 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6859 (tt0) REVERT: L 109 VAL cc_start: 0.7960 (t) cc_final: 0.7608 (m) REVERT: L 129 GLU cc_start: 0.6286 (mm-30) cc_final: 0.5947 (tp30) REVERT: G 40 ILE cc_start: 0.8085 (mt) cc_final: 0.7525 (mm) REVERT: G 43 ARG cc_start: 0.7618 (ttm110) cc_final: 0.6970 (mtp85) REVERT: B 128 ARG cc_start: 0.5848 (mtt90) cc_final: 0.5518 (mtp180) REVERT: B 217 ARG cc_start: 0.7293 (mmm160) cc_final: 0.6601 (ttm-80) REVERT: B 222 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7237 (p) REVERT: B 227 LYS cc_start: 0.7542 (pttp) cc_final: 0.7279 (mmtm) REVERT: B 299 SER cc_start: 0.8753 (m) cc_final: 0.8504 (p) REVERT: B 371 GLU cc_start: 0.6979 (pm20) cc_final: 0.6710 (tt0) REVERT: B 509 ARG cc_start: 0.7501 (ttp80) cc_final: 0.6984 (mtt-85) REVERT: B 533 TRP cc_start: 0.7995 (m100) cc_final: 0.7749 (m100) REVERT: B 554 SER cc_start: 0.8246 (t) cc_final: 0.7845 (p) REVERT: B 654 SER cc_start: 0.6952 (t) cc_final: 0.6605 (p) REVERT: B 698 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7782 (mm-30) REVERT: C 170 ARG cc_start: 0.7905 (tpp80) cc_final: 0.6943 (tmm160) REVERT: C 210 MET cc_start: 0.9166 (ttp) cc_final: 0.8883 (ttm) REVERT: C 222 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7444 (p) REVERT: C 227 LYS cc_start: 0.7863 (pttp) cc_final: 0.7391 (mttp) REVERT: C 262 ASN cc_start: 0.8513 (t0) cc_final: 0.8211 (t0) REVERT: C 404 CYS cc_start: 0.6844 (m) cc_final: 0.6544 (m) REVERT: C 411 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7111 (tm-30) REVERT: C 556 ARG cc_start: 0.7495 (ttp-110) cc_final: 0.6884 (ptm160) REVERT: C 578 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5942 (mt0) REVERT: C 661 VAL cc_start: 0.8671 (m) cc_final: 0.8416 (p) REVERT: C 718 ARG cc_start: 0.5977 (mtt180) cc_final: 0.5357 (mtm180) outliers start: 76 outliers final: 56 residues processed: 290 average time/residue: 0.3425 time to fit residues: 146.9163 Evaluate side-chains 284 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 223 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 579 ASN Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 ASP 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 95 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 120 TYR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 672 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 0.0770 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20064 Z= 0.243 Angle : 0.524 9.689 27273 Z= 0.274 Chirality : 0.042 0.141 2970 Planarity : 0.004 0.040 3513 Dihedral : 4.354 20.595 2736 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.47 % Allowed : 12.91 % Favored : 83.62 % 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: -0.08 (0.17), residues: 2418 helix: 0.71 (0.28), residues: 342 sheet: -0.07 (0.18), residues: 834 loop : -0.13 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 533 HIS 0.011 0.001 HIS C 510 PHE 0.033 0.002 PHE B 635 TYR 0.031 0.001 TYR B 647 ARG 0.008 0.000 ARG A 124 *********************** 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 297 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 223 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7851 (t-90) cc_final: 0.7091 (p-80) REVERT: A 225 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8252 (mp0) REVERT: A 509 ARG cc_start: 0.7309 (ttp80) cc_final: 0.6929 (ttt180) REVERT: A 524 GLU cc_start: 0.8269 (tp30) cc_final: 0.7968 (mt-10) REVERT: A 582 ARG cc_start: 0.6530 (mmt180) cc_final: 0.6148 (mmm-85) REVERT: D 78 LYS cc_start: 0.7564 (mtmm) cc_final: 0.7038 (mtmt) REVERT: D 124 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6765 (mtm110) REVERT: E 46 GLN cc_start: 0.6940 (mt0) cc_final: 0.6164 (tt0) REVERT: E 101 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.6942 (mtp85) REVERT: H 133 GLN cc_start: 0.7818 (pm20) cc_final: 0.7412 (mm-40) REVERT: F 32 LYS cc_start: 0.7672 (mtpp) cc_final: 0.7185 (mptt) REVERT: F 43 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.6879 (m-80) REVERT: F 121 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.7183 (m-10) REVERT: L 46 GLN cc_start: 0.7589 (mt0) cc_final: 0.7083 (tt0) REVERT: L 103 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6861 (tt0) REVERT: L 109 VAL cc_start: 0.7966 (t) cc_final: 0.7617 (m) REVERT: L 129 GLU cc_start: 0.6383 (mm-30) cc_final: 0.6042 (tp30) REVERT: G 40 ILE cc_start: 0.8063 (mt) cc_final: 0.7498 (mm) REVERT: G 43 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7103 (mtp85) REVERT: B 128 ARG cc_start: 0.5856 (mtt90) cc_final: 0.5525 (mtp180) REVERT: B 217 ARG cc_start: 0.7244 (mmm160) cc_final: 0.6581 (ttm-80) REVERT: B 222 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7066 (p) REVERT: B 299 SER cc_start: 0.8745 (m) cc_final: 0.8487 (p) REVERT: B 371 GLU cc_start: 0.6973 (pm20) cc_final: 0.6702 (tt0) REVERT: B 528 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.7602 (t70) REVERT: B 533 TRP cc_start: 0.7984 (m100) cc_final: 0.7752 (m100) REVERT: B 554 SER cc_start: 0.8250 (t) cc_final: 0.7875 (p) REVERT: B 654 SER cc_start: 0.7099 (t) cc_final: 0.6732 (p) REVERT: B 698 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7647 (mm-30) REVERT: C 210 MET cc_start: 0.9147 (ttp) cc_final: 0.8865 (ttm) REVERT: C 227 LYS cc_start: 0.7859 (pttp) cc_final: 0.7399 (mttp) REVERT: C 262 ASN cc_start: 0.8498 (t0) cc_final: 0.8208 (t0) REVERT: C 404 CYS cc_start: 0.6858 (m) cc_final: 0.6586 (m) REVERT: C 411 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6854 (tm-30) REVERT: C 556 ARG cc_start: 0.7558 (ttp-110) cc_final: 0.6939 (ptm160) REVERT: C 578 GLN cc_start: 0.6176 (OUTLIER) cc_final: 0.5873 (mt0) REVERT: C 661 VAL cc_start: 0.8685 (m) cc_final: 0.8433 (p) REVERT: C 718 ARG cc_start: 0.6204 (mtt180) cc_final: 0.5454 (mtm180) outliers start: 74 outliers final: 60 residues processed: 281 average time/residue: 0.3296 time to fit residues: 139.7983 Evaluate side-chains 278 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 212 time to evaluate : 2.145 ------------------------------------------------------------------------------- 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 575 VAL Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 ASP 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 31 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 92 LYS Chi-restraints excluded: chain F residue 95 SER 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 52 ASN Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 528 HIS Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 528 HIS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 599 ARG 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 224 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 197 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 506 HIS ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20064 Z= 0.383 Angle : 0.601 9.164 27273 Z= 0.316 Chirality : 0.044 0.154 2970 Planarity : 0.005 0.040 3513 Dihedral : 4.636 24.612 2736 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.33 % Allowed : 13.38 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.17), residues: 2418 helix: 0.56 (0.28), residues: 342 sheet: -0.25 (0.18), residues: 834 loop : -0.25 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 533 HIS 0.011 0.001 HIS C 510 PHE 0.022 0.002 PHE A 151 TYR 0.043 0.002 TYR B 647 ARG 0.005 0.001 ARG A 701 *********************** 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 292 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 221 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7875 (t-90) cc_final: 0.7107 (p-80) REVERT: A 225 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8224 (mp0) REVERT: A 509 ARG cc_start: 0.7337 (ttp80) cc_final: 0.6960 (ttt180) REVERT: A 524 GLU cc_start: 0.8266 (tp30) cc_final: 0.7978 (mt-10) REVERT: A 582 ARG cc_start: 0.6012 (mmt180) cc_final: 0.5710 (mmm-85) REVERT: D 78 LYS cc_start: 0.7527 (mtmm) cc_final: 0.7003 (mtmt) REVERT: D 124 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6719 (mtm110) REVERT: E 46 GLN cc_start: 0.7040 (mt0) cc_final: 0.6197 (tt0) REVERT: E 101 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.6987 (mtp85) REVERT: H 133 GLN cc_start: 0.8217 (pm20) cc_final: 0.7829 (mm-40) REVERT: F 32 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7115 (mptt) REVERT: F 43 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: F 121 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.7244 (m-10) REVERT: L 46 GLN cc_start: 0.7565 (mt0) cc_final: 0.7061 (tt0) REVERT: L 103 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6915 (mt-10) REVERT: L 109 VAL cc_start: 0.7944 (t) cc_final: 0.7585 (m) REVERT: L 129 GLU cc_start: 0.6115 (mm-30) cc_final: 0.5745 (tp30) REVERT: G 40 ILE cc_start: 0.7978 (mt) cc_final: 0.7446 (mm) REVERT: G 43 ARG cc_start: 0.7597 (ttm110) cc_final: 0.6947 (mtp85) REVERT: B 128 ARG cc_start: 0.5657 (mtt90) cc_final: 0.5314 (mtp180) REVERT: B 217 ARG cc_start: 0.7296 (mmm160) cc_final: 0.6782 (ttm-80) REVERT: B 289 MET cc_start: 0.8833 (ttp) cc_final: 0.8600 (ttp) REVERT: B 299 SER cc_start: 0.8785 (m) cc_final: 0.8479 (p) REVERT: B 528 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7679 (t70) REVERT: B 554 SER cc_start: 0.8428 (t) cc_final: 0.7981 (p) REVERT: B 632 ARG cc_start: 0.5882 (mtp-110) cc_final: 0.5601 (ptt-90) REVERT: B 654 SER cc_start: 0.6946 (t) cc_final: 0.6599 (p) REVERT: B 698 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7706 (mm-30) REVERT: C 227 LYS cc_start: 0.7899 (pttp) cc_final: 0.7413 (mttp) REVERT: C 262 ASN cc_start: 0.8531 (t0) cc_final: 0.8232 (t0) REVERT: C 404 CYS cc_start: 0.6901 (m) cc_final: 0.6635 (m) REVERT: C 411 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7169 (tm-30) REVERT: C 578 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5927 (mt0) REVERT: C 661 VAL cc_start: 0.8750 (m) cc_final: 0.8505 (p) REVERT: C 718 ARG cc_start: 0.6091 (mtt180) cc_final: 0.5441 (mtm180) outliers start: 71 outliers final: 58 residues processed: 274 average time/residue: 0.3333 time to fit residues: 137.4013 Evaluate side-chains 278 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 215 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 290 SER 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 424 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 579 ASN Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 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 95 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 121 TYR Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain G residue 36 GLU Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 528 HIS Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 599 ARG 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 230 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 109 optimal weight: 0.0470 chunk 160 optimal weight: 1.9990 chunk 242 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 192 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN B 508 GLN ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20064 Z= 0.187 Angle : 0.518 10.165 27273 Z= 0.272 Chirality : 0.041 0.150 2970 Planarity : 0.004 0.043 3513 Dihedral : 4.417 24.714 2736 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.68 % Allowed : 14.04 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2418 helix: 0.63 (0.28), residues: 342 sheet: -0.09 (0.19), residues: 795 loop : -0.19 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 533 HIS 0.021 0.001 HIS A 528 PHE 0.037 0.002 PHE B 635 TYR 0.043 0.001 TYR B 647 ARG 0.004 0.000 ARG C 556 ********************** 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 277 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 220 time to evaluate : 2.326 Fit side-chains revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7854 (t-90) cc_final: 0.7092 (p-80) REVERT: A 225 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8220 (mp0) REVERT: A 509 ARG cc_start: 0.7262 (ttp80) cc_final: 0.6874 (ttt180) REVERT: A 524 GLU cc_start: 0.8272 (tp30) cc_final: 0.7986 (mt-10) REVERT: A 582 ARG cc_start: 0.6508 (mmt180) cc_final: 0.6146 (mmm-85) REVERT: D 78 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7011 (mtmt) REVERT: D 124 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6777 (mtm110) REVERT: E 46 GLN cc_start: 0.6946 (mt0) cc_final: 0.6173 (tt0) REVERT: E 101 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.6940 (mtp85) REVERT: H 133 GLN cc_start: 0.8139 (pm20) cc_final: 0.7696 (mm-40) REVERT: F 32 LYS cc_start: 0.7691 (mtpp) cc_final: 0.7150 (mptt) REVERT: F 121 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.7195 (m-10) REVERT: L 46 GLN cc_start: 0.7582 (mt0) cc_final: 0.7070 (tt0) REVERT: L 103 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6737 (tt0) REVERT: L 109 VAL cc_start: 0.7956 (t) cc_final: 0.7608 (m) REVERT: L 129 GLU cc_start: 0.6329 (mm-30) cc_final: 0.6005 (tp30) REVERT: G 40 ILE cc_start: 0.7938 (mt) cc_final: 0.7412 (mm) REVERT: G 43 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7061 (mtp85) REVERT: B 128 ARG cc_start: 0.5643 (mtt90) cc_final: 0.5282 (mtp180) REVERT: B 217 ARG cc_start: 0.7232 (mmm160) cc_final: 0.6636 (ttm-80) REVERT: B 289 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8354 (ttp) REVERT: B 299 SER cc_start: 0.8740 (m) cc_final: 0.8442 (p) REVERT: B 528 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7640 (t70) REVERT: B 554 SER cc_start: 0.8337 (t) cc_final: 0.7968 (p) REVERT: B 654 SER cc_start: 0.6969 (t) cc_final: 0.6616 (p) REVERT: B 698 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7624 (mm-30) REVERT: C 170 ARG cc_start: 0.7915 (tpp80) cc_final: 0.6934 (tmm160) REVERT: C 210 MET cc_start: 0.9150 (ttp) cc_final: 0.8873 (ttm) REVERT: C 227 LYS cc_start: 0.7829 (pttp) cc_final: 0.7379 (mttp) REVERT: C 262 ASN cc_start: 0.8368 (t0) cc_final: 0.8157 (t0) REVERT: C 404 CYS cc_start: 0.6927 (m) cc_final: 0.6669 (m) REVERT: C 411 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6873 (tm-30) REVERT: C 556 ARG cc_start: 0.7538 (ttp-110) cc_final: 0.7253 (ttp-110) REVERT: C 578 GLN cc_start: 0.6083 (OUTLIER) cc_final: 0.5789 (mt0) REVERT: C 599 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6788 (ptt-90) REVERT: C 661 VAL cc_start: 0.8760 (m) cc_final: 0.8512 (p) REVERT: C 718 ARG cc_start: 0.6085 (mtt180) cc_final: 0.5432 (mtm180) outliers start: 57 outliers final: 44 residues processed: 263 average time/residue: 0.3363 time to fit residues: 131.6631 Evaluate side-chains 263 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 213 time to evaluate : 2.054 ------------------------------------------------------------------------------- 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 424 THR Chi-restraints excluded: chain A residue 579 ASN Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain D residue 124 ARG 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 121 TYR Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 94 ASP Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain G residue 36 GLU 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 162 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 223 ASP Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 528 HIS Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 528 HIS Chi-restraints excluded: chain C residue 578 GLN Chi-restraints excluded: chain C residue 599 ARG 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 205 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 198 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS E 52 ASN B 121 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 631 HIS ** 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 = 0.3679 r_free = 0.3679 target = 0.121744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.101541 restraints weight = 33838.737| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.46 r_work: 0.3248 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20064 Z= 0.250 Angle : 0.536 9.716 27273 Z= 0.279 Chirality : 0.042 0.153 2970 Planarity : 0.004 0.044 3513 Dihedral : 4.412 24.913 2736 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.63 % Allowed : 14.08 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.17), residues: 2418 helix: 0.94 (0.28), residues: 324 sheet: -0.09 (0.19), residues: 795 loop : -0.11 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 533 HIS 0.013 0.001 HIS C 510 PHE 0.017 0.002 PHE A 598 TYR 0.028 0.001 TYR A 647 ARG 0.003 0.000 ARG C 552 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4172.92 seconds wall clock time: 75 minutes 12.65 seconds (4512.65 seconds total)