Starting phenix.real_space_refine on Thu Feb 5 12:35:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j4c_61131/02_2026/9j4c_61131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j4c_61131/02_2026/9j4c_61131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j4c_61131/02_2026/9j4c_61131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j4c_61131/02_2026/9j4c_61131.map" model { file = "/net/cci-nas-00/data/ceres_data/9j4c_61131/02_2026/9j4c_61131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j4c_61131/02_2026/9j4c_61131.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.055 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 10672 2.51 5 N 2876 2.21 5 O 3314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16958 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5117 Classifications: {'peptide': 655} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 617} Chain: "L" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1643 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "H" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1719 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 212} Restraints were copied for chains: B, C, D Time building chain proxies: 5.58, per 1000 atoms: 0.33 Number of scatterers: 16958 At special positions: 0 Unit cell: (127.224, 129.276, 183.654, 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 3314 8.00 N 2876 7.00 C 10672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 138 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 617 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 670 " - pdb=" SG CYS A 686 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS L 213 " - pdb=" SG CYS H 224 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 138 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 532 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 547 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 617 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 677 " distance=2.03 Simple disulfide: pdb=" SG CYS B 670 " - pdb=" SG CYS B 686 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS D 224 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 149 " - pdb=" SG CYS D 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 736.9 milliseconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4072 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 50 sheets defined 8.3% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.753A pdb=" N ILE A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 321 through 328 Processing helix chain 'A' and resid 362 through 379 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 666 through 672 Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.549A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 127 removed outlier: 3.606A pdb=" N SER L 126 " --> pdb=" O GLU L 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.600A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 142 removed outlier: 3.708A pdb=" N GLN H 140 " --> pdb=" O GLY H 136 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR H 141 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 136 through 142' Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.753A pdb=" N ILE B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 362 through 379 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 621 through 626 Processing helix chain 'B' and resid 666 through 672 Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.549A pdb=" N ALA C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA C 83 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.606A pdb=" N SER C 126 " --> pdb=" O GLU C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.599A pdb=" N ASP D 90 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 142 removed outlier: 3.708A pdb=" N GLN D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 136 through 142' Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing sheet with id=1, first strand: chain 'A' and resid 43 through 45 removed outlier: 4.088A pdb=" N VAL A 491 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 51 through 56 removed outlier: 3.512A pdb=" N ARG A 70 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=4, first strand: chain 'A' and resid 117 through 121 removed outlier: 7.173A pdb=" N PHE A 140 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 172 through 173 Processing sheet with id=6, first strand: chain 'A' and resid 249 through 252 removed outlier: 3.576A pdb=" N GLN A 262 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 13.946A pdb=" N PHE A 278 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N CYS A 302 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER A 280 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 18.202A pdb=" N PHE A 298 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 13.723A pdb=" N GLN A 313 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N ILE A 300 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 311 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 304 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL A 312 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA A 342 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 314 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 317 through 318 removed outlier: 3.824A pdb=" N ASP A 314 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA A 342 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL A 312 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 304 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 311 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 10.231A pdb=" N ILE A 300 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 13.723A pdb=" N GLN A 313 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 18.202A pdb=" N PHE A 298 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 434 through 440 removed outlier: 3.916A pdb=" N ARG A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU A 476 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 461 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA A 474 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 534 through 535 Processing sheet with id=10, first strand: chain 'A' and resid 584 through 585 Processing sheet with id=11, first strand: chain 'A' and resid 596 through 598 removed outlier: 3.646A pdb=" N LYS A 643 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL A 654 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 642 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 652 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 678 through 680 Processing sheet with id=13, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.155A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS L 23 " --> pdb=" O PHE L 70 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.704A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=14 Processing sheet with id=15, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.704A pdb=" N LYS L 44 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TYR L 48 " --> pdb=" O MET L 32 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET L 32 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'L' and resid 115 through 117 Processing sheet with id=17, first strand: chain 'L' and resid 152 through 153 removed outlier: 6.251A pdb=" N HIS L 197 " --> pdb=" O SER L 202 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N SER L 202 " --> pdb=" O HIS L 197 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'L' and resid 152 through 153 Processing sheet with id=19, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.581A pdb=" N GLN H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.581A pdb=" N GLN H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'H' and resid 45 through 50 removed outlier: 6.719A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN H 98 " --> pdb=" O TYR H 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR H 111 " --> pdb=" O GLN H 98 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'H' and resid 45 through 50 removed outlier: 6.719A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA H 92 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'H' and resid 145 through 154 removed outlier: 3.832A pdb=" N VAL H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY H 153 " --> pdb=" O TYR H 184 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR H 184 " --> pdb=" O GLY H 153 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'H' and resid 145 through 154 removed outlier: 3.832A pdb=" N VAL H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY H 153 " --> pdb=" O TYR H 184 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR H 184 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR H 185 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL H 178 " --> pdb=" O THR H 185 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'H' and resid 160 through 163 removed outlier: 4.012A pdb=" N THR H 162 " --> pdb=" O ASN H 205 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'B' and resid 43 through 45 removed outlier: 4.088A pdb=" N VAL B 491 " --> pdb=" O TYR B 500 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'B' and resid 51 through 56 removed outlier: 3.512A pdb=" N ARG B 70 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'B' and resid 89 through 91 Processing sheet with id=29, first strand: chain 'B' and resid 117 through 121 removed outlier: 7.173A pdb=" N PHE B 140 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=31, first strand: chain 'B' and resid 249 through 252 removed outlier: 3.576A pdb=" N GLN B 262 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 13.947A pdb=" N PHE B 278 " --> pdb=" O CYS B 302 " (cutoff:3.500A) removed outlier: 10.944A pdb=" N CYS B 302 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER B 280 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 18.201A pdb=" N PHE B 298 " --> pdb=" O GLN B 313 " (cutoff:3.500A) removed outlier: 13.723A pdb=" N GLN B 313 " --> pdb=" O PHE B 298 " (cutoff:3.500A) removed outlier: 10.232A pdb=" N ILE B 300 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU B 311 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 304 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL B 312 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA B 342 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B 314 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.824A pdb=" N ASP B 314 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA B 342 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL B 312 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 304 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU B 311 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 10.232A pdb=" N ILE B 300 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 13.723A pdb=" N GLN B 313 " --> pdb=" O PHE B 298 " (cutoff:3.500A) removed outlier: 18.201A pdb=" N PHE B 298 " --> pdb=" O GLN B 313 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'B' and resid 434 through 440 removed outlier: 3.917A pdb=" N ARG B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU B 476 " --> pdb=" O LYS B 459 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU B 461 " --> pdb=" O ALA B 474 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA B 474 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'B' and resid 534 through 535 Processing sheet with id=35, first strand: chain 'B' and resid 584 through 585 Processing sheet with id=36, first strand: chain 'B' and resid 596 through 598 removed outlier: 3.646A pdb=" N LYS B 643 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL B 654 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 642 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 652 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'B' and resid 678 through 680 Processing sheet with id=38, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.156A pdb=" N SER C 7 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER C 22 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 19 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS C 23 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE C 70 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.704A pdb=" N LEU C 11 " --> pdb=" O GLU C 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=39 Processing sheet with id=40, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.705A pdb=" N LYS C 44 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TRP C 34 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR C 48 " --> pdb=" O MET C 32 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET C 32 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER C 96 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'C' and resid 115 through 117 Processing sheet with id=42, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.251A pdb=" N HIS C 197 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N SER C 202 " --> pdb=" O HIS C 197 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=44, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.581A pdb=" N GLN D 5 " --> pdb=" O LYS D 23 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.581A pdb=" N GLN D 5 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.719A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN D 98 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR D 111 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.719A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA D 92 " --> pdb=" O VAL D 118 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'D' and resid 145 through 154 removed outlier: 3.833A pdb=" N VAL D 145 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU D 147 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY D 153 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR D 184 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'D' and resid 145 through 154 removed outlier: 3.833A pdb=" N VAL D 145 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU D 147 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY D 153 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR D 184 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 185 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 178 " --> pdb=" O THR D 185 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'D' and resid 160 through 163 removed outlier: 4.011A pdb=" N THR D 162 " --> pdb=" O ASN D 205 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5554 1.34 - 1.46: 3977 1.46 - 1.58: 7715 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 17366 Sorted by residual: bond pdb=" N THR L 73 " pdb=" CA THR L 73 " ideal model delta sigma weight residual 1.454 1.477 -0.022 1.27e-02 6.20e+03 3.10e+00 bond pdb=" N THR C 73 " pdb=" CA THR C 73 " ideal model delta sigma weight residual 1.454 1.476 -0.022 1.27e-02 6.20e+03 2.98e+00 bond pdb=" C GLU D 157 " pdb=" N PRO D 158 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.82e-01 bond pdb=" C GLU H 157 " pdb=" N PRO H 158 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.80e-01 bond pdb=" CG1 ILE B 137 " pdb=" CD1 ILE B 137 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.77e-01 ... (remaining 17361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 23195 1.75 - 3.50: 355 3.50 - 5.25: 40 5.25 - 7.00: 11 7.00 - 8.75: 5 Bond angle restraints: 23606 Sorted by residual: angle pdb=" N LEU A 267 " pdb=" CA LEU A 267 " pdb=" C LEU A 267 " ideal model delta sigma weight residual 114.56 109.88 4.68 1.27e+00 6.20e-01 1.36e+01 angle pdb=" N LEU B 267 " pdb=" CA LEU B 267 " pdb=" C LEU B 267 " ideal model delta sigma weight residual 114.56 109.89 4.67 1.27e+00 6.20e-01 1.35e+01 angle pdb=" N ILE L 74 " pdb=" CA ILE L 74 " pdb=" CB ILE L 74 " ideal model delta sigma weight residual 111.41 106.50 4.91 1.38e+00 5.25e-01 1.27e+01 angle pdb=" N ILE C 74 " pdb=" CA ILE C 74 " pdb=" CB ILE C 74 " ideal model delta sigma weight residual 111.41 106.50 4.91 1.38e+00 5.25e-01 1.26e+01 angle pdb=" N GLY A 136 " pdb=" CA GLY A 136 " pdb=" C GLY A 136 " ideal model delta sigma weight residual 113.18 119.34 -6.16 2.37e+00 1.78e-01 6.76e+00 ... (remaining 23601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 8823 18.33 - 36.67: 1251 36.67 - 55.00: 342 55.00 - 73.33: 46 73.33 - 91.67: 32 Dihedral angle restraints: 10494 sinusoidal: 4136 harmonic: 6358 Sorted by residual: dihedral pdb=" CB CYS D 149 " pdb=" SG CYS D 149 " pdb=" SG CYS D 204 " pdb=" CB CYS D 204 " ideal model delta sinusoidal sigma weight residual -86.00 -176.30 90.30 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS H 149 " pdb=" SG CYS H 149 " pdb=" SG CYS H 204 " pdb=" CB CYS H 204 " ideal model delta sinusoidal sigma weight residual -86.00 -176.27 90.27 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS A 302 " pdb=" SG CYS A 302 " pdb=" SG CYS A 358 " pdb=" CB CYS A 358 " ideal model delta sinusoidal sigma weight residual -86.00 -32.98 -53.02 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 10491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2148 0.051 - 0.103: 375 0.103 - 0.154: 73 0.154 - 0.206: 8 0.206 - 0.257: 2 Chirality restraints: 2606 Sorted by residual: chirality pdb=" CA ILE L 74 " pdb=" N ILE L 74 " pdb=" C ILE L 74 " pdb=" CB ILE L 74 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE C 74 " pdb=" N ILE C 74 " pdb=" C ILE C 74 " pdb=" CB ILE C 74 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU L 72 " pdb=" N LEU L 72 " pdb=" C LEU L 72 " pdb=" CB LEU L 72 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2603 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 131 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO D 132 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 131 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.24e+00 pdb=" N PRO H 132 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO H 132 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 132 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 162 " -0.010 2.00e-02 2.50e+03 8.56e-03 1.83e+00 pdb=" CG TRP L 162 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP L 162 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP L 162 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP L 162 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 162 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP L 162 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 162 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 162 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 162 " 0.000 2.00e-02 2.50e+03 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.42: 12 1.42 - 2.29: 50 2.29 - 3.16: 14601 3.16 - 4.03: 47612 4.03 - 4.90: 83891 Warning: very small nonbonded interaction distances. Nonbonded interactions: 146166 Sorted by model distance: nonbonded pdb=" OE2 GLU A 211 " pdb=" C SER B 100 " model vdw 0.555 3.270 nonbonded pdb=" C SER A 100 " pdb=" OE2 GLU B 211 " model vdw 0.555 3.270 nonbonded pdb=" O SER A 100 " pdb=" CG GLU B 211 " model vdw 0.691 3.440 nonbonded pdb=" CG GLU A 211 " pdb=" O SER B 100 " model vdw 0.691 3.440 nonbonded pdb=" CD GLU A 211 " pdb=" C SER B 100 " model vdw 0.722 3.500 ... (remaining 146161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'L' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.010 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.660 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5346 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 : 0.002 0.042 17400 Z= 0.110 Angle : 0.558 8.745 23674 Z= 0.285 Chirality : 0.043 0.257 2606 Planarity : 0.003 0.049 3068 Dihedral : 18.131 91.666 6320 Min Nonbonded Distance : 0.555 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.11 % Allowed : 34.23 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 2178 helix: -0.42 (0.43), residues: 160 sheet: -1.20 (0.20), residues: 744 loop : -0.66 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 204 TYR 0.014 0.001 TYR C 31 PHE 0.011 0.001 PHE A 218 TRP 0.023 0.002 TRP L 162 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00246 (17366) covalent geometry : angle 0.55668 (23606) SS BOND : bond 0.00172 ( 34) SS BOND : angle 0.86726 ( 68) hydrogen bonds : bond 0.29145 ( 398) hydrogen bonds : angle 12.48420 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 429 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 THR cc_start: 0.7549 (t) cc_final: 0.7154 (m) REVERT: A 332 GLU cc_start: 0.7118 (tp30) cc_final: 0.6782 (tt0) REVERT: L 97 PHE cc_start: 0.6754 (m-10) cc_final: 0.6287 (m-80) REVERT: L 169 ASP cc_start: 0.7882 (p0) cc_final: 0.7514 (p0) REVERT: L 174 MET cc_start: -0.0709 (tpt) cc_final: -0.1460 (mmm) REVERT: L 209 ASN cc_start: 0.7086 (m-40) cc_final: 0.6728 (t0) REVERT: H 31 GLU cc_start: 0.6295 (tm-30) cc_final: 0.5734 (mp0) REVERT: C 117 PHE cc_start: 0.3275 (m-10) cc_final: 0.3022 (m-10) REVERT: C 146 LYS cc_start: 0.7859 (mmtt) cc_final: 0.7527 (mtmt) outliers start: 2 outliers final: 0 residues processed: 431 average time/residue: 0.1637 time to fit residues: 100.6400 Evaluate side-chains 218 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 0.0030 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN L 6 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 GLN B 53 HIS ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 262 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.198181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.163715 restraints weight = 41160.455| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 3.83 r_work: 0.4470 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17400 Z= 0.165 Angle : 0.718 8.705 23674 Z= 0.372 Chirality : 0.047 0.284 2606 Planarity : 0.005 0.075 3068 Dihedral : 4.928 33.344 2382 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.52 % Allowed : 29.65 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.18), residues: 2178 helix: -0.83 (0.39), residues: 170 sheet: -1.39 (0.19), residues: 720 loop : -0.71 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 310 TYR 0.022 0.002 TYR A 293 PHE 0.036 0.002 PHE B 218 TRP 0.017 0.002 TRP H 36 HIS 0.007 0.001 HIS L 188 Details of bonding type rmsd covalent geometry : bond 0.00370 (17366) covalent geometry : angle 0.71559 (23606) SS BOND : bond 0.00342 ( 34) SS BOND : angle 1.35674 ( 68) hydrogen bonds : bond 0.05337 ( 398) hydrogen bonds : angle 9.08768 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 259 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6918 (tt0) REVERT: A 277 PHE cc_start: 0.7071 (m-80) cc_final: 0.6742 (m-80) REVERT: A 332 GLU cc_start: 0.7368 (tp30) cc_final: 0.6906 (tt0) REVERT: A 489 ASP cc_start: 0.5535 (OUTLIER) cc_final: 0.5283 (t70) REVERT: A 509 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6688 (ttp80) REVERT: A 575 VAL cc_start: 0.4112 (OUTLIER) cc_final: 0.3853 (m) REVERT: L 21 MET cc_start: 0.5361 (ttm) cc_final: 0.4714 (ptm) REVERT: L 77 MET cc_start: 0.6224 (tmm) cc_final: 0.5991 (tmm) REVERT: L 97 PHE cc_start: 0.7361 (m-10) cc_final: 0.7150 (m-80) REVERT: L 209 ASN cc_start: 0.7274 (m-40) cc_final: 0.6946 (t0) REVERT: H 31 GLU cc_start: 0.6491 (tm-30) cc_final: 0.5697 (mp0) REVERT: H 52 SER cc_start: 0.7054 (OUTLIER) cc_final: 0.6576 (p) REVERT: H 72 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8028 (t) REVERT: H 109 LEU cc_start: 0.8237 (tt) cc_final: 0.8014 (mp) REVERT: H 157 GLU cc_start: 0.8879 (tp30) cc_final: 0.8617 (tp30) REVERT: B 174 ILE cc_start: 0.4556 (mp) cc_final: 0.4346 (mp) REVERT: B 282 ILE cc_start: 0.4275 (tt) cc_final: 0.3859 (mt) REVERT: B 317 LEU cc_start: 0.4673 (OUTLIER) cc_final: 0.3675 (tp) REVERT: B 377 TYR cc_start: 0.3227 (m-80) cc_final: 0.2981 (m-80) REVERT: B 383 LEU cc_start: 0.4819 (OUTLIER) cc_final: 0.4469 (mm) REVERT: B 504 GLU cc_start: 0.7333 (mp0) cc_final: 0.7115 (mp0) REVERT: B 675 PHE cc_start: 0.1401 (OUTLIER) cc_final: 0.0228 (m-80) REVERT: D 101 TYR cc_start: 0.4816 (m-80) cc_final: 0.4605 (m-80) REVERT: D 179 LEU cc_start: 0.4268 (OUTLIER) cc_final: 0.4031 (tt) REVERT: D 214 LYS cc_start: 0.7168 (mmtp) cc_final: 0.6949 (mmtm) outliers start: 105 outliers final: 43 residues processed: 343 average time/residue: 0.1362 time to fit residues: 70.1608 Evaluate side-chains 245 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 180 GLN Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 675 PHE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 185 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 208 optimal weight: 50.0000 chunk 90 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 205 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS C 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.182955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.140103 restraints weight = 39249.961| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 4.60 r_work: 0.4073 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 17400 Z= 0.329 Angle : 0.889 12.820 23674 Z= 0.459 Chirality : 0.050 0.197 2606 Planarity : 0.006 0.068 3068 Dihedral : 5.748 30.458 2382 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 6.62 % Allowed : 27.39 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.18), residues: 2178 helix: -1.21 (0.39), residues: 156 sheet: -1.53 (0.19), residues: 726 loop : -1.02 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 142 TYR 0.048 0.003 TYR A 246 PHE 0.041 0.003 PHE B 406 TRP 0.028 0.002 TRP D 112 HIS 0.012 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00742 (17366) covalent geometry : angle 0.88738 (23606) SS BOND : bond 0.00525 ( 34) SS BOND : angle 1.43235 ( 68) hydrogen bonds : bond 0.05006 ( 398) hydrogen bonds : angle 8.11125 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 249 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7027 (mt) REVERT: A 332 GLU cc_start: 0.7913 (tp30) cc_final: 0.7482 (tt0) REVERT: A 489 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8192 (t70) REVERT: A 491 VAL cc_start: 0.8571 (p) cc_final: 0.8225 (m) REVERT: L 21 MET cc_start: 0.6040 (ttm) cc_final: 0.5714 (mtm) REVERT: L 31 TYR cc_start: 0.8466 (m-80) cc_final: 0.7979 (m-80) REVERT: L 32 MET cc_start: 0.7972 (tmm) cc_final: 0.7541 (tmm) REVERT: L 70 PHE cc_start: 0.8262 (m-80) cc_final: 0.7895 (m-80) REVERT: L 184 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7032 (pt0) REVERT: L 209 ASN cc_start: 0.6912 (m-40) cc_final: 0.6611 (t0) REVERT: H 31 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6701 (pp20) REVERT: H 157 GLU cc_start: 0.9036 (tp30) cc_final: 0.8711 (tp30) REVERT: B 206 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6955 (mp) REVERT: B 346 LYS cc_start: 0.7804 (ptmm) cc_final: 0.7472 (ptmm) REVERT: B 368 LYS cc_start: 0.7360 (mttp) cc_final: 0.6543 (tttm) REVERT: B 675 PHE cc_start: 0.1364 (OUTLIER) cc_final: 0.0220 (m-80) REVERT: C 21 MET cc_start: 0.4785 (mmm) cc_final: 0.4542 (mmm) REVERT: C 32 MET cc_start: 0.6426 (ppp) cc_final: 0.6179 (ppp) REVERT: C 174 MET cc_start: 0.6630 (ppp) cc_final: 0.5169 (mmt) REVERT: C 189 ASN cc_start: 0.6418 (t0) cc_final: 0.6014 (p0) REVERT: D 20 ILE cc_start: 0.4256 (mm) cc_final: 0.4031 (mm) outliers start: 126 outliers final: 64 residues processed: 349 average time/residue: 0.1277 time to fit residues: 68.6552 Evaluate side-chains 264 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 194 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 TRP Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 184 GLU Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 144 MET Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 675 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 110 optimal weight: 0.0370 chunk 193 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 139 GLN A 562 GLN ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.185768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.144360 restraints weight = 38747.963| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 4.25 r_work: 0.4149 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17400 Z= 0.147 Angle : 0.702 9.556 23674 Z= 0.356 Chirality : 0.046 0.168 2606 Planarity : 0.005 0.052 3068 Dihedral : 5.376 34.687 2382 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.94 % Allowed : 28.71 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.18), residues: 2178 helix: -1.28 (0.38), residues: 160 sheet: -1.36 (0.20), residues: 672 loop : -0.98 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 319 TYR 0.023 0.002 TYR A 500 PHE 0.024 0.002 PHE B 406 TRP 0.022 0.002 TRP B 49 HIS 0.005 0.001 HIS L 188 Details of bonding type rmsd covalent geometry : bond 0.00340 (17366) covalent geometry : angle 0.69954 (23606) SS BOND : bond 0.00452 ( 34) SS BOND : angle 1.22281 ( 68) hydrogen bonds : bond 0.03768 ( 398) hydrogen bonds : angle 7.55852 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 194 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6787 (mt0) REVERT: A 252 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7749 (m) REVERT: A 253 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7026 (tt0) REVERT: A 332 GLU cc_start: 0.7800 (tp30) cc_final: 0.7310 (tt0) REVERT: A 491 VAL cc_start: 0.7879 (p) cc_final: 0.7617 (m) REVERT: A 577 MET cc_start: 0.7925 (ptp) cc_final: 0.7665 (mpp) REVERT: L 21 MET cc_start: 0.6066 (ttm) cc_final: 0.5588 (mtm) REVERT: L 70 PHE cc_start: 0.7976 (m-80) cc_final: 0.7705 (m-10) REVERT: L 209 ASN cc_start: 0.7178 (m-40) cc_final: 0.6837 (t0) REVERT: H 36 TRP cc_start: 0.7771 (m100) cc_final: 0.7356 (m100) REVERT: H 157 GLU cc_start: 0.9031 (tp30) cc_final: 0.8649 (tp30) REVERT: B 277 PHE cc_start: 0.7032 (m-80) cc_final: 0.6813 (m-10) REVERT: B 368 LYS cc_start: 0.7333 (mttp) cc_final: 0.6452 (tttm) REVERT: B 675 PHE cc_start: 0.1373 (OUTLIER) cc_final: 0.0261 (m-80) REVERT: C 103 LEU cc_start: 0.5742 (tp) cc_final: 0.5440 (tp) REVERT: C 174 MET cc_start: 0.6709 (ppp) cc_final: 0.5250 (mmt) REVERT: D 30 THR cc_start: 0.5215 (OUTLIER) cc_final: 0.4886 (m) REVERT: D 80 TYR cc_start: 0.6462 (OUTLIER) cc_final: 0.5720 (t80) REVERT: D 101 TYR cc_start: 0.6127 (m-80) cc_final: 0.5332 (m-80) outliers start: 94 outliers final: 58 residues processed: 273 average time/residue: 0.1173 time to fit residues: 50.7685 Evaluate side-chains 229 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 166 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 TRP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 675 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 145 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 0.0010 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.184341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.141605 restraints weight = 38314.137| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 4.48 r_work: 0.4107 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17400 Z= 0.154 Angle : 0.665 10.696 23674 Z= 0.335 Chirality : 0.044 0.168 2606 Planarity : 0.004 0.057 3068 Dihedral : 5.151 32.028 2382 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.84 % Allowed : 28.65 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.18), residues: 2178 helix: -1.27 (0.37), residues: 170 sheet: -1.31 (0.20), residues: 676 loop : -0.97 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 107 TYR 0.027 0.002 TYR A 197 PHE 0.018 0.002 PHE B 406 TRP 0.021 0.001 TRP B 49 HIS 0.009 0.001 HIS B 276 Details of bonding type rmsd covalent geometry : bond 0.00359 (17366) covalent geometry : angle 0.66426 (23606) SS BOND : bond 0.00330 ( 34) SS BOND : angle 0.79853 ( 68) hydrogen bonds : bond 0.03540 ( 398) hydrogen bonds : angle 7.07767 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 195 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LEU cc_start: 0.7205 (mm) cc_final: 0.6824 (mt) REVERT: A 207 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7931 (mmm) REVERT: A 252 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7829 (m) REVERT: A 285 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6628 (mt) REVERT: A 295 TYR cc_start: 0.7750 (t80) cc_final: 0.7426 (t80) REVERT: A 332 GLU cc_start: 0.7839 (tp30) cc_final: 0.7144 (tp30) REVERT: A 491 VAL cc_start: 0.7997 (p) cc_final: 0.7630 (m) REVERT: A 577 MET cc_start: 0.8115 (ptp) cc_final: 0.7712 (mpp) REVERT: L 21 MET cc_start: 0.5763 (ttm) cc_final: 0.5549 (mtm) REVERT: L 36 GLN cc_start: 0.7092 (pt0) cc_final: 0.6781 (tt0) REVERT: L 209 ASN cc_start: 0.7067 (m-40) cc_final: 0.6722 (t0) REVERT: H 36 TRP cc_start: 0.7828 (m100) cc_final: 0.7509 (m100) REVERT: H 157 GLU cc_start: 0.9051 (tp30) cc_final: 0.8626 (tp30) REVERT: B 207 MET cc_start: 0.5161 (ptp) cc_final: 0.4672 (ptm) REVERT: B 262 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.5802 (pt0) REVERT: B 322 ARG cc_start: 0.6362 (mpt-90) cc_final: 0.5794 (mmt90) REVERT: B 368 LYS cc_start: 0.7437 (mttp) cc_final: 0.6458 (tttm) REVERT: B 383 LEU cc_start: 0.5547 (mm) cc_final: 0.5274 (mm) REVERT: B 675 PHE cc_start: 0.1250 (OUTLIER) cc_final: 0.0177 (m-80) REVERT: C 20 THR cc_start: 0.6423 (p) cc_final: 0.6102 (t) REVERT: C 89 GLN cc_start: 0.5357 (OUTLIER) cc_final: 0.4271 (pp30) REVERT: C 103 LEU cc_start: 0.5881 (tp) cc_final: 0.5521 (tp) REVERT: C 174 MET cc_start: 0.6971 (ppp) cc_final: 0.5547 (mmt) REVERT: D 30 THR cc_start: 0.5282 (OUTLIER) cc_final: 0.5060 (m) REVERT: D 80 TYR cc_start: 0.6515 (OUTLIER) cc_final: 0.5781 (t80) outliers start: 92 outliers final: 60 residues processed: 274 average time/residue: 0.1221 time to fit residues: 52.5457 Evaluate side-chains 238 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 170 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 TRP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 142 ASP Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 675 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 77 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 15 optimal weight: 0.4980 chunk 146 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN A 397 ASN ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.171950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.124673 restraints weight = 36837.492| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 3.69 r_work: 0.3898 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.7479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 17400 Z= 0.346 Angle : 0.878 13.344 23674 Z= 0.451 Chirality : 0.051 0.274 2606 Planarity : 0.006 0.089 3068 Dihedral : 5.863 30.399 2382 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.05 % Allowed : 28.34 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.17), residues: 2178 helix: -1.34 (0.37), residues: 168 sheet: -1.50 (0.19), residues: 698 loop : -1.20 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 126 TYR 0.047 0.003 TYR B 475 PHE 0.035 0.003 PHE H 64 TRP 0.028 0.003 TRP B 49 HIS 0.009 0.002 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00789 (17366) covalent geometry : angle 0.87619 (23606) SS BOND : bond 0.00596 ( 34) SS BOND : angle 1.37034 ( 68) hydrogen bonds : bond 0.04618 ( 398) hydrogen bonds : angle 7.57222 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 221 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7025 (mt) REVERT: A 332 GLU cc_start: 0.7980 (tp30) cc_final: 0.7172 (tp30) REVERT: A 577 MET cc_start: 0.8146 (ptp) cc_final: 0.7718 (mpp) REVERT: L 143 ILE cc_start: 0.6896 (tt) cc_final: 0.6462 (tt) REVERT: H 36 TRP cc_start: 0.8105 (m100) cc_final: 0.7837 (m100) REVERT: B 78 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8310 (mp) REVERT: B 125 ASN cc_start: 0.7955 (p0) cc_final: 0.7737 (t0) REVERT: B 473 LEU cc_start: 0.7200 (mp) cc_final: 0.6894 (tt) REVERT: B 475 TYR cc_start: 0.4898 (OUTLIER) cc_final: 0.4313 (p90) REVERT: B 675 PHE cc_start: 0.1189 (OUTLIER) cc_final: 0.0119 (m-80) REVERT: C 45 ARG cc_start: 0.6007 (ttp80) cc_final: 0.5659 (ttp80) REVERT: C 174 MET cc_start: 0.7187 (ppp) cc_final: 0.5795 (mmt) REVERT: D 80 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6403 (t80) outliers start: 115 outliers final: 70 residues processed: 310 average time/residue: 0.1214 time to fit residues: 59.1831 Evaluate side-chains 248 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 173 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 TRP Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 675 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 30 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 ASN ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 HIS B 597 ASN C 88 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.175342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.130750 restraints weight = 36678.771| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 4.27 r_work: 0.3963 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17400 Z= 0.170 Angle : 0.718 11.282 23674 Z= 0.365 Chirality : 0.046 0.171 2606 Planarity : 0.005 0.080 3068 Dihedral : 5.403 28.804 2382 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.68 % Allowed : 30.02 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.18), residues: 2178 helix: -1.32 (0.37), residues: 172 sheet: -1.32 (0.20), residues: 680 loop : -1.06 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 555 TYR 0.024 0.002 TYR A 246 PHE 0.034 0.002 PHE A 360 TRP 0.023 0.002 TRP A 49 HIS 0.009 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00406 (17366) covalent geometry : angle 0.71792 (23606) SS BOND : bond 0.00294 ( 34) SS BOND : angle 0.85970 ( 68) hydrogen bonds : bond 0.03664 ( 398) hydrogen bonds : angle 6.92869 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 206 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6796 (mt) REVERT: A 298 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7874 (t80) REVERT: A 332 GLU cc_start: 0.7936 (tp30) cc_final: 0.7008 (tp30) REVERT: A 540 ILE cc_start: 0.8127 (tp) cc_final: 0.7760 (mm) REVERT: A 577 MET cc_start: 0.8064 (ptp) cc_final: 0.7692 (mpp) REVERT: L 143 ILE cc_start: 0.7214 (tt) cc_final: 0.6906 (tt) REVERT: H 157 GLU cc_start: 0.8999 (tp30) cc_final: 0.8452 (tp30) REVERT: B 78 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8034 (tp) REVERT: B 125 ASN cc_start: 0.7944 (p0) cc_final: 0.7686 (t0) REVERT: B 200 THR cc_start: 0.8091 (t) cc_final: 0.7609 (m) REVERT: B 473 LEU cc_start: 0.7203 (mp) cc_final: 0.6865 (tt) REVERT: B 475 TYR cc_start: 0.5143 (OUTLIER) cc_final: 0.3584 (p90) REVERT: B 675 PHE cc_start: 0.1073 (OUTLIER) cc_final: 0.0035 (m-80) REVERT: C 174 MET cc_start: 0.7209 (ppp) cc_final: 0.5842 (mmt) REVERT: D 80 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6517 (t80) outliers start: 89 outliers final: 64 residues processed: 276 average time/residue: 0.1068 time to fit residues: 47.9060 Evaluate side-chains 257 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 187 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 TRP Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 675 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 208 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 115 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.171896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.125495 restraints weight = 37725.327| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 4.59 r_work: 0.3855 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.8242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17400 Z= 0.251 Angle : 0.761 11.041 23674 Z= 0.389 Chirality : 0.047 0.192 2606 Planarity : 0.005 0.063 3068 Dihedral : 5.547 29.560 2382 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.15 % Allowed : 29.39 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.18), residues: 2178 helix: -1.10 (0.38), residues: 168 sheet: -1.43 (0.20), residues: 686 loop : -1.07 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG B 549 TYR 0.023 0.003 TYR A 246 PHE 0.032 0.003 PHE A 360 TRP 0.024 0.002 TRP A 49 HIS 0.008 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00590 (17366) covalent geometry : angle 0.75948 (23606) SS BOND : bond 0.00460 ( 34) SS BOND : angle 1.14210 ( 68) hydrogen bonds : bond 0.03879 ( 398) hydrogen bonds : angle 6.88033 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 200 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.7983 (m-30) cc_final: 0.7769 (m-30) REVERT: A 285 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.6908 (mt) REVERT: A 298 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7945 (t80) REVERT: A 332 GLU cc_start: 0.8051 (tp30) cc_final: 0.7137 (tp30) REVERT: A 540 ILE cc_start: 0.8419 (tp) cc_final: 0.8081 (mm) REVERT: A 577 MET cc_start: 0.8127 (ptp) cc_final: 0.7775 (mpp) REVERT: L 32 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7669 (ppp) REVERT: L 36 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: L 133 CYS cc_start: 0.3023 (t) cc_final: 0.2211 (t) REVERT: L 143 ILE cc_start: 0.7240 (tt) cc_final: 0.6942 (tt) REVERT: H 54 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6902 (t0) REVERT: H 62 GLN cc_start: 0.8399 (pm20) cc_final: 0.8188 (pm20) REVERT: H 157 GLU cc_start: 0.9072 (tp30) cc_final: 0.8531 (tp30) REVERT: B 125 ASN cc_start: 0.8129 (p0) cc_final: 0.7679 (t0) REVERT: B 137 ILE cc_start: 0.8299 (mp) cc_final: 0.7786 (mp) REVERT: B 409 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6495 (tp-100) REVERT: B 675 PHE cc_start: 0.1211 (OUTLIER) cc_final: 0.0182 (m-80) REVERT: C 94 PRO cc_start: 0.7921 (Cg_endo) cc_final: 0.7563 (Cg_exo) REVERT: C 174 MET cc_start: 0.7451 (ppp) cc_final: 0.6062 (mmt) REVERT: D 80 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6576 (t80) REVERT: D 98 GLN cc_start: 0.7898 (pm20) cc_final: 0.7459 (pm20) outliers start: 98 outliers final: 73 residues processed: 272 average time/residue: 0.1078 time to fit residues: 48.1299 Evaluate side-chains 267 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 186 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 46 TRP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 101 TYR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 675 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 46 TRP Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 185 optimal weight: 0.0470 chunk 89 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 128 optimal weight: 0.0980 chunk 165 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 183 optimal weight: 0.4980 chunk 64 optimal weight: 0.0060 chunk 170 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN A 506 GLN ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN B 579 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.177586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.133964 restraints weight = 37570.496| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 4.41 r_work: 0.4015 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.8334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17400 Z= 0.139 Angle : 0.710 13.737 23674 Z= 0.357 Chirality : 0.046 0.208 2606 Planarity : 0.005 0.063 3068 Dihedral : 5.255 27.558 2382 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.00 % Allowed : 30.70 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.18), residues: 2178 helix: -1.11 (0.38), residues: 160 sheet: -1.17 (0.21), residues: 632 loop : -1.01 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 549 TYR 0.035 0.002 TYR L 31 PHE 0.017 0.002 PHE A 360 TRP 0.036 0.002 TRP D 47 HIS 0.006 0.001 HIS L 188 Details of bonding type rmsd covalent geometry : bond 0.00329 (17366) covalent geometry : angle 0.70904 (23606) SS BOND : bond 0.00266 ( 34) SS BOND : angle 0.97413 ( 68) hydrogen bonds : bond 0.03337 ( 398) hydrogen bonds : angle 6.54005 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 212 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 TYR cc_start: 0.7401 (t80) cc_final: 0.7129 (t80) REVERT: A 298 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.8004 (t80) REVERT: A 332 GLU cc_start: 0.7985 (tp30) cc_final: 0.6990 (tp30) REVERT: A 491 VAL cc_start: 0.7590 (p) cc_final: 0.7183 (m) REVERT: A 540 ILE cc_start: 0.8461 (tp) cc_final: 0.7671 (pt) REVERT: A 577 MET cc_start: 0.8091 (ptp) cc_final: 0.7736 (mpp) REVERT: L 36 GLN cc_start: 0.6820 (OUTLIER) cc_final: 0.6604 (tt0) REVERT: L 60 ARG cc_start: 0.7617 (ptm-80) cc_final: 0.7242 (ptm-80) REVERT: L 133 CYS cc_start: 0.2810 (t) cc_final: 0.2109 (t) REVERT: L 143 ILE cc_start: 0.7109 (tt) cc_final: 0.6796 (tt) REVERT: H 54 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6710 (t0) REVERT: H 62 GLN cc_start: 0.8447 (pm20) cc_final: 0.8239 (pm20) REVERT: H 157 GLU cc_start: 0.8985 (tp30) cc_final: 0.8439 (tp30) REVERT: B 48 ASP cc_start: 0.7501 (p0) cc_final: 0.6796 (p0) REVERT: B 78 LEU cc_start: 0.8001 (tp) cc_final: 0.7719 (tp) REVERT: B 125 ASN cc_start: 0.8042 (p0) cc_final: 0.7665 (t0) REVERT: B 153 HIS cc_start: 0.7623 (p-80) cc_final: 0.7129 (p-80) REVERT: B 473 LEU cc_start: 0.7134 (mp) cc_final: 0.6588 (tt) REVERT: B 675 PHE cc_start: 0.1148 (OUTLIER) cc_final: 0.0163 (m-80) REVERT: C 94 PRO cc_start: 0.7693 (Cg_endo) cc_final: 0.7324 (Cg_exo) REVERT: C 174 MET cc_start: 0.7483 (ppp) cc_final: 0.6242 (mmt) REVERT: D 50 ASP cc_start: 0.3534 (p0) cc_final: 0.2889 (p0) REVERT: D 80 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6572 (t80) REVERT: D 98 GLN cc_start: 0.7353 (pm20) cc_final: 0.7007 (pm20) REVERT: D 101 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6198 (m-80) outliers start: 76 outliers final: 60 residues processed: 274 average time/residue: 0.1122 time to fit residues: 49.3611 Evaluate side-chains 260 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 194 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 46 TRP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 675 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 184 optimal weight: 30.0000 chunk 45 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 chunk 154 optimal weight: 0.1980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.177209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.132002 restraints weight = 37602.942| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 3.77 r_work: 0.4038 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.8470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17400 Z= 0.143 Angle : 0.702 12.383 23674 Z= 0.352 Chirality : 0.045 0.190 2606 Planarity : 0.005 0.102 3068 Dihedral : 5.155 26.574 2382 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.73 % Allowed : 30.70 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.18), residues: 2178 helix: -0.61 (0.41), residues: 148 sheet: -1.23 (0.21), residues: 648 loop : -1.06 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 549 TYR 0.028 0.002 TYR D 27 PHE 0.021 0.002 PHE H 64 TRP 0.055 0.002 TRP D 47 HIS 0.005 0.001 HIS L 188 Details of bonding type rmsd covalent geometry : bond 0.00344 (17366) covalent geometry : angle 0.70203 (23606) SS BOND : bond 0.00206 ( 34) SS BOND : angle 0.82171 ( 68) hydrogen bonds : bond 0.03215 ( 398) hydrogen bonds : angle 6.44914 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 200 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6662 (mt) REVERT: A 295 TYR cc_start: 0.7619 (t80) cc_final: 0.7248 (t80) REVERT: A 298 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7929 (t80) REVERT: A 332 GLU cc_start: 0.7985 (tp30) cc_final: 0.6976 (tp30) REVERT: A 363 ARG cc_start: 0.7911 (tpp80) cc_final: 0.7701 (tpp80) REVERT: A 491 VAL cc_start: 0.7960 (p) cc_final: 0.7620 (m) REVERT: A 540 ILE cc_start: 0.8475 (tp) cc_final: 0.7676 (pt) REVERT: A 577 MET cc_start: 0.7944 (ptp) cc_final: 0.7602 (mpp) REVERT: L 31 TYR cc_start: 0.8508 (m-80) cc_final: 0.8301 (m-10) REVERT: L 133 CYS cc_start: 0.2867 (t) cc_final: 0.2254 (t) REVERT: L 143 ILE cc_start: 0.7085 (tt) cc_final: 0.6757 (tt) REVERT: H 39 GLN cc_start: 0.7812 (tt0) cc_final: 0.7418 (tp40) REVERT: H 54 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6588 (t0) REVERT: H 84 ARG cc_start: 0.8910 (tmm-80) cc_final: 0.8609 (ptt-90) REVERT: H 157 GLU cc_start: 0.8900 (tp30) cc_final: 0.8117 (tp30) REVERT: B 48 ASP cc_start: 0.7440 (p0) cc_final: 0.6710 (p0) REVERT: B 78 LEU cc_start: 0.8044 (tp) cc_final: 0.7686 (tp) REVERT: B 125 ASN cc_start: 0.7953 (p0) cc_final: 0.7483 (t0) REVERT: B 143 LEU cc_start: 0.7829 (mp) cc_final: 0.7601 (mt) REVERT: B 153 HIS cc_start: 0.7458 (p-80) cc_final: 0.6999 (p-80) REVERT: B 473 LEU cc_start: 0.7156 (mp) cc_final: 0.6628 (tt) REVERT: B 675 PHE cc_start: 0.1003 (OUTLIER) cc_final: -0.0015 (m-80) REVERT: C 94 PRO cc_start: 0.7803 (Cg_endo) cc_final: 0.7460 (Cg_exo) REVERT: C 97 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7248 (t80) REVERT: C 174 MET cc_start: 0.7449 (ppp) cc_final: 0.6188 (mmt) REVERT: D 34 MET cc_start: 0.5480 (tpp) cc_final: 0.4731 (tmm) REVERT: D 50 ASP cc_start: 0.3347 (p0) cc_final: 0.3061 (p0) REVERT: D 80 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.6592 (t80) REVERT: D 98 GLN cc_start: 0.7481 (pm20) cc_final: 0.6957 (pm20) REVERT: D 101 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6215 (m-80) outliers start: 71 outliers final: 56 residues processed: 255 average time/residue: 0.1062 time to fit residues: 43.9079 Evaluate side-chains 251 residues out of total 1902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 TRP Chi-restraints excluded: chain L residue 84 THR Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 286 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 CYS Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 427 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 675 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 97 PHE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 101 TYR Chi-restraints excluded: chain D residue 131 TYR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 192 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 99 optimal weight: 7.9990 chunk 210 optimal weight: 0.3980 chunk 151 optimal weight: 0.9990 chunk 147 optimal weight: 0.0980 chunk 202 optimal weight: 0.0010 chunk 66 optimal weight: 0.0050 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 119 optimal weight: 0.9980 overall best weight: 0.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.180247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.137410 restraints weight = 37859.890| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 4.40 r_work: 0.4073 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.8561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17400 Z= 0.126 Angle : 0.692 11.282 23674 Z= 0.346 Chirality : 0.045 0.191 2606 Planarity : 0.005 0.065 3068 Dihedral : 5.066 24.406 2382 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.42 % Allowed : 31.18 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2178 helix: -0.63 (0.41), residues: 148 sheet: -1.19 (0.20), residues: 664 loop : -1.00 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 45 TYR 0.029 0.002 TYR D 27 PHE 0.014 0.002 PHE B 338 TRP 0.059 0.002 TRP D 47 HIS 0.005 0.001 HIS L 188 Details of bonding type rmsd covalent geometry : bond 0.00295 (17366) covalent geometry : angle 0.69220 (23606) SS BOND : bond 0.00215 ( 34) SS BOND : angle 0.76722 ( 68) hydrogen bonds : bond 0.03111 ( 398) hydrogen bonds : angle 6.30054 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6158.82 seconds wall clock time: 105 minutes 57.90 seconds (6357.90 seconds total)