Starting phenix.real_space_refine on Wed Jan 22 20:46:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rh2_19166/01_2025/8rh2_19166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rh2_19166/01_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_19166/01_2025/8rh2_19166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rh2_19166/01_2025/8rh2_19166.map" model { file = "/net/cci-nas-00/data/ceres_data/8rh2_19166/01_2025/8rh2_19166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rh2_19166/01_2025/8rh2_19166.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 10.91, per 1000 atoms: 0.57 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: 4.51 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 3.18 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: 7.80 Time building geometry restraints manager: 5.25 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: 3.120 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: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 44.060 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.810 ------------------------------------------------------------------------------- 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 19614 Z= 0.330 Angle : 0.577 6.797 26643 Z= 0.339 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (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 TRP 0.013 0.003 TRP B 533 HIS 0.015 0.003 HIS C 506 PHE 0.019 0.003 PHE H 34 TYR 0.039 0.003 TYR E 48 ARG 0.021 0.002 ARG D 24 *********************** 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 : 2.090 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: 0.3747 time to fit residues: 155.9954 Evaluate side-chains 244 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 2.9990 chunk 179 optimal weight: 0.0470 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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** 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 = 0.3532 r_free = 0.3532 target = 0.132425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.105576 restraints weight = 23654.964| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.43 r_work: 0.2987 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19614 Z= 0.227 Angle : 0.504 5.541 26643 Z= 0.274 Chirality : 0.043 0.196 2889 Planarity : 0.004 0.041 3477 Dihedral : 4.114 18.645 2715 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.68 % Allowed : 6.19 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2397 helix: 1.01 (0.29), residues: 324 sheet: 0.10 (0.17), residues: 837 loop : 0.26 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 533 HIS 0.012 0.001 HIS A 631 PHE 0.018 0.002 PHE C 279 TYR 0.030 0.001 TYR E 48 ARG 0.005 0.000 ARG B 618 *********************** 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 266 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7966 (t70) cc_final: 0.7600 (t70) REVERT: A 187 GLU cc_start: 0.8094 (pp20) cc_final: 0.7508 (pp20) REVERT: A 191 ASP cc_start: 0.8416 (m-30) cc_final: 0.8180 (m-30) REVERT: C 136 GLU cc_start: 0.8306 (tp30) cc_final: 0.8026 (tp30) REVERT: C 175 MET cc_start: 0.9264 (mmt) cc_final: 0.8783 (mmt) REVERT: C 210 MET cc_start: 0.9326 (ttt) cc_final: 0.8810 (ttt) REVERT: C 591 TYR cc_start: 0.7032 (m-10) cc_final: 0.6640 (m-10) REVERT: C 647 TYR cc_start: 0.8077 (m-80) cc_final: 0.7855 (m-80) REVERT: H 51 GLU cc_start: 0.8307 (tt0) cc_final: 0.8080 (tt0) REVERT: D 62 ASN cc_start: 0.9065 (m-40) cc_final: 0.8527 (m110) REVERT: D 89 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7660 (mtm-85) REVERT: D 95 ASP cc_start: 0.8432 (m-30) cc_final: 0.7765 (m-30) REVERT: F 23 VAL cc_start: 0.8921 (t) cc_final: 0.8719 (p) REVERT: F 78 ASN cc_start: 0.7658 (t0) cc_final: 0.7276 (t0) outliers start: 14 outliers final: 13 residues processed: 265 average time/residue: 0.3689 time to fit residues: 143.1813 Evaluate side-chains 248 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 235 time to evaluate : 2.043 ------------------------------------------------------------------------------- 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 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 30 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 F residue 80 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 133 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 118 optimal weight: 0.0050 chunk 218 optimal weight: 0.0770 chunk 53 optimal weight: 0.2980 chunk 160 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.3752 ------------------------------------------------------------------------------- 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** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 HIS H 40 ASN G 68 ASN D 62 ASN F 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106502 restraints weight = 23507.554| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.33 r_work: 0.3041 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19614 Z= 0.157 Angle : 0.461 5.181 26643 Z= 0.251 Chirality : 0.041 0.170 2889 Planarity : 0.004 0.045 3477 Dihedral : 3.958 18.852 2715 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.73 % Allowed : 8.53 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2397 helix: 1.13 (0.29), residues: 327 sheet: 0.20 (0.17), residues: 849 loop : 0.23 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 52 HIS 0.011 0.001 HIS A 631 PHE 0.014 0.001 PHE C 279 TYR 0.022 0.001 TYR B 647 ARG 0.008 0.000 ARG B 556 *********************** 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 271 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 256 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 HIS cc_start: 0.7891 (t70) cc_final: 0.7508 (t70) REVERT: A 187 GLU cc_start: 0.8071 (pp20) cc_final: 0.7436 (pp20) REVERT: A 191 ASP cc_start: 0.8500 (m-30) cc_final: 0.8250 (m-30) REVERT: A 421 TYR cc_start: 0.7753 (m-10) cc_final: 0.6792 (m-10) REVERT: B 170 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7372 (mmt180) REVERT: B 578 GLN cc_start: 0.7831 (tp40) cc_final: 0.7562 (tp40) REVERT: C 175 MET cc_start: 0.9287 (mmt) cc_final: 0.8807 (mmt) REVERT: C 591 TYR cc_start: 0.6926 (m-10) cc_final: 0.6685 (m-10) REVERT: C 646 GLU cc_start: 0.7611 (tp30) cc_final: 0.7365 (mp0) REVERT: H 43 ARG cc_start: 0.8963 (ptt180) cc_final: 0.8761 (ptt180) REVERT: H 51 GLU cc_start: 0.8304 (tt0) cc_final: 0.8074 (tt0) REVERT: H 75 MET cc_start: 0.8694 (mtt) cc_final: 0.8170 (mtt) REVERT: D 62 ASN cc_start: 0.9089 (m110) cc_final: 0.8547 (m110) REVERT: D 89 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7652 (mtm-85) REVERT: D 95 ASP cc_start: 0.8370 (m-30) cc_final: 0.7767 (m-30) REVERT: F 78 ASN cc_start: 0.7821 (t0) cc_final: 0.7281 (t0) outliers start: 15 outliers final: 11 residues processed: 269 average time/residue: 0.3707 time to fit residues: 144.4677 Evaluate side-chains 248 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 237 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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 C residue 339 THR Chi-restraints excluded: chain H residue 16 VAL 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 Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 156 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 187 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 652 GLN A 668 ASN ** B 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN C 240 HIS ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN G 68 ASN F 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102925 restraints weight = 23722.695| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.38 r_work: 0.2988 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19614 Z= 0.326 Angle : 0.521 5.729 26643 Z= 0.282 Chirality : 0.044 0.220 2889 Planarity : 0.004 0.042 3477 Dihedral : 4.137 17.666 2715 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.56 % Allowed : 9.02 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2397 helix: 1.10 (0.29), residues: 324 sheet: 0.09 (0.17), residues: 858 loop : 0.12 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 52 HIS 0.009 0.001 HIS A 631 PHE 0.022 0.002 PHE C 279 TYR 0.037 0.002 TYR L 48 ARG 0.009 0.001 ARG B 556 *********************** 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 267 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 2.058 Fit side-chains REVERT: A 187 GLU cc_start: 0.8134 (pp20) cc_final: 0.7522 (pp20) REVERT: B 408 ASP cc_start: 0.7634 (m-30) cc_final: 0.7383 (m-30) REVERT: C 175 MET cc_start: 0.9297 (mmt) cc_final: 0.8805 (mmt) REVERT: C 416 MET cc_start: 0.8944 (ptp) cc_final: 0.8488 (ptp) REVERT: C 528 HIS cc_start: 0.8782 (OUTLIER) cc_final: 0.8578 (t-90) REVERT: C 632 ARG cc_start: 0.7115 (ptt-90) cc_final: 0.6496 (mtm-85) REVERT: H 75 MET cc_start: 0.8847 (mtt) cc_final: 0.8451 (mtt) REVERT: L 48 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8758 (p90) REVERT: D 62 ASN cc_start: 0.9117 (m110) cc_final: 0.8568 (m110) REVERT: D 89 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7747 (mtm-85) REVERT: D 95 ASP cc_start: 0.8530 (m-30) cc_final: 0.7780 (m-30) REVERT: F 78 ASN cc_start: 0.7940 (t0) cc_final: 0.7577 (t0) outliers start: 32 outliers final: 25 residues processed: 261 average time/residue: 0.3558 time to fit residues: 137.4213 Evaluate side-chains 257 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 614 ASN 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 C residue 133 ASN Chi-restraints excluded: chain C residue 162 VAL 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 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 79 ILE 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 206 optimal weight: 0.0370 chunk 158 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- 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** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.101560 restraints weight = 23870.310| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.39 r_work: 0.2971 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 19614 Z= 0.374 Angle : 0.541 6.058 26643 Z= 0.293 Chirality : 0.045 0.252 2889 Planarity : 0.004 0.043 3477 Dihedral : 4.297 18.752 2715 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.10 % Allowed : 9.41 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2397 helix: 1.04 (0.29), residues: 324 sheet: 0.07 (0.17), residues: 834 loop : 0.03 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 52 HIS 0.009 0.001 HIS A 631 PHE 0.023 0.002 PHE C 279 TYR 0.041 0.002 TYR L 48 ARG 0.007 0.001 ARG B 556 *********************** 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 279 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 2.136 Fit side-chains REVERT: A 187 GLU cc_start: 0.8079 (pp20) cc_final: 0.7517 (pp20) REVERT: C 175 MET cc_start: 0.9320 (mmt) cc_final: 0.8852 (mmt) REVERT: C 416 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8515 (ptp) REVERT: C 595 LEU cc_start: 0.8304 (mp) cc_final: 0.8050 (mp) REVERT: C 632 ARG cc_start: 0.7156 (ptt-90) cc_final: 0.6523 (mtm-85) REVERT: C 646 GLU cc_start: 0.7940 (tp30) cc_final: 0.7418 (mp0) REVERT: H 17 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7550 (mmtp) REVERT: H 68 GLN cc_start: 0.8203 (pm20) cc_final: 0.7848 (pm20) REVERT: D 62 ASN cc_start: 0.9113 (m110) cc_final: 0.8578 (m110) REVERT: D 95 ASP cc_start: 0.8507 (m-30) cc_final: 0.7706 (m-30) REVERT: F 22 SER cc_start: 0.8496 (p) cc_final: 0.8273 (p) REVERT: F 87 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8081 (tt0) outliers start: 43 outliers final: 34 residues processed: 268 average time/residue: 0.3629 time to fit residues: 143.5477 Evaluate side-chains 268 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 614 ASN 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 227 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 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 = 0.3482 r_free = 0.3482 target = 0.128441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101274 restraints weight = 23863.113| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.39 r_work: 0.2974 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19614 Z= 0.267 Angle : 0.501 5.418 26643 Z= 0.272 Chirality : 0.043 0.216 2889 Planarity : 0.004 0.043 3477 Dihedral : 4.209 18.518 2715 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.14 % Allowed : 10.23 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2397 helix: 1.12 (0.29), residues: 324 sheet: -0.09 (0.17), residues: 864 loop : 0.18 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 533 HIS 0.008 0.001 HIS A 631 PHE 0.019 0.002 PHE C 279 TYR 0.033 0.001 TYR L 48 ARG 0.008 0.000 ARG B 556 *********************** 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 280 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 2.229 Fit side-chains REVERT: A 169 HIS cc_start: 0.8030 (t70) cc_final: 0.7742 (t70) REVERT: A 187 GLU cc_start: 0.8112 (pp20) cc_final: 0.7574 (pp20) REVERT: A 420 LYS cc_start: 0.8741 (tttp) cc_final: 0.8508 (tttm) REVERT: A 629 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.8079 (p) REVERT: C 175 MET cc_start: 0.9330 (mmt) cc_final: 0.8903 (mmt) REVERT: C 210 MET cc_start: 0.9367 (ttt) cc_final: 0.8962 (ttt) REVERT: C 416 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8528 (ptp) REVERT: C 632 ARG cc_start: 0.7104 (ptt-90) cc_final: 0.6453 (mtm-85) REVERT: C 646 GLU cc_start: 0.7809 (tp30) cc_final: 0.7580 (mp0) REVERT: H 17 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7525 (mmtp) REVERT: H 68 GLN cc_start: 0.8215 (pm20) cc_final: 0.7829 (pm20) REVERT: D 62 ASN cc_start: 0.9114 (m110) cc_final: 0.8542 (m110) REVERT: D 89 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7693 (mtm-85) REVERT: D 95 ASP cc_start: 0.8446 (m-30) cc_final: 0.7703 (m-30) REVERT: F 22 SER cc_start: 0.8435 (p) cc_final: 0.8195 (p) REVERT: F 87 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7933 (tt0) outliers start: 44 outliers final: 33 residues processed: 269 average time/residue: 0.3623 time to fit residues: 144.6678 Evaluate side-chains 269 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 2.356 ------------------------------------------------------------------------------- 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 645 GLU 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 B residue 636 ILE 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 212 THR Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 42 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 196 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3494 r_free = 0.3494 target = 0.129467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.102796 restraints weight = 23706.492| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.36 r_work: 0.2913 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19614 Z= 0.253 Angle : 0.495 5.455 26643 Z= 0.269 Chirality : 0.043 0.207 2889 Planarity : 0.004 0.042 3477 Dihedral : 4.169 18.407 2715 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.39 % Allowed : 10.96 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2397 helix: 1.16 (0.29), residues: 324 sheet: 0.04 (0.17), residues: 849 loop : 0.14 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 52 HIS 0.007 0.001 HIS B 528 PHE 0.018 0.002 PHE C 279 TYR 0.032 0.001 TYR G 48 ARG 0.008 0.000 ARG B 556 *********************** 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 289 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 2.103 Fit side-chains REVERT: A 104 GLN cc_start: 0.7229 (tt0) cc_final: 0.6960 (tt0) REVERT: A 169 HIS cc_start: 0.8025 (t70) cc_final: 0.7765 (t70) REVERT: A 187 GLU cc_start: 0.8134 (pp20) cc_final: 0.7621 (pp20) REVERT: A 629 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8197 (p) REVERT: B 252 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: C 175 MET cc_start: 0.9308 (mmt) cc_final: 0.8884 (mmt) REVERT: C 210 MET cc_start: 0.9382 (ttt) cc_final: 0.8963 (ttt) REVERT: C 416 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8541 (ptp) REVERT: C 595 LEU cc_start: 0.8353 (mp) cc_final: 0.8120 (mp) REVERT: C 632 ARG cc_start: 0.7120 (ptt-90) cc_final: 0.6472 (mtm-85) REVERT: C 646 GLU cc_start: 0.7636 (tp30) cc_final: 0.7342 (mp0) REVERT: H 17 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7529 (mmtp) REVERT: H 68 GLN cc_start: 0.8221 (pm20) cc_final: 0.7822 (pm20) REVERT: D 62 ASN cc_start: 0.9105 (m110) cc_final: 0.8503 (m110) REVERT: D 95 ASP cc_start: 0.8446 (m-30) cc_final: 0.7687 (m-30) REVERT: F 22 SER cc_start: 0.8423 (p) cc_final: 0.8171 (p) REVERT: F 87 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7990 (tt0) outliers start: 49 outliers final: 39 residues processed: 278 average time/residue: 0.3729 time to fit residues: 152.1388 Evaluate side-chains 278 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 645 GLU 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 62 ASN Chi-restraints excluded: chain F residue 80 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 189 optimal weight: 1.9990 chunk 2 optimal weight: 0.0060 chunk 138 optimal weight: 0.1980 chunk 144 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 220 optimal weight: 0.2980 chunk 147 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.131600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.104996 restraints weight = 23737.400| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.36 r_work: 0.3015 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19614 Z= 0.159 Angle : 0.461 5.633 26643 Z= 0.251 Chirality : 0.041 0.174 2889 Planarity : 0.004 0.041 3477 Dihedral : 4.019 18.284 2715 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.56 % Allowed : 11.70 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2397 helix: 1.20 (0.29), residues: 327 sheet: 0.19 (0.17), residues: 825 loop : 0.13 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 533 HIS 0.008 0.001 HIS A 631 PHE 0.014 0.001 PHE F 34 TYR 0.023 0.001 TYR B 421 ARG 0.009 0.000 ARG B 556 *********************** 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 274 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 2.341 Fit side-chains REVERT: A 104 GLN cc_start: 0.7257 (tt0) cc_final: 0.6982 (tt0) REVERT: A 169 HIS cc_start: 0.7959 (t70) cc_final: 0.7742 (t70) REVERT: B 269 ASP cc_start: 0.8064 (m-30) cc_final: 0.7770 (t70) REVERT: C 210 MET cc_start: 0.9347 (ttt) cc_final: 0.8907 (ttt) REVERT: C 416 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8608 (ptp) REVERT: C 632 ARG cc_start: 0.7122 (ptt-90) cc_final: 0.6481 (mtm-85) REVERT: H 17 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7533 (mmtp) REVERT: D 48 GLN cc_start: 0.8400 (mp10) cc_final: 0.8199 (mp10) REVERT: D 62 ASN cc_start: 0.9086 (m110) cc_final: 0.8549 (m110) REVERT: D 89 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7899 (mtm-85) REVERT: D 95 ASP cc_start: 0.8383 (m-30) cc_final: 0.7709 (m-30) REVERT: F 22 SER cc_start: 0.8397 (p) cc_final: 0.8154 (p) outliers start: 32 outliers final: 26 residues processed: 269 average time/residue: 0.3826 time to fit residues: 149.9924 Evaluate side-chains 264 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 2.221 ------------------------------------------------------------------------------- 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 645 GLU 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 213 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 389 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 280 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 538 LYS Chi-restraints excluded: chain H residue 16 VAL 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 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 44 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 133 optimal weight: 0.0770 chunk 119 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN F 8 GLN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.130720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104126 restraints weight = 23734.563| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.39 r_work: 0.2916 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19614 Z= 0.210 Angle : 0.480 7.819 26643 Z= 0.261 Chirality : 0.042 0.181 2889 Planarity : 0.004 0.041 3477 Dihedral : 4.025 20.086 2715 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.66 % Allowed : 12.13 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2397 helix: 1.20 (0.29), residues: 327 sheet: 0.16 (0.17), residues: 834 loop : 0.12 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 52 HIS 0.008 0.001 HIS A 631 PHE 0.016 0.001 PHE F 34 TYR 0.028 0.001 TYR G 48 ARG 0.008 0.000 ARG B 556 *********************** 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 274 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 2.586 Fit side-chains REVERT: A 104 GLN cc_start: 0.7203 (tt0) cc_final: 0.6950 (tt0) REVERT: A 367 MET cc_start: 0.7730 (mtm) cc_final: 0.7486 (mtp) REVERT: B 269 ASP cc_start: 0.8095 (m-30) cc_final: 0.7769 (t70) REVERT: C 210 MET cc_start: 0.9365 (ttt) cc_final: 0.8927 (ttt) REVERT: C 416 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8512 (ptp) REVERT: C 595 LEU cc_start: 0.8390 (mp) cc_final: 0.8095 (mp) REVERT: C 632 ARG cc_start: 0.7119 (ptt-90) cc_final: 0.6441 (mtm-85) REVERT: H 17 LYS cc_start: 0.7915 (mmmt) cc_final: 0.7469 (mmtp) REVERT: H 51 GLU cc_start: 0.8422 (tt0) cc_final: 0.8185 (tt0) REVERT: D 48 GLN cc_start: 0.8404 (mp10) cc_final: 0.8169 (mp10) REVERT: D 62 ASN cc_start: 0.9105 (m110) cc_final: 0.8533 (m110) REVERT: D 89 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: D 95 ASP cc_start: 0.8376 (m-30) cc_final: 0.7699 (m-30) REVERT: F 22 SER cc_start: 0.8546 (p) cc_final: 0.8230 (p) REVERT: F 78 ASN cc_start: 0.7934 (t0) cc_final: 0.7321 (t0) outliers start: 34 outliers final: 28 residues processed: 270 average time/residue: 0.3664 time to fit residues: 145.1511 Evaluate side-chains 267 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 659 THR 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 333 THR Chi-restraints excluded: chain B residue 389 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 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 C residue 538 LYS Chi-restraints excluded: chain H residue 16 VAL 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 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 117 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 198 optimal weight: 0.0980 chunk 120 optimal weight: 0.1980 chunk 148 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3500 r_free = 0.3500 target = 0.129881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.102890 restraints weight = 23688.288| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.36 r_work: 0.2929 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19614 Z= 0.252 Angle : 0.495 7.966 26643 Z= 0.268 Chirality : 0.043 0.197 2889 Planarity : 0.004 0.042 3477 Dihedral : 4.088 19.992 2715 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.51 % Allowed : 12.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2397 helix: 1.15 (0.29), residues: 327 sheet: 0.20 (0.17), residues: 825 loop : 0.12 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 52 HIS 0.008 0.001 HIS B 528 PHE 0.018 0.001 PHE C 279 TYR 0.033 0.001 TYR G 48 ARG 0.009 0.000 ARG B 556 ********************** 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 264 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 2.100 Fit side-chains REVERT: A 104 GLN cc_start: 0.7244 (tt0) cc_final: 0.6983 (tt0) REVERT: A 367 MET cc_start: 0.7844 (mtm) cc_final: 0.7589 (mtp) REVERT: B 269 ASP cc_start: 0.8070 (m-30) cc_final: 0.7703 (t70) REVERT: C 210 MET cc_start: 0.9362 (ttt) cc_final: 0.8964 (ttt) REVERT: C 416 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8569 (ptp) REVERT: C 632 ARG cc_start: 0.7114 (ptt-90) cc_final: 0.6437 (mtm-85) REVERT: H 17 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7531 (mmtp) REVERT: H 51 GLU cc_start: 0.8417 (tt0) cc_final: 0.8205 (tt0) REVERT: D 48 GLN cc_start: 0.8446 (mp10) cc_final: 0.8230 (mp10) REVERT: D 62 ASN cc_start: 0.9105 (m110) cc_final: 0.8534 (m110) REVERT: D 89 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7850 (mtm-85) REVERT: D 95 ASP cc_start: 0.8433 (m-30) cc_final: 0.7696 (m-30) REVERT: F 22 SER cc_start: 0.8598 (p) cc_final: 0.8286 (p) REVERT: F 78 ASN cc_start: 0.7967 (t0) cc_final: 0.7373 (t0) outliers start: 31 outliers final: 29 residues processed: 260 average time/residue: 0.3570 time to fit residues: 136.1025 Evaluate side-chains 263 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 659 THR 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 333 THR Chi-restraints excluded: chain B residue 389 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 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 C residue 538 LYS Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 26 SER 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 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 141 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 225 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 120 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104483 restraints weight = 23837.777| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.39 r_work: 0.2939 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19614 Z= 0.183 Angle : 0.471 8.337 26643 Z= 0.256 Chirality : 0.042 0.178 2889 Planarity : 0.004 0.041 3477 Dihedral : 4.011 19.861 2715 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.75 % Allowed : 12.18 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2397 helix: 1.19 (0.29), residues: 327 sheet: 0.24 (0.17), residues: 825 loop : 0.15 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 52 HIS 0.008 0.001 HIS A 631 PHE 0.015 0.001 PHE C 279 TYR 0.025 0.001 TYR G 48 ARG 0.009 0.000 ARG B 556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11539.97 seconds wall clock time: 207 minutes 50.33 seconds (12470.33 seconds total)