Starting phenix.real_space_refine on Thu Sep 18 18:29:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh2_19166/09_2025/8rh2_19166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh2_19166/09_2025/8rh2_19166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rh2_19166/09_2025/8rh2_19166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh2_19166/09_2025/8rh2_19166.map" model { file = "/net/cci-nas-00/data/ceres_data/8rh2_19166/09_2025/8rh2_19166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh2_19166/09_2025/8rh2_19166.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 12036 2.51 5 N 3390 2.21 5 O 3630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19152 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: "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 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "G" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 773 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "D" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Time building chain proxies: 4.15, per 1000 atoms: 0.22 Number of scatterers: 19152 At special positions: 0 Unit cell: (190.565, 169.963, 160.95, 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 3630 8.00 N 3390 7.00 C 12036 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=2.06 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 263 " distance=2.04 Simple disulfide: pdb=" SG CYS A 356 " - pdb=" SG CYS A 404 " distance=2.04 Simple disulfide: pdb=" SG CYS A 590 " - pdb=" SG CYS A 627 " distance=2.05 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 567 " distance=2.04 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 523 " distance=2.08 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 263 " distance=2.04 Simple disulfide: pdb=" SG CYS B 356 " - pdb=" SG CYS B 404 " distance=2.03 Simple disulfide: pdb=" SG CYS B 590 " - pdb=" SG CYS B 627 " distance=2.05 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=2.07 Simple disulfide: pdb=" SG CYS C 199 " - pdb=" SG CYS C 263 " distance=2.04 Simple disulfide: pdb=" SG CYS C 356 " - pdb=" SG CYS C 404 " distance=2.04 Simple disulfide: pdb=" SG CYS C 590 " - pdb=" SG CYS C 627 " distance=2.05 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 101 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 101 " distance=2.04 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 101 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 829.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4476 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 49 sheets defined 18.5% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 185 through 192 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 298 through 302 removed outlier: 3.653A pdb=" N THR A 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) 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 420 removed outlier: 4.643A pdb=" N GLY A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 540 removed outlier: 4.085A pdb=" N GLY A 516 " --> pdb=" O ASN A 512 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 550 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 691 Processing helix chain 'A' and resid 695 through 704 Processing helix chain 'A' and resid 705 through 711 Processing helix chain 'B' and resid 185 through 190 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 298 through 302 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: 4.389A pdb=" N GLY B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 540 removed outlier: 4.279A pdb=" N THR B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 532 " --> pdb=" O HIS B 528 " (cutoff:3.500A) removed outlier: 3.707A 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 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 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 190 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 298 through 302 removed outlier: 3.520A pdb=" N THR C 301 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 302 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' 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 404 through 420 Processing helix chain 'C' and resid 495 through 540 removed outlier: 4.368A pdb=" N THR C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C 532 " --> pdb=" O HIS C 528 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS C 538 " --> pdb=" O ASN C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 550 removed outlier: 3.734A 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 removed outlier: 3.523A pdb=" N VAL C 658 " --> pdb=" O ARG C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 691 Processing helix chain 'C' and resid 695 through 705 Processing helix chain 'C' and resid 705 through 711 removed outlier: 3.503A pdb=" N ALA C 711 " --> pdb=" O ASP C 707 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 70 removed outlier: 3.530A pdb=" N GLN H 70 " --> pdb=" O ARG H 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 67 through 70' Processing helix chain 'H' and resid 92 through 95 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.892A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.753A pdb=" N GLU E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.751A pdb=" N GLU G 82 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 70 removed outlier: 3.718A pdb=" N GLN D 70 " --> pdb=" O ARG D 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 67 through 70' Processing helix chain 'D' and resid 92 through 95 Processing helix chain 'F' and resid 67 through 70 removed outlier: 3.618A pdb=" N GLN F 70 " --> pdb=" O ARG F 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 70' Processing helix chain 'F' and resid 92 through 95 Processing sheet with id=AA1, first strand: chain 'A' and resid 568 through 570 removed outlier: 7.551A 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: 6.687A pdb=" N VAL A 116 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 661 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN A 118 " --> pdb=" O VAL C 661 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 364 removed outlier: 5.356A pdb=" N LYS A 360 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LYS A 143 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 364 removed outlier: 5.356A pdb=" N LYS A 360 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LYS A 143 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 183 removed outlier: 6.326A pdb=" N GLN A 164 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE A 177 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 162 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A 179 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 160 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 181 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS A 158 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N TYR A 156 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 227 through 228 removed outlier: 7.190A pdb=" N LYS A 152 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP A 347 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N THR A 332 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 316 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 198 through 200 Processing sheet with id=AA9, first strand: chain 'A' and resid 202 through 207 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: 6.919A pdb=" N TYR A 641 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLN A 652 " --> pdb=" O TYR A 641 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR A 643 " --> pdb=" O SER A 650 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 659 through 661 removed outlier: 3.997A pdb=" N THR A 659 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 568 through 570 removed outlier: 7.636A pdb=" N TYR B 106 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 364 removed outlier: 5.374A pdb=" N LYS B 360 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS B 143 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 358 through 364 removed outlier: 5.374A pdb=" N LYS B 360 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS B 143 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 183 removed outlier: 6.413A pdb=" N GLN B 164 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE B 177 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 162 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU B 179 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 160 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG B 181 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS B 158 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N TYR B 156 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 227 through 228 removed outlier: 7.196A pdb=" N LYS B 152 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP B 347 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N THR B 332 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 316 " --> pdb=" O THR B 332 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 198 through 200 Processing sheet with id=AC1, first strand: chain 'B' and resid 202 through 207 Processing sheet with id=AC2, first strand: chain 'B' and resid 367 through 372 Processing sheet with id=AC3, first strand: chain 'B' and resid 589 through 591 Processing sheet with id=AC4, first strand: chain 'B' and resid 632 through 637 removed outlier: 5.245A pdb=" N GLU B 645 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 659 through 661 removed outlier: 3.918A pdb=" N THR B 659 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 568 through 570 removed outlier: 7.389A pdb=" N TYR C 106 " --> pdb=" O LEU C 617 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 358 through 364 removed outlier: 5.266A pdb=" N LYS C 360 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS C 143 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 358 through 364 removed outlier: 5.266A pdb=" N LYS C 360 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS C 143 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 172 through 183 removed outlier: 6.135A pdb=" N GLN C 164 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE C 177 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL C 162 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU C 179 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL C 160 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG C 181 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LYS C 158 " --> pdb=" O ARG C 181 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N TYR C 156 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 227 through 228 removed outlier: 7.062A pdb=" N LYS C 152 " --> pdb=" O ASP C 347 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP C 347 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR C 332 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY C 316 " --> pdb=" O THR C 332 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AD3, first strand: chain 'C' and resid 202 through 206 Processing sheet with id=AD4, first strand: chain 'C' and resid 367 through 372 Processing sheet with id=AD5, first strand: chain 'C' and resid 589 through 591 Processing sheet with id=AD6, first strand: chain 'C' and resid 632 through 637 removed outlier: 5.231A pdb=" N GLU C 645 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TYR C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 8 through 11 Processing sheet with id=AD8, first strand: chain 'H' and resid 15 through 16 removed outlier: 6.644A pdb=" N GLU H 15 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE H 39 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP H 55 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 41 " --> pdb=" O MET H 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.537A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AE3, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.628A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AE5, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AE6, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.645A pdb=" N VAL G 10 " --> pdb=" O THR G 104 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP G 34 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.645A pdb=" N VAL G 10 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE9, first strand: chain 'D' and resid 8 through 11 Processing sheet with id=AF1, first strand: chain 'D' and resid 15 through 16 removed outlier: 6.659A pdb=" N GLU D 15 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG D 43 " --> pdb=" O TRP D 52 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TRP D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA D 45 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU D 50 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 8 through 11 Processing sheet with id=AF3, first strand: chain 'F' and resid 15 through 16 removed outlier: 5.823A pdb=" N ARG F 43 " --> pdb=" O TRP F 52 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TRP F 52 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA F 45 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU F 50 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 15 through 16 removed outlier: 4.467A pdb=" N VAL F 116 " --> pdb=" O ARG F 103 " (cutoff:3.500A) 861 hydrogen bonds defined for protein. 2250 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: 3.73 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6357 1.34 - 1.47: 5049 1.47 - 1.59: 8058 1.59 - 1.71: 0 1.71 - 1.84: 150 Bond restraints: 19614 Sorted by residual: bond pdb=" CE1 HIS D 32 " pdb=" NE2 HIS D 32 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS H 32 " pdb=" NE2 HIS H 32 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.26e+01 bond pdb=" CE1 HIS C 220 " pdb=" NE2 HIS C 220 " ideal model delta sigma weight residual 1.321 1.355 -0.034 1.00e-02 1.00e+04 1.12e+01 bond pdb=" CE1 HIS C 169 " pdb=" NE2 HIS C 169 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.12e+01 bond pdb=" CE1 HIS B 220 " pdb=" NE2 HIS B 220 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.09e+01 ... (remaining 19609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 25739 1.36 - 2.72: 784 2.72 - 4.08: 105 4.08 - 5.44: 12 5.44 - 6.80: 3 Bond angle restraints: 26643 Sorted by residual: angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 113.53 110.76 2.77 9.80e-01 1.04e+00 8.00e+00 angle pdb=" C SER G 92 " pdb=" CA SER G 92 " pdb=" CB SER G 92 " ideal model delta sigma weight residual 110.42 115.98 -5.56 1.99e+00 2.53e-01 7.80e+00 angle pdb=" C TYR G 49 " pdb=" N ASP G 50 " pdb=" CA ASP G 50 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 angle pdb=" N VAL G 95 " pdb=" CA VAL G 95 " pdb=" CB VAL G 95 " ideal model delta sigma weight residual 111.00 113.73 -2.73 1.14e+00 7.69e-01 5.73e+00 angle pdb=" C TYR L 49 " pdb=" N ASP L 50 " pdb=" CA ASP L 50 " ideal model delta sigma weight residual 121.54 125.98 -4.44 1.91e+00 2.74e-01 5.41e+00 ... (remaining 26638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10543 17.96 - 35.92: 854 35.92 - 53.89: 176 53.89 - 71.85: 47 71.85 - 89.81: 26 Dihedral angle restraints: 11646 sinusoidal: 4638 harmonic: 7008 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 -169.93 83.93 1 1.00e+01 1.00e-02 8.58e+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 -86.00 -169.36 83.36 1 1.00e+01 1.00e-02 8.49e+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 -86.00 -168.51 82.51 1 1.00e+01 1.00e-02 8.35e+01 ... (remaining 11643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1809 0.040 - 0.081: 821 0.081 - 0.121: 224 0.121 - 0.161: 34 0.161 - 0.202: 1 Chirality restraints: 2889 Sorted by residual: chirality pdb=" CB VAL L 95 " pdb=" CA VAL L 95 " pdb=" CG1 VAL L 95 " pdb=" CG2 VAL L 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU B 297 " pdb=" N GLU B 297 " pdb=" C GLU B 297 " pdb=" CB GLU B 297 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CB VAL G 95 " pdb=" CA VAL G 95 " pdb=" CG1 VAL G 95 " pdb=" CG2 VAL G 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 2886 not shown) Planarity restraints: 3477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 48 " 0.016 2.00e-02 2.50e+03 1.66e-02 5.48e+00 pdb=" CG TYR E 48 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E 48 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 48 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 48 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR E 48 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 48 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR E 48 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 568 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO B 569 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 569 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 569 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 509 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.28e+00 pdb=" C ARG A 509 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG A 509 " -0.013 2.00e-02 2.50e+03 pdb=" N HIS A 510 " -0.012 2.00e-02 2.50e+03 ... (remaining 3474 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1589 2.74 - 3.28: 17858 3.28 - 3.82: 32252 3.82 - 4.36: 39371 4.36 - 4.90: 69166 Nonbonded interactions: 160236 Sorted by model distance: nonbonded pdb=" OH TYR C 274 " pdb=" OD2 ASP C 400 " model vdw 2.205 3.040 nonbonded pdb=" O THR A 135 " pdb=" OH TYR A 444 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A 157 " pdb=" OE2 GLU A 266 " model vdw 2.213 3.040 nonbonded pdb=" NH1 ARG B 655 " pdb=" OE1 GLN C 118 " model vdw 2.235 3.120 nonbonded pdb=" O THR B 135 " pdb=" OH TYR B 444 " model vdw 2.251 3.040 ... (remaining 160231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.520 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.005 0.048 19635 Z= 0.290 Angle : 0.581 6.797 26685 Z= 0.340 Chirality : 0.047 0.202 2889 Planarity : 0.006 0.076 3477 Dihedral : 14.367 89.810 7107 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.05 % Allowed : 0.63 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.16), residues: 2397 helix: 0.44 (0.29), residues: 312 sheet: 0.14 (0.17), residues: 834 loop : 0.02 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG D 24 TYR 0.039 0.003 TYR E 48 PHE 0.019 0.003 PHE H 34 TRP 0.013 0.003 TRP B 533 HIS 0.015 0.003 HIS C 506 Details of bonding type rmsd covalent geometry : bond 0.00502 (19614) covalent geometry : angle 0.57736 (26643) SS BOND : bond 0.01785 ( 21) SS BOND : angle 1.69998 ( 42) hydrogen bonds : bond 0.12796 ( 759) hydrogen bonds : angle 6.47714 ( 2250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.6519 (mtm-85) cc_final: 0.5935 (mtp85) REVERT: A 187 GLU cc_start: 0.7811 (pp20) cc_final: 0.6770 (pp20) REVERT: A 430 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8278 (mm110) REVERT: B 170 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7084 (mmt180) REVERT: B 421 TYR cc_start: 0.7806 (m-80) cc_final: 0.7570 (m-80) REVERT: C 136 GLU cc_start: 0.8318 (tp30) cc_final: 0.8086 (tp30) REVERT: C 175 MET cc_start: 0.9309 (mmt) cc_final: 0.8593 (mmt) REVERT: C 210 MET cc_start: 0.9282 (ttt) cc_final: 0.8673 (ttt) REVERT: C 578 GLN cc_start: 0.7440 (mp10) cc_final: 0.7194 (mp10) REVERT: D 38 ASP cc_start: 0.8566 (m-30) cc_final: 0.8361 (m-30) REVERT: D 62 ASN cc_start: 0.9129 (m-40) cc_final: 0.8470 (m-40) REVERT: D 95 ASP cc_start: 0.8667 (m-30) cc_final: 0.7945 (m-30) REVERT: F 78 ASN cc_start: 0.7616 (t0) cc_final: 0.7292 (t0) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.1649 time to fit residues: 69.1176 Evaluate side-chains 243 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.0370 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.3980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN A 668 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 GLN G 68 ASN F 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106066 restraints weight = 23637.075| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.37 r_work: 0.3036 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19635 Z= 0.137 Angle : 0.496 5.551 26685 Z= 0.270 Chirality : 0.042 0.181 2889 Planarity : 0.004 0.042 3477 Dihedral : 4.079 18.589 2715 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.49 % Allowed : 6.19 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.17), residues: 2397 helix: 1.02 (0.29), residues: 324 sheet: 0.11 (0.17), residues: 837 loop : 0.28 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 170 TYR 0.028 0.001 TYR E 48 PHE 0.017 0.001 PHE C 279 TRP 0.011 0.001 TRP B 533 HIS 0.011 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00315 (19614) covalent geometry : angle 0.49605 (26643) SS BOND : bond 0.00181 ( 21) SS BOND : angle 0.69931 ( 42) hydrogen bonds : bond 0.04051 ( 759) hydrogen bonds : angle 5.18437 ( 2250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 250 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7947 (t70) cc_final: 0.7597 (t70) REVERT: A 187 GLU cc_start: 0.8068 (pp20) cc_final: 0.7507 (pp20) REVERT: A 191 ASP cc_start: 0.8489 (m-30) cc_final: 0.8256 (m-30) REVERT: C 136 GLU cc_start: 0.8289 (tp30) cc_final: 0.8010 (tp30) REVERT: C 175 MET cc_start: 0.9268 (mmt) cc_final: 0.8776 (mmt) REVERT: C 210 MET cc_start: 0.9314 (ttt) cc_final: 0.8771 (ttt) REVERT: C 551 ARG cc_start: 0.7859 (ptt-90) cc_final: 0.7656 (ptt90) REVERT: H 51 GLU cc_start: 0.8281 (tt0) cc_final: 0.8043 (tt0) REVERT: D 62 ASN cc_start: 0.9047 (m-40) cc_final: 0.8524 (m110) REVERT: D 89 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7633 (mtm-85) REVERT: D 95 ASP cc_start: 0.8435 (m-30) cc_final: 0.7769 (m-30) REVERT: F 78 ASN cc_start: 0.7647 (t0) cc_final: 0.7274 (t0) outliers start: 10 outliers final: 9 residues processed: 259 average time/residue: 0.1621 time to fit residues: 61.3827 Evaluate side-chains 243 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 234 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 66 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 118 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 303 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN D 62 ASN F 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104120 restraints weight = 23873.477| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.41 r_work: 0.3017 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19635 Z= 0.152 Angle : 0.489 5.061 26685 Z= 0.266 Chirality : 0.042 0.187 2889 Planarity : 0.004 0.044 3477 Dihedral : 4.059 18.215 2715 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.02 % Allowed : 8.04 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.17), residues: 2397 helix: 1.14 (0.29), residues: 324 sheet: 0.20 (0.17), residues: 846 loop : 0.16 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 556 TYR 0.028 0.001 TYR L 48 PHE 0.018 0.001 PHE C 279 TRP 0.009 0.001 TRP H 52 HIS 0.011 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00352 (19614) covalent geometry : angle 0.48908 (26643) SS BOND : bond 0.00152 ( 21) SS BOND : angle 0.63914 ( 42) hydrogen bonds : bond 0.03823 ( 759) hydrogen bonds : angle 4.96018 ( 2250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7955 (t70) cc_final: 0.7560 (t70) REVERT: A 187 GLU cc_start: 0.8126 (pp20) cc_final: 0.7562 (pp20) REVERT: C 175 MET cc_start: 0.9291 (mmt) cc_final: 0.8813 (mmt) REVERT: C 591 TYR cc_start: 0.6983 (m-10) cc_final: 0.6656 (m-10) REVERT: C 646 GLU cc_start: 0.7837 (tp30) cc_final: 0.7475 (mp0) REVERT: H 51 GLU cc_start: 0.8360 (tt0) cc_final: 0.8111 (tt0) REVERT: H 75 MET cc_start: 0.8746 (mtt) cc_final: 0.8275 (mtt) REVERT: D 62 ASN cc_start: 0.9110 (m110) cc_final: 0.8572 (m110) REVERT: D 89 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7683 (mtm-85) REVERT: D 95 ASP cc_start: 0.8428 (m-30) cc_final: 0.7645 (m-30) REVERT: F 78 ASN cc_start: 0.7864 (t0) cc_final: 0.7620 (t0) outliers start: 21 outliers final: 17 residues processed: 268 average time/residue: 0.1618 time to fit residues: 63.2244 Evaluate side-chains 253 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 37 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 652 GLN A 668 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN C 240 HIS C 528 HIS H 40 ASN G 26 ASN G 68 ASN F 8 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.100291 restraints weight = 23953.024| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.47 r_work: 0.2936 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 19635 Z= 0.270 Angle : 0.568 6.571 26685 Z= 0.306 Chirality : 0.046 0.255 2889 Planarity : 0.005 0.050 3477 Dihedral : 4.340 18.676 2715 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.71 % Allowed : 9.21 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.17), residues: 2397 helix: 1.02 (0.29), residues: 324 sheet: -0.01 (0.17), residues: 858 loop : 0.05 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 296 TYR 0.045 0.002 TYR L 48 PHE 0.024 0.002 PHE C 279 TRP 0.012 0.002 TRP H 52 HIS 0.011 0.002 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.00642 (19614) covalent geometry : angle 0.56741 (26643) SS BOND : bond 0.00250 ( 21) SS BOND : angle 0.96574 ( 42) hydrogen bonds : bond 0.04227 ( 759) hydrogen bonds : angle 5.04295 ( 2250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.591 Fit side-chains REVERT: A 187 GLU cc_start: 0.8078 (pp20) cc_final: 0.7478 (pp20) REVERT: C 175 MET cc_start: 0.9323 (mmt) cc_final: 0.8795 (mmt) REVERT: C 416 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8485 (ptp) REVERT: C 632 ARG cc_start: 0.7143 (ptt-90) cc_final: 0.6489 (mtm-85) REVERT: C 646 GLU cc_start: 0.7904 (tp30) cc_final: 0.7458 (mp0) REVERT: H 17 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7534 (mmtp) REVERT: H 68 GLN cc_start: 0.8208 (pm20) cc_final: 0.7831 (pm20) REVERT: H 75 MET cc_start: 0.8867 (mtt) cc_final: 0.8529 (mtt) REVERT: D 62 ASN cc_start: 0.9140 (m110) cc_final: 0.8593 (m110) REVERT: D 95 ASP cc_start: 0.8533 (m-30) cc_final: 0.7727 (m-30) REVERT: F 22 SER cc_start: 0.8457 (p) cc_final: 0.8223 (p) REVERT: F 78 ASN cc_start: 0.7982 (t0) cc_final: 0.7563 (t0) REVERT: F 87 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8092 (tt0) outliers start: 35 outliers final: 27 residues processed: 270 average time/residue: 0.1554 time to fit residues: 61.8829 Evaluate side-chains 261 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 673 GLU 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 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 168 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.0270 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 HIS G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.102556 restraints weight = 23708.310| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.33 r_work: 0.2995 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19635 Z= 0.141 Angle : 0.482 5.031 26685 Z= 0.262 Chirality : 0.042 0.193 2889 Planarity : 0.004 0.042 3477 Dihedral : 4.132 18.416 2715 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.46 % Allowed : 10.14 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2397 helix: 1.13 (0.29), residues: 324 sheet: 0.06 (0.17), residues: 843 loop : 0.19 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 556 TYR 0.027 0.001 TYR L 48 PHE 0.017 0.001 PHE C 279 TRP 0.011 0.001 TRP B 533 HIS 0.009 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00330 (19614) covalent geometry : angle 0.48042 (26643) SS BOND : bond 0.00208 ( 21) SS BOND : angle 0.99611 ( 42) hydrogen bonds : bond 0.03682 ( 759) hydrogen bonds : angle 4.86244 ( 2250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.496 Fit side-chains REVERT: A 169 HIS cc_start: 0.7981 (t70) cc_final: 0.7743 (t70) REVERT: A 187 GLU cc_start: 0.8031 (pp20) cc_final: 0.7584 (pp20) REVERT: B 535 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7703 (mm-30) REVERT: C 175 MET cc_start: 0.9286 (mmt) cc_final: 0.8875 (mmt) REVERT: C 416 MET cc_start: 0.8980 (ptp) cc_final: 0.8616 (ptp) REVERT: C 595 LEU cc_start: 0.8299 (mp) cc_final: 0.8060 (mp) REVERT: C 632 ARG cc_start: 0.7079 (ptt-90) cc_final: 0.6444 (mtm-85) REVERT: C 646 GLU cc_start: 0.7738 (tp30) cc_final: 0.7484 (mp0) REVERT: H 17 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7545 (mmtp) REVERT: H 75 MET cc_start: 0.8809 (mtt) cc_final: 0.8398 (mtt) REVERT: L 5 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8571 (t) REVERT: D 62 ASN cc_start: 0.9097 (m110) cc_final: 0.8548 (m110) REVERT: D 95 ASP cc_start: 0.8457 (m-30) cc_final: 0.7677 (m-30) REVERT: F 22 SER cc_start: 0.8432 (p) cc_final: 0.8183 (p) REVERT: F 78 ASN cc_start: 0.7976 (t0) cc_final: 0.7549 (t0) outliers start: 30 outliers final: 22 residues processed: 262 average time/residue: 0.1513 time to fit residues: 58.1471 Evaluate side-chains 257 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 157 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 chunk 196 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN F 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.102609 restraints weight = 23652.613| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.42 r_work: 0.2960 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19635 Z= 0.142 Angle : 0.479 5.833 26685 Z= 0.260 Chirality : 0.042 0.186 2889 Planarity : 0.004 0.041 3477 Dihedral : 4.076 18.241 2715 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.95 % Allowed : 10.48 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2397 helix: 1.21 (0.29), residues: 324 sheet: 0.10 (0.17), residues: 843 loop : 0.14 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 556 TYR 0.029 0.001 TYR L 48 PHE 0.017 0.001 PHE C 279 TRP 0.012 0.001 TRP H 52 HIS 0.008 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00333 (19614) covalent geometry : angle 0.47763 (26643) SS BOND : bond 0.00164 ( 21) SS BOND : angle 0.88343 ( 42) hydrogen bonds : bond 0.03623 ( 759) hydrogen bonds : angle 4.79598 ( 2250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.763 Fit side-chains REVERT: A 169 HIS cc_start: 0.8026 (t70) cc_final: 0.7768 (t70) REVERT: B 223 ASP cc_start: 0.8388 (m-30) cc_final: 0.7948 (m-30) REVERT: B 529 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7411 (mt-10) REVERT: C 416 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8594 (ptp) REVERT: C 632 ARG cc_start: 0.7113 (ptt-90) cc_final: 0.6479 (mtm-85) REVERT: C 646 GLU cc_start: 0.7689 (tp30) cc_final: 0.7397 (mp0) REVERT: H 17 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7548 (mmtp) REVERT: L 5 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8574 (t) REVERT: D 62 ASN cc_start: 0.9115 (m110) cc_final: 0.8480 (m110) REVERT: D 89 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7808 (mtm-85) REVERT: D 95 ASP cc_start: 0.8399 (m-30) cc_final: 0.7620 (m-30) REVERT: F 22 SER cc_start: 0.8431 (p) cc_final: 0.8144 (p) REVERT: F 78 ASN cc_start: 0.7964 (t0) cc_final: 0.7533 (t0) outliers start: 40 outliers final: 34 residues processed: 263 average time/residue: 0.1623 time to fit residues: 62.6193 Evaluate side-chains 266 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 673 GLU 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 235 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 168 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 221 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN F 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.101139 restraints weight = 23868.412| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.36 r_work: 0.2940 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19635 Z= 0.201 Angle : 0.513 6.421 26685 Z= 0.278 Chirality : 0.043 0.218 2889 Planarity : 0.004 0.042 3477 Dihedral : 4.174 18.348 2715 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.39 % Allowed : 10.72 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.17), residues: 2397 helix: 1.16 (0.29), residues: 324 sheet: 0.03 (0.17), residues: 846 loop : 0.09 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 556 TYR 0.039 0.002 TYR G 48 PHE 0.021 0.002 PHE C 279 TRP 0.013 0.001 TRP H 52 HIS 0.008 0.001 HIS F 32 Details of bonding type rmsd covalent geometry : bond 0.00477 (19614) covalent geometry : angle 0.51151 (26643) SS BOND : bond 0.00279 ( 21) SS BOND : angle 1.08618 ( 42) hydrogen bonds : bond 0.03847 ( 759) hydrogen bonds : angle 4.87931 ( 2250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 0.718 Fit side-chains REVERT: A 104 GLN cc_start: 0.7235 (tt0) cc_final: 0.6960 (tt0) REVERT: A 169 HIS cc_start: 0.8056 (t70) cc_final: 0.7806 (t70) REVERT: B 223 ASP cc_start: 0.8363 (m-30) cc_final: 0.7927 (m-30) REVERT: B 252 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: C 416 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8600 (ptp) REVERT: C 595 LEU cc_start: 0.8379 (mp) cc_final: 0.8139 (mp) REVERT: C 632 ARG cc_start: 0.7104 (ptt-90) cc_final: 0.6463 (mtm-85) REVERT: C 646 GLU cc_start: 0.7750 (tp30) cc_final: 0.7502 (mp0) REVERT: H 17 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7559 (mmtp) REVERT: D 62 ASN cc_start: 0.9126 (m110) cc_final: 0.8563 (m110) REVERT: D 89 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7767 (mtm-85) REVERT: D 95 ASP cc_start: 0.8495 (m-30) cc_final: 0.7740 (m-30) REVERT: F 22 SER cc_start: 0.8462 (p) cc_final: 0.8173 (p) REVERT: F 78 ASN cc_start: 0.7995 (t0) cc_final: 0.7565 (t0) outliers start: 49 outliers final: 39 residues processed: 273 average time/residue: 0.1580 time to fit residues: 63.7965 Evaluate side-chains 271 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 673 GLU 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 235 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN D 32 HIS F 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.103246 restraints weight = 23708.834| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.45 r_work: 0.2990 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19635 Z= 0.146 Angle : 0.487 5.995 26685 Z= 0.264 Chirality : 0.042 0.187 2889 Planarity : 0.004 0.041 3477 Dihedral : 4.116 18.260 2715 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.24 % Allowed : 11.31 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.17), residues: 2397 helix: 1.21 (0.28), residues: 324 sheet: 0.11 (0.17), residues: 843 loop : 0.12 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 556 TYR 0.030 0.001 TYR G 48 PHE 0.017 0.001 PHE C 644 TRP 0.013 0.001 TRP H 52 HIS 0.008 0.001 HIS B 528 Details of bonding type rmsd covalent geometry : bond 0.00342 (19614) covalent geometry : angle 0.48282 (26643) SS BOND : bond 0.00255 ( 21) SS BOND : angle 1.68333 ( 42) hydrogen bonds : bond 0.03614 ( 759) hydrogen bonds : angle 4.79812 ( 2250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 0.696 Fit side-chains REVERT: A 104 GLN cc_start: 0.7269 (tt0) cc_final: 0.6988 (tt0) REVERT: B 252 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: C 416 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8621 (ptp) REVERT: C 529 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8120 (mm-30) REVERT: C 646 GLU cc_start: 0.7613 (tp30) cc_final: 0.7367 (mp0) REVERT: H 17 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7522 (mmtp) REVERT: H 53 MET cc_start: 0.9153 (mtp) cc_final: 0.8901 (mtm) REVERT: D 62 ASN cc_start: 0.9110 (m110) cc_final: 0.8496 (m110) REVERT: D 89 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7860 (mtm-85) REVERT: D 95 ASP cc_start: 0.8458 (m-30) cc_final: 0.7642 (m-30) REVERT: F 22 SER cc_start: 0.8439 (p) cc_final: 0.8141 (p) outliers start: 46 outliers final: 39 residues processed: 270 average time/residue: 0.1592 time to fit residues: 63.0274 Evaluate side-chains 272 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 673 GLU 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 235 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 528 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 4 optimal weight: 0.3980 chunk 230 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 215 optimal weight: 0.3980 chunk 208 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN F 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.102483 restraints weight = 23703.531| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.36 r_work: 0.2986 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19635 Z= 0.173 Angle : 0.505 9.558 26685 Z= 0.272 Chirality : 0.043 0.209 2889 Planarity : 0.004 0.042 3477 Dihedral : 4.145 18.435 2715 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.14 % Allowed : 11.74 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.17), residues: 2397 helix: 1.21 (0.28), residues: 324 sheet: 0.09 (0.17), residues: 843 loop : 0.10 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 556 TYR 0.035 0.001 TYR G 48 PHE 0.019 0.002 PHE C 279 TRP 0.011 0.001 TRP B 533 HIS 0.009 0.001 HIS B 528 Details of bonding type rmsd covalent geometry : bond 0.00409 (19614) covalent geometry : angle 0.50189 (26643) SS BOND : bond 0.00241 ( 21) SS BOND : angle 1.38588 ( 42) hydrogen bonds : bond 0.03719 ( 759) hydrogen bonds : angle 4.81436 ( 2250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 0.744 Fit side-chains REVERT: A 104 GLN cc_start: 0.7288 (tt0) cc_final: 0.7010 (tt0) REVERT: B 252 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: C 416 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8598 (ptp) REVERT: C 595 LEU cc_start: 0.8389 (mp) cc_final: 0.8131 (mp) REVERT: C 632 ARG cc_start: 0.7071 (ptt-90) cc_final: 0.6714 (mtm110) REVERT: H 17 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7527 (mmtp) REVERT: H 68 GLN cc_start: 0.8207 (pm20) cc_final: 0.7872 (pm20) REVERT: D 62 ASN cc_start: 0.9108 (m110) cc_final: 0.8515 (m110) REVERT: D 89 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: D 95 ASP cc_start: 0.8473 (m-30) cc_final: 0.7773 (m-30) REVERT: F 22 SER cc_start: 0.8445 (p) cc_final: 0.8146 (p) outliers start: 44 outliers final: 39 residues processed: 266 average time/residue: 0.1634 time to fit residues: 63.5681 Evaluate side-chains 266 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 673 GLU 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 235 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 528 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 168 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 169 HIS ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN D 32 HIS F 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.128151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101426 restraints weight = 23831.821| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.40 r_work: 0.2959 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 19635 Z= 0.238 Angle : 0.547 9.350 26685 Z= 0.295 Chirality : 0.045 0.238 2889 Planarity : 0.004 0.045 3477 Dihedral : 4.299 19.024 2715 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.14 % Allowed : 11.99 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2397 helix: 1.16 (0.29), residues: 324 sheet: -0.01 (0.17), residues: 846 loop : 0.05 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 556 TYR 0.046 0.002 TYR G 48 PHE 0.022 0.002 PHE C 279 TRP 0.018 0.002 TRP H 52 HIS 0.011 0.001 HIS B 528 Details of bonding type rmsd covalent geometry : bond 0.00568 (19614) covalent geometry : angle 0.54498 (26643) SS BOND : bond 0.00277 ( 21) SS BOND : angle 1.42342 ( 42) hydrogen bonds : bond 0.04000 ( 759) hydrogen bonds : angle 4.92307 ( 2250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4794 Ramachandran restraints generated. 2397 Oldfield, 0 Emsley, 2397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.732 Fit side-chains REVERT: A 104 GLN cc_start: 0.7333 (tt0) cc_final: 0.7045 (tt0) REVERT: B 169 HIS cc_start: 0.8152 (t-90) cc_final: 0.7880 (t-90) REVERT: B 252 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8255 (tm-30) REVERT: B 618 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7819 (mtp-110) REVERT: C 416 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8565 (ptp) REVERT: C 632 ARG cc_start: 0.7080 (ptt-90) cc_final: 0.6697 (mtm110) REVERT: H 17 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7611 (mmtp) REVERT: H 68 GLN cc_start: 0.8220 (pm20) cc_final: 0.7902 (pm20) REVERT: D 62 ASN cc_start: 0.9145 (m110) cc_final: 0.8605 (m110) REVERT: D 89 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7871 (mtm-85) REVERT: D 95 ASP cc_start: 0.8515 (m-30) cc_final: 0.7769 (m-30) REVERT: F 22 SER cc_start: 0.8464 (p) cc_final: 0.8182 (p) outliers start: 44 outliers final: 40 residues processed: 266 average time/residue: 0.1515 time to fit residues: 59.7002 Evaluate side-chains 267 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 327 ARG Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 673 GLU 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 235 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 528 HIS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 124 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 214 optimal weight: 0.0870 chunk 106 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN F 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103217 restraints weight = 23684.659| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.37 r_work: 0.2953 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19635 Z= 0.134 Angle : 0.489 9.183 26685 Z= 0.265 Chirality : 0.042 0.187 2889 Planarity : 0.004 0.041 3477 Dihedral : 4.146 18.809 2715 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.05 % Allowed : 12.23 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.17), residues: 2397 helix: 1.24 (0.28), residues: 324 sheet: 0.06 (0.17), residues: 843 loop : 0.11 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 556 TYR 0.029 0.001 TYR G 48 PHE 0.017 0.001 PHE C 279 TRP 0.016 0.001 TRP H 52 HIS 0.008 0.001 HIS B 528 Details of bonding type rmsd covalent geometry : bond 0.00312 (19614) covalent geometry : angle 0.48778 (26643) SS BOND : bond 0.00199 ( 21) SS BOND : angle 1.08146 ( 42) hydrogen bonds : bond 0.03580 ( 759) hydrogen bonds : angle 4.79602 ( 2250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5677.96 seconds wall clock time: 97 minutes 27.63 seconds (5847.63 seconds total)