Starting phenix.real_space_refine on Wed Feb 4 23:34:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qcn_53016/02_2026/9qcn_53016.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qcn_53016/02_2026/9qcn_53016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qcn_53016/02_2026/9qcn_53016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qcn_53016/02_2026/9qcn_53016.map" model { file = "/net/cci-nas-00/data/ceres_data/9qcn_53016/02_2026/9qcn_53016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qcn_53016/02_2026/9qcn_53016.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 18 5.16 5 C 8587 2.51 5 N 2196 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s 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: 13415 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4439 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 23, 'TRANS': 546} Chain breaks: 7 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 7, 'GLN:plan1': 5, 'GLU:plan': 6, 'ASN:plan1': 8, 'ARG:plan': 4, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 121 Chain: "B" Number of atoms: 4488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4488 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 537} Chain breaks: 7 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 4488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4488 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 22, 'TRANS': 539} Chain breaks: 7 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Time building chain proxies: 2.64, per 1000 atoms: 0.20 Number of scatterers: 13415 At special positions: 0 Unit cell: (154.008, 167.256, 63.756, 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 18 16.00 O 2614 8.00 N 2196 7.00 C 8587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.95 Conformation dependent library (CDL) restraints added in 409.3 milliseconds 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 27 sheets defined 9.2% alpha, 53.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.643A pdb=" N ASN A 68 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.656A pdb=" N ASN A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.942A pdb=" N TYR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.598A pdb=" N VAL B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.885A pdb=" N TYR B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 Processing helix chain 'B' and resid 502 through 508 Processing helix chain 'C' and resid 80 through 92 removed outlier: 3.589A pdb=" N VAL C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.887A pdb=" N TYR C 168 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 502 through 508 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 53 removed outlier: 3.937A pdb=" N ASN A 116 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 149 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 126 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR A 128 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR A 145 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 130 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL A 143 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LYS A 132 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG A 141 " --> pdb=" O LYS A 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 138 through 157 current: chain 'A' and resid 181 through 185 removed outlier: 5.981A pdb=" N PHE A 181 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 removed outlier: 6.026A pdb=" N ARG A 141 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LYS A 132 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL A 143 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 130 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR A 145 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR A 128 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE A 126 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 149 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN A 116 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA4, first strand: chain 'A' and resid 57 through 64 removed outlier: 3.536A pdb=" N ILE A 103 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 293 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 103 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE C 293 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 103 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 293 " --> pdb=" O GLN B 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 262 removed outlier: 5.170A pdb=" N ILE A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN A 322 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN A 328 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A 313 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP A 223 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS A 315 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 262 removed outlier: 5.170A pdb=" N ILE A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN A 322 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN A 328 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A 313 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP A 223 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS A 315 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 216 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 222 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLU A 369 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 23.617A pdb=" N GLU A 370 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 18.805A pdb=" N THR A 459 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 11.809A pdb=" N VAL A 372 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N TYR A 457 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 374 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE A 431 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 430 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN A 381 " --> pdb=" O TYR A 407 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU A 409 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLN A 383 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 233 through 239 Processing sheet with id=AA8, first strand: chain 'A' and resid 392 through 396 removed outlier: 5.171A pdb=" N ALA A 422 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER A 468 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N SER A 511 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU A 540 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASN A 513 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N THR A 542 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 609 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN A 563 " --> pdb=" O THR A 611 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A 568 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN A 585 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ARG A 570 " --> pdb=" O ILE A 583 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE A 583 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 442 through 443 removed outlier: 6.078A pdb=" N ARG C 141 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYS C 132 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL C 143 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 130 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TYR C 145 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR C 128 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE C 126 " --> pdb=" O PRO C 147 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 149 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN C 116 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 49 through 53 removed outlier: 4.030A pdb=" N ASN C 116 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 149 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE C 126 " --> pdb=" O PRO C 147 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR C 128 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TYR C 145 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 130 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL C 143 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LYS C 132 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG C 141 " --> pdb=" O LYS C 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 138 through 157 current: chain 'C' and resid 181 through 185 removed outlier: 5.984A pdb=" N PHE C 181 " --> pdb=" O THR C 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 529 removed outlier: 4.337A pdb=" N LYS A 619 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 554 through 556 Processing sheet with id=AB4, first strand: chain 'B' and resid 49 through 53 removed outlier: 7.052A pdb=" N ASN B 116 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU B 156 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR B 118 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 154 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR B 120 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL B 152 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY B 150 " --> pdb=" O GLN B 122 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR B 124 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 140 " --> pdb=" O LYS B 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 138 through 157 current: chain 'B' and resid 181 through 186 removed outlier: 5.973A pdb=" N PHE B 181 " --> pdb=" O THR B 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 72 through 74 removed outlier: 3.751A pdb=" N GLU B 140 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR B 124 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY B 150 " --> pdb=" O GLN B 122 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL B 152 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N TYR B 120 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 154 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR B 118 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU B 156 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN B 116 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB7, first strand: chain 'B' and resid 233 through 239 removed outlier: 6.071A pdb=" N LEU B 233 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN B 311 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 11.459A pdb=" N ALA B 309 " --> pdb=" O ARG B 227 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N ARG B 227 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN B 311 " --> pdb=" O TYR B 225 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR B 225 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 313 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP B 223 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS B 315 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 259 through 262 removed outlier: 5.158A pdb=" N ILE B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN B 322 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN B 328 " --> pdb=" O ASP B 320 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR B 312 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY B 338 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR B 310 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS B 340 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 308 " --> pdb=" O CYS B 340 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL B 342 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N CYS B 306 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 11.459A pdb=" N ALA B 309 " --> pdb=" O ARG B 227 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N ARG B 227 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN B 311 " --> pdb=" O TYR B 225 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR B 225 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 313 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP B 223 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS B 315 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 216 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N VAL B 372 " --> pdb=" O TYR B 457 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR B 457 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 374 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE B 431 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 430 " --> pdb=" O ARG B 483 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN B 381 " --> pdb=" O TYR B 407 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 409 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN B 383 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 392 through 396 removed outlier: 4.709A pdb=" N ILE B 417 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N SER B 511 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLU B 540 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN B 513 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N THR B 542 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE B 515 " --> pdb=" O THR B 542 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN B 563 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 525 through 529 removed outlier: 4.381A pdb=" N LYS B 619 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 558 " --> pdb=" O HIS B 621 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AC3, first strand: chain 'C' and resid 259 through 262 removed outlier: 5.177A pdb=" N ILE C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN C 322 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN C 328 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR C 313 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP C 223 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS C 315 " --> pdb=" O LYS C 221 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 262 removed outlier: 5.177A pdb=" N ILE C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN C 322 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN C 328 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR C 313 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASP C 223 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS C 315 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C 216 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY C 222 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU C 369 " --> pdb=" O GLY C 222 " (cutoff:3.500A) removed outlier: 23.601A pdb=" N GLU C 370 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 18.802A pdb=" N THR C 459 " --> pdb=" O GLU C 370 " (cutoff:3.500A) removed outlier: 11.807A pdb=" N VAL C 372 " --> pdb=" O TYR C 457 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR C 457 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 374 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N TYR C 457 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU C 433 " --> pdb=" O TYR C 457 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR C 459 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN C 381 " --> pdb=" O TYR C 407 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU C 409 " --> pdb=" O ASN C 381 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN C 383 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 233 through 239 removed outlier: 3.507A pdb=" N GLY C 235 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 392 through 396 removed outlier: 5.164A pdb=" N ALA C 422 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER C 468 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER C 511 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU C 540 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASN C 513 " --> pdb=" O GLU C 540 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N THR C 542 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE C 603 " --> pdb=" O VAL C 571 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 392 through 396 removed outlier: 5.164A pdb=" N ALA C 422 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER C 468 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER C 511 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU C 540 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASN C 513 " --> pdb=" O GLU C 540 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N THR C 542 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 609 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN C 563 " --> pdb=" O THR C 611 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 525 through 529 removed outlier: 4.378A pdb=" N LYS C 619 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 560 " --> pdb=" O LYS C 619 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR C 558 " --> pdb=" O HIS C 621 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 553 through 555 551 hydrogen bonds defined for protein. 1455 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: 2.44 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3086 1.32 - 1.45: 2869 1.45 - 1.58: 7692 1.58 - 1.70: 2 1.70 - 1.83: 24 Bond restraints: 13673 Sorted by residual: bond pdb=" CA GLN B 45 " pdb=" C GLN B 45 " ideal model delta sigma weight residual 1.527 1.607 -0.080 1.32e-02 5.74e+03 3.66e+01 bond pdb=" C ASN A 87 " pdb=" O ASN A 87 " ideal model delta sigma weight residual 1.237 1.303 -0.066 1.19e-02 7.06e+03 3.09e+01 bond pdb=" N ILE B 46 " pdb=" CA ILE B 46 " ideal model delta sigma weight residual 1.459 1.502 -0.043 9.10e-03 1.21e+04 2.22e+01 bond pdb=" N GLY B 150 " pdb=" CA GLY B 150 " ideal model delta sigma weight residual 1.442 1.472 -0.030 7.70e-03 1.69e+04 1.50e+01 bond pdb=" CA ASN B 68 " pdb=" C ASN B 68 " ideal model delta sigma weight residual 1.524 1.608 -0.084 2.25e-02 1.98e+03 1.41e+01 ... (remaining 13668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 18117 2.67 - 5.35: 458 5.35 - 8.02: 11 8.02 - 10.70: 3 10.70 - 13.37: 2 Bond angle restraints: 18591 Sorted by residual: angle pdb=" N ILE B 46 " pdb=" CA ILE B 46 " pdb=" C ILE B 46 " ideal model delta sigma weight residual 113.47 100.10 13.37 1.01e+00 9.80e-01 1.75e+02 angle pdb=" N ALA B 69 " pdb=" CA ALA B 69 " pdb=" CB ALA B 69 " ideal model delta sigma weight residual 110.95 122.69 -11.74 1.44e+00 4.82e-01 6.65e+01 angle pdb=" N ILE B 46 " pdb=" CA ILE B 46 " pdb=" CB ILE B 46 " ideal model delta sigma weight residual 112.33 120.52 -8.19 1.19e+00 7.06e-01 4.74e+01 angle pdb=" N ASP B 67 " pdb=" CA ASP B 67 " pdb=" C ASP B 67 " ideal model delta sigma weight residual 111.36 118.26 -6.90 1.09e+00 8.42e-01 4.00e+01 angle pdb=" N ASN C 493 " pdb=" CA ASN C 493 " pdb=" CB ASN C 493 " ideal model delta sigma weight residual 110.46 119.45 -8.99 1.55e+00 4.16e-01 3.36e+01 ... (remaining 18586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7173 17.71 - 35.42: 782 35.42 - 53.12: 150 53.12 - 70.83: 39 70.83 - 88.54: 13 Dihedral angle restraints: 8157 sinusoidal: 3162 harmonic: 4995 Sorted by residual: dihedral pdb=" CD ARG B 64 " pdb=" NE ARG B 64 " pdb=" CZ ARG B 64 " pdb=" NH1 ARG B 64 " ideal model delta sinusoidal sigma weight residual 0.00 48.71 -48.71 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" N ALA B 69 " pdb=" C ALA B 69 " pdb=" CA ALA B 69 " pdb=" CB ALA B 69 " ideal model delta harmonic sigma weight residual 122.90 134.75 -11.85 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" CA ASN B 588 " pdb=" C ASN B 588 " pdb=" N LEU B 589 " pdb=" CA LEU B 589 " ideal model delta harmonic sigma weight residual -180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 8154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1503 0.086 - 0.173: 588 0.173 - 0.259: 20 0.259 - 0.345: 5 0.345 - 0.432: 3 Chirality restraints: 2119 Sorted by residual: chirality pdb=" CA GLN B 45 " pdb=" N GLN B 45 " pdb=" C GLN B 45 " pdb=" CB GLN B 45 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA ASN B 68 " pdb=" N ASN B 68 " pdb=" C ASN B 68 " pdb=" CB ASN B 68 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CA ASN B 44 " pdb=" N ASN B 44 " pdb=" C ASN B 44 " pdb=" CB ASN B 44 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 2116 not shown) Planarity restraints: 2407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 64 " -0.821 9.50e-02 1.11e+02 3.68e-01 8.23e+01 pdb=" NE ARG B 64 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG B 64 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 64 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 64 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 45 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C GLN B 45 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN B 45 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE B 46 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 395 " 0.030 2.00e-02 2.50e+03 2.13e-02 9.09e+00 pdb=" CG TYR B 395 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 395 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 395 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 395 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 395 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 395 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR B 395 " 0.006 2.00e-02 2.50e+03 ... (remaining 2404 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 107 2.56 - 3.14: 9793 3.14 - 3.73: 20005 3.73 - 4.31: 30864 4.31 - 4.90: 50806 Nonbonded interactions: 111575 Sorted by model distance: nonbonded pdb=" OG SER C 463 " pdb=" OD1 ASN C 465 " model vdw 1.973 3.040 nonbonded pdb=" OD1 ASN C 402 " pdb=" ND2 ASN C 403 " model vdw 2.076 3.120 nonbonded pdb=" OG1 THR B 312 " pdb=" O LEU B 337 " model vdw 2.107 3.040 nonbonded pdb=" OD1 ASN B 493 " pdb=" N GLN B 494 " model vdw 2.126 3.120 nonbonded pdb=" OG SER C 244 " pdb=" OE1 GLU C 298 " model vdw 2.172 3.040 ... (remaining 111570 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 139 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or resid 141 through 463 or resid 465 through 489 or \ (resid 490 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 1 or (resid 492 and (name N or name CA or name C or name O or name CB )) or resi \ d 493 through 519 or resid 524 through 544 or resid 552 through 553 or (resid 55 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 555 or (resi \ d 556 and (name N or name CA or name C or name O or name CB )) or resid 557 thro \ ugh 584 or (resid 585 and (name N or name CA or name C or name O or name CB )) o \ r resid 586 through 596 or resid 599 through 621)) selection = (chain 'B' and (resid 22 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 134 or (resid 135 and (name N o \ r name CA or name C or name O or name CB )) or resid 136 through 139 or (resid 1 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 141 through \ 160 or (resid 161 through 162 and (name N or name CA or name C or name O or nam \ e CB )) or resid 163 through 164 or (resid 165 through 166 and (name N or name C \ A or name C or name O or name CB )) or resid 167 through 177 or (resid 178 and ( \ name N or name CA or name C or name O or name CB )) or resid 179 through 187 or \ (resid 208 and (name N or name CA or name C or name O or name CB )) or resid 209 \ through 252 or (resid 253 and (name N or name CA or name C or name O or name CB \ )) or resid 254 through 270 or (resid 271 and (name N or name CA or name C or n \ ame O or name CB )) or resid 272 through 301 or (resid 302 and (name N or name C \ A or name C or name O or name CB )) or resid 303 through 322 or (resid 323 and ( \ name N or name CA or name C or name O or name CB )) or resid 324 through 348 or \ (resid 349 and (name N or name CA or name C or name O or name CB )) or resid 350 \ through 390 or (resid 391 and (name N or name CA or name C or name O or name CB \ )) or resid 392 through 396 or (resid 397 and (name N or name CA or name C or n \ ame O or name CB )) or resid 398 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 or (resid 402 through 403 and (name N or na \ me CA or name C or name O or name CB )) or resid 404 through 422 or (resid 423 t \ hrough 424 and (name N or name CA or name C or name O or name CB )) or resid 425 \ through 432 or (resid 433 through 434 and (name N or name CA or name C or name \ O or name CB )) or resid 435 through 442 or (resid 443 and (name N or name CA or \ name C or name O or name CB )) or resid 444 through 448 or (resid 449 through 4 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 452 through \ 463 or (resid 465 through 466 and (name N or name CA or name C or name O or nam \ e CB )) or resid 467 through 476 or (resid 477 and (name N or name CA or name C \ or name O or name CB )) or resid 478 through 533 or (resid 534 and (name N or na \ me CA or name C or name O or name CB )) or resid 535 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 or (resid 5 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 557 through \ 562 or (resid 563 and (name N or name CA or name C or name O or name CB )) or r \ esid 564 through 571 or (resid 578 through 579 and (name N or name CA or name C \ or name O or name CB )) or resid 580 through 611 or (resid 612 and (name N or na \ me CA or name C or name O or name CB )) or resid 613 through 618 or (resid 619 a \ nd (name N or name CA or name C or name O or name CB )) or resid 620 through 621 \ )) selection = (chain 'C' and (resid 22 through 114 or (resid 115 and (name N or name CA or nam \ e C or name O or name CB )) or resid 116 through 134 or (resid 135 and (name N o \ r name CA or name C or name O or name CB )) or resid 136 through 160 or (resid 1 \ 61 through 162 and (name N or name CA or name C or name O or name CB )) or resid \ 163 through 165 or (resid 166 and (name N or name CA or name C or name O or nam \ e CB )) or resid 167 through 177 or (resid 178 and (name N or name CA or name C \ or name O or name CB )) or resid 179 through 252 or (resid 253 and (name N or na \ me CA or name C or name O or name CB )) or resid 254 through 266 or (resid 267 a \ nd (name N or name CA or name C or name O or name CB )) or resid 268 through 270 \ or (resid 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 301 or (resid 302 and (name N or name CA or name C or name O or nam \ e CB )) or resid 303 through 322 or (resid 323 and (name N or name CA or name C \ or name O or name CB )) or resid 324 through 348 or (resid 349 and (name N or na \ me CA or name C or name O or name CB )) or resid 350 through 358 or (resid 359 a \ nd (name N or name CA or name C or name O or name CB )) or resid 360 through 390 \ or (resid 391 and (name N or name CA or name C or name O or name CB )) or resid \ 392 through 396 or (resid 397 and (name N or name CA or name C or name O or nam \ e CB )) or resid 398 or (resid 400 and (name N or name CA or name C or name O or \ name CB )) or resid 401 or (resid 402 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or resid 404 through 422 or (resid 423 through 424 a \ nd (name N or name CA or name C or name O or name CB )) or resid 425 through 432 \ or (resid 433 through 434 and (name N or name CA or name C or name O or name CB \ )) or resid 435 through 442 or (resid 443 and (name N or name CA or name C or n \ ame O or name CB )) or resid 444 through 448 or (resid 449 through 451 and (name \ N or name CA or name C or name O or name CB )) or resid 452 through 463 or (res \ id 465 through 466 and (name N or name CA or name C or name O or name CB )) or r \ esid 467 through 476 or (resid 477 and (name N or name CA or name C or name O or \ name CB )) or resid 478 through 491 or (resid 492 and (name N or name CA or nam \ e C or name O or name CB )) or resid 493 through 569 or (resid 570 and (name N o \ r name CA or name C or name O or name CB )) or resid 571 or (resid 578 through 5 \ 79 and (name N or name CA or name C or name O or name CB )) or resid 580 through \ 584 or (resid 585 and (name N or name CA or name C or name O or name CB )) or r \ esid 586 through 596 or resid 599 through 611 or (resid 612 and (name N or name \ CA or name C or name O or name CB )) or resid 613 through 618 or (resid 619 and \ (name N or name CA or name C or name O or name CB )) or resid 620 through 621)) } 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.150 Find NCS groups from input model: 0.220 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.012 0.084 13673 Z= 0.867 Angle : 1.167 13.373 18591 Z= 0.799 Chirality : 0.078 0.432 2119 Planarity : 0.010 0.368 2407 Dihedral : 15.478 88.538 4959 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.81 % Allowed : 18.27 % Favored : 80.92 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.20), residues: 1645 helix: 1.66 (0.63), residues: 77 sheet: 0.25 (0.18), residues: 717 loop : -1.03 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.003 ARG B 257 TYR 0.048 0.006 TYR B 395 PHE 0.029 0.006 PHE A 169 TRP 0.016 0.005 TRP C 38 HIS 0.011 0.003 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.01209 (13673) covalent geometry : angle 1.16651 (18591) hydrogen bonds : bond 0.22035 ( 460) hydrogen bonds : angle 9.43772 ( 1455) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 556 ARG cc_start: 0.7250 (ttt180) cc_final: 0.5253 (pmt170) REVERT: C 584 GLN cc_start: 0.7597 (mm110) cc_final: 0.7248 (mm110) outliers start: 12 outliers final: 1 residues processed: 148 average time/residue: 0.3569 time to fit residues: 60.9646 Evaluate side-chains 90 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 413 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN B 614 ASN C 271 GLN C 424 ASN C 582 ASN C 584 GLN C 617 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.132896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.111871 restraints weight = 22032.377| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.34 r_work: 0.3641 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13673 Z= 0.134 Angle : 0.543 8.652 18591 Z= 0.302 Chirality : 0.047 0.153 2119 Planarity : 0.003 0.036 2407 Dihedral : 4.702 46.054 1848 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.71 % Allowed : 17.93 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.19), residues: 1645 helix: 1.93 (0.59), residues: 78 sheet: 0.44 (0.18), residues: 713 loop : -1.00 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 127 TYR 0.013 0.001 TYR C 120 PHE 0.024 0.002 PHE C 497 TRP 0.003 0.001 TRP A 38 HIS 0.001 0.000 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00294 (13673) covalent geometry : angle 0.54324 (18591) hydrogen bonds : bond 0.04263 ( 460) hydrogen bonds : angle 6.43251 ( 1455) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.395 Fit side-chains REVERT: A 246 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8820 (t) REVERT: A 586 ASN cc_start: 0.8289 (m-40) cc_final: 0.7579 (t0) REVERT: B 166 ASP cc_start: 0.7616 (t0) cc_final: 0.7334 (t0) REVERT: B 403 ASN cc_start: 0.8169 (m-40) cc_final: 0.7948 (m110) REVERT: C 161 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: C 246 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8730 (t) outliers start: 40 outliers final: 12 residues processed: 127 average time/residue: 0.2731 time to fit residues: 41.3345 Evaluate side-chains 98 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 487 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 115 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 554 ASN A 614 ASN A 617 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN C 45 GLN C 180 GLN C 402 ASN C 465 ASN C 584 GLN C 585 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.123344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102047 restraints weight = 22612.867| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.36 r_work: 0.3493 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 13673 Z= 0.336 Angle : 0.679 7.894 18591 Z= 0.374 Chirality : 0.051 0.197 2119 Planarity : 0.004 0.042 2407 Dihedral : 5.311 24.777 1846 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.40 % Allowed : 17.52 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.49 (0.19), residues: 1645 helix: 1.45 (0.57), residues: 78 sheet: 0.42 (0.18), residues: 694 loop : -1.14 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 141 TYR 0.022 0.002 TYR B 120 PHE 0.019 0.002 PHE C 497 TRP 0.003 0.002 TRP B 38 HIS 0.002 0.001 HIS C 621 Details of bonding type rmsd covalent geometry : bond 0.00793 (13673) covalent geometry : angle 0.67916 (18591) hydrogen bonds : bond 0.04923 ( 460) hydrogen bonds : angle 6.41534 ( 1455) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 69 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 360 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8277 (p0) REVERT: A 492 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7189 (tp30) REVERT: A 586 ASN cc_start: 0.8153 (m-40) cc_final: 0.7611 (t0) REVERT: B 166 ASP cc_start: 0.7825 (t0) cc_final: 0.7504 (t0) REVERT: B 403 ASN cc_start: 0.8221 (m-40) cc_final: 0.7924 (m110) REVERT: B 447 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8658 (tp) REVERT: B 462 ASP cc_start: 0.7548 (t0) cc_final: 0.7286 (m-30) REVERT: B 584 GLN cc_start: 0.7548 (mm-40) cc_final: 0.7249 (mp10) outliers start: 65 outliers final: 28 residues processed: 125 average time/residue: 0.3066 time to fit residues: 44.7928 Evaluate side-chains 96 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 533 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 7 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN C 465 ASN C 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.126656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.105493 restraints weight = 22260.961| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.37 r_work: 0.3546 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13673 Z= 0.141 Angle : 0.523 7.504 18591 Z= 0.294 Chirality : 0.047 0.164 2119 Planarity : 0.003 0.037 2407 Dihedral : 4.912 21.128 1846 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.91 % Allowed : 19.22 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.19), residues: 1645 helix: 1.32 (0.56), residues: 78 sheet: 0.46 (0.18), residues: 711 loop : -1.08 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 597 TYR 0.019 0.001 TYR B 561 PHE 0.018 0.002 PHE C 497 TRP 0.003 0.001 TRP A 38 HIS 0.001 0.000 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00324 (13673) covalent geometry : angle 0.52299 (18591) hydrogen bonds : bond 0.03589 ( 460) hydrogen bonds : angle 5.94062 ( 1455) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 72 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 586 ASN cc_start: 0.8167 (m-40) cc_final: 0.7532 (t0) REVERT: B 50 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8417 (m) REVERT: B 166 ASP cc_start: 0.7796 (t0) cc_final: 0.7501 (t0) REVERT: B 424 ASN cc_start: 0.8030 (t0) cc_final: 0.7346 (t0) REVERT: B 462 ASP cc_start: 0.7366 (t0) cc_final: 0.7068 (m-30) REVERT: B 584 GLN cc_start: 0.7428 (mm-40) cc_final: 0.6893 (mp10) REVERT: C 413 ASN cc_start: 0.9255 (OUTLIER) cc_final: 0.8913 (m-40) outliers start: 43 outliers final: 19 residues processed: 109 average time/residue: 0.2945 time to fit residues: 37.6109 Evaluate side-chains 86 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 467 LYS Chi-restraints excluded: chain C residue 583 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN C 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.125662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.104538 restraints weight = 22321.645| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.36 r_work: 0.3533 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13673 Z= 0.174 Angle : 0.541 8.640 18591 Z= 0.299 Chirality : 0.047 0.183 2119 Planarity : 0.003 0.036 2407 Dihedral : 4.888 20.781 1846 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.79 % Allowed : 18.88 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.19), residues: 1645 helix: 1.22 (0.55), residues: 78 sheet: 0.41 (0.18), residues: 731 loop : -1.05 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 597 TYR 0.016 0.001 TYR B 120 PHE 0.016 0.002 PHE C 497 TRP 0.002 0.001 TRP A 38 HIS 0.001 0.000 HIS C 621 Details of bonding type rmsd covalent geometry : bond 0.00407 (13673) covalent geometry : angle 0.54053 (18591) hydrogen bonds : bond 0.03633 ( 460) hydrogen bonds : angle 5.81404 ( 1455) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 67 time to evaluate : 0.537 Fit side-chains REVERT: A 100 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: A 404 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7795 (m110) REVERT: A 584 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6984 (pm20) REVERT: B 50 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8280 (m) REVERT: B 166 ASP cc_start: 0.7820 (t0) cc_final: 0.7507 (t0) REVERT: B 298 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: B 424 ASN cc_start: 0.8085 (t0) cc_final: 0.7681 (t0) REVERT: B 584 GLN cc_start: 0.7446 (mm-40) cc_final: 0.7158 (mp10) REVERT: C 135 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8449 (mp10) REVERT: C 253 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7788 (mtt180) REVERT: C 593 THR cc_start: 0.8697 (p) cc_final: 0.8483 (t) REVERT: C 598 LEU cc_start: 0.8011 (mm) cc_final: 0.7609 (mm) outliers start: 56 outliers final: 21 residues processed: 116 average time/residue: 0.3271 time to fit residues: 43.8727 Evaluate side-chains 89 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 467 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 ASN C 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.127266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106269 restraints weight = 22185.993| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.36 r_work: 0.3560 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13673 Z= 0.126 Angle : 0.497 7.172 18591 Z= 0.277 Chirality : 0.046 0.173 2119 Planarity : 0.003 0.036 2407 Dihedral : 4.701 18.626 1846 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.91 % Allowed : 19.96 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.19), residues: 1645 helix: 1.19 (0.55), residues: 78 sheet: 0.46 (0.17), residues: 738 loop : -0.96 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 440 TYR 0.018 0.001 TYR B 561 PHE 0.015 0.001 PHE C 497 TRP 0.002 0.001 TRP A 38 HIS 0.001 0.000 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00289 (13673) covalent geometry : angle 0.49725 (18591) hydrogen bonds : bond 0.03228 ( 460) hydrogen bonds : angle 5.61216 ( 1455) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 66 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: B 166 ASP cc_start: 0.7795 (t0) cc_final: 0.7481 (t0) REVERT: B 424 ASN cc_start: 0.8110 (t0) cc_final: 0.7741 (t0) REVERT: B 462 ASP cc_start: 0.7581 (t0) cc_final: 0.7330 (m-30) REVERT: B 584 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7097 (mp10) REVERT: C 246 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8797 (t) REVERT: C 492 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7423 (tp30) REVERT: C 593 THR cc_start: 0.8698 (p) cc_final: 0.8459 (t) REVERT: C 598 LEU cc_start: 0.8005 (mm) cc_final: 0.7703 (mm) outliers start: 43 outliers final: 23 residues processed: 101 average time/residue: 0.3319 time to fit residues: 38.9270 Evaluate side-chains 89 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 467 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 74 optimal weight: 0.6980 chunk 2 optimal weight: 0.0370 chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 0.0370 chunk 42 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 ASN C 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.129298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.108431 restraints weight = 22187.120| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.35 r_work: 0.3596 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13673 Z= 0.092 Angle : 0.470 6.045 18591 Z= 0.262 Chirality : 0.045 0.146 2119 Planarity : 0.003 0.034 2407 Dihedral : 4.474 18.186 1846 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.37 % Allowed : 20.16 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.19), residues: 1645 helix: 1.19 (0.55), residues: 78 sheet: 0.52 (0.18), residues: 729 loop : -0.87 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 597 TYR 0.013 0.001 TYR A 310 PHE 0.016 0.001 PHE C 569 TRP 0.002 0.000 TRP A 38 HIS 0.001 0.000 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00198 (13673) covalent geometry : angle 0.47037 (18591) hydrogen bonds : bond 0.02883 ( 460) hydrogen bonds : angle 5.40108 ( 1455) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.340 Fit side-chains REVERT: A 100 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: A 246 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8810 (t) REVERT: B 50 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8299 (m) REVERT: B 166 ASP cc_start: 0.7733 (t0) cc_final: 0.7405 (t0) REVERT: B 424 ASN cc_start: 0.8077 (t0) cc_final: 0.7661 (t0) REVERT: B 462 ASP cc_start: 0.7390 (t0) cc_final: 0.7136 (m-30) REVERT: B 584 GLN cc_start: 0.7284 (mm-40) cc_final: 0.6998 (mp10) REVERT: C 246 SER cc_start: 0.8986 (OUTLIER) cc_final: 0.8773 (t) REVERT: C 253 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7772 (mtt180) REVERT: C 492 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7440 (tp30) REVERT: C 593 THR cc_start: 0.8719 (p) cc_final: 0.8476 (t) REVERT: C 598 LEU cc_start: 0.7899 (mm) cc_final: 0.7652 (mm) outliers start: 35 outliers final: 10 residues processed: 100 average time/residue: 0.3407 time to fit residues: 39.6471 Evaluate side-chains 82 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 253 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 116 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 141 optimal weight: 0.0770 chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.123963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102873 restraints weight = 22399.204| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.33 r_work: 0.3506 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13673 Z= 0.264 Angle : 0.604 6.975 18591 Z= 0.333 Chirality : 0.049 0.227 2119 Planarity : 0.004 0.036 2407 Dihedral : 5.094 21.417 1846 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.25 % Allowed : 19.49 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.19), residues: 1645 helix: 1.23 (0.56), residues: 78 sheet: 0.45 (0.18), residues: 721 loop : -1.00 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 141 TYR 0.022 0.002 TYR B 120 PHE 0.017 0.002 PHE C 497 TRP 0.003 0.001 TRP B 38 HIS 0.002 0.000 HIS C 621 Details of bonding type rmsd covalent geometry : bond 0.00625 (13673) covalent geometry : angle 0.60423 (18591) hydrogen bonds : bond 0.04019 ( 460) hydrogen bonds : angle 5.85878 ( 1455) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 67 time to evaluate : 0.477 Fit side-chains REVERT: A 100 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7582 (mt0) REVERT: A 130 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8637 (mm) REVERT: A 593 THR cc_start: 0.8854 (p) cc_final: 0.8584 (t) REVERT: B 166 ASP cc_start: 0.7876 (t0) cc_final: 0.7551 (t0) REVERT: B 424 ASN cc_start: 0.8132 (t0) cc_final: 0.7763 (t0) REVERT: B 584 GLN cc_start: 0.7445 (mm-40) cc_final: 0.7179 (mp10) REVERT: C 135 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8533 (mp10) REVERT: C 253 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7849 (mtt180) REVERT: C 359 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8076 (mm-30) REVERT: C 413 ASN cc_start: 0.9258 (OUTLIER) cc_final: 0.8953 (m-40) REVERT: C 584 GLN cc_start: 0.7269 (mm110) cc_final: 0.6880 (mp10) REVERT: C 598 LEU cc_start: 0.7900 (mm) cc_final: 0.7611 (mm) outliers start: 48 outliers final: 19 residues processed: 109 average time/residue: 0.3159 time to fit residues: 40.5514 Evaluate side-chains 86 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 581 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN C 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.126685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.105729 restraints weight = 22161.515| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.35 r_work: 0.3551 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13673 Z= 0.133 Angle : 0.515 9.607 18591 Z= 0.285 Chirality : 0.046 0.215 2119 Planarity : 0.003 0.035 2407 Dihedral : 4.778 19.001 1846 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.17 % Allowed : 20.70 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.19), residues: 1645 helix: 1.21 (0.55), residues: 78 sheet: 0.45 (0.18), residues: 724 loop : -0.93 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.017 0.001 TYR C 432 PHE 0.015 0.001 PHE C 569 TRP 0.002 0.001 TRP A 38 HIS 0.001 0.000 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00305 (13673) covalent geometry : angle 0.51484 (18591) hydrogen bonds : bond 0.03251 ( 460) hydrogen bonds : angle 5.59134 ( 1455) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 100 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: A 237 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 593 THR cc_start: 0.8854 (p) cc_final: 0.8577 (t) REVERT: B 50 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8298 (m) REVERT: B 166 ASP cc_start: 0.7820 (t0) cc_final: 0.7471 (t0) REVERT: B 424 ASN cc_start: 0.8067 (t0) cc_final: 0.7705 (t0) REVERT: B 584 GLN cc_start: 0.7349 (mm-40) cc_final: 0.7084 (mp10) REVERT: C 246 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8804 (t) REVERT: C 359 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8054 (mm-30) REVERT: C 413 ASN cc_start: 0.9275 (OUTLIER) cc_final: 0.9005 (m-40) REVERT: C 492 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7285 (tp30) REVERT: C 598 LEU cc_start: 0.7961 (mm) cc_final: 0.7629 (mm) outliers start: 32 outliers final: 18 residues processed: 95 average time/residue: 0.3054 time to fit residues: 34.2975 Evaluate side-chains 87 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 583 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 77 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 157 optimal weight: 0.0570 chunk 30 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.125387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.104381 restraints weight = 22198.400| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.35 r_work: 0.3530 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13673 Z= 0.185 Angle : 0.552 9.275 18591 Z= 0.303 Chirality : 0.047 0.206 2119 Planarity : 0.003 0.035 2407 Dihedral : 4.888 19.966 1846 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.89 % Allowed : 20.91 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.19), residues: 1645 helix: 1.20 (0.55), residues: 78 sheet: 0.42 (0.18), residues: 725 loop : -0.93 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 34 TYR 0.020 0.002 TYR B 561 PHE 0.016 0.002 PHE C 497 TRP 0.002 0.001 TRP A 38 HIS 0.001 0.000 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00436 (13673) covalent geometry : angle 0.55236 (18591) hydrogen bonds : bond 0.03539 ( 460) hydrogen bonds : angle 5.65086 ( 1455) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.544 Fit side-chains REVERT: A 100 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: A 119 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8531 (ptt) REVERT: A 237 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 593 THR cc_start: 0.8879 (p) cc_final: 0.8584 (t) REVERT: B 50 SER cc_start: 0.8582 (OUTLIER) cc_final: 0.8299 (m) REVERT: B 166 ASP cc_start: 0.7860 (t0) cc_final: 0.7521 (t0) REVERT: B 424 ASN cc_start: 0.8118 (t0) cc_final: 0.7751 (t0) REVERT: B 584 GLN cc_start: 0.7378 (mm-40) cc_final: 0.7120 (mp10) REVERT: C 253 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7797 (mtt180) REVERT: C 359 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8022 (mm-30) REVERT: C 413 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.8998 (m-40) REVERT: C 492 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7365 (tp30) REVERT: C 584 GLN cc_start: 0.7196 (mm110) cc_final: 0.6793 (mm110) REVERT: C 598 LEU cc_start: 0.7916 (mm) cc_final: 0.7667 (mm) outliers start: 28 outliers final: 16 residues processed: 91 average time/residue: 0.2932 time to fit residues: 31.9084 Evaluate side-chains 88 residues out of total 1538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 413 ASN Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 146 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 116 optimal weight: 0.0060 chunk 48 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.127086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106171 restraints weight = 22335.944| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.36 r_work: 0.3558 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13673 Z= 0.127 Angle : 0.506 8.672 18591 Z= 0.279 Chirality : 0.046 0.195 2119 Planarity : 0.003 0.035 2407 Dihedral : 4.683 18.655 1846 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.10 % Allowed : 20.70 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.19), residues: 1645 helix: 1.18 (0.55), residues: 78 sheet: 0.44 (0.17), residues: 738 loop : -0.86 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 127 TYR 0.017 0.001 TYR C 432 PHE 0.015 0.001 PHE C 569 TRP 0.001 0.001 TRP A 38 HIS 0.001 0.000 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00293 (13673) covalent geometry : angle 0.50600 (18591) hydrogen bonds : bond 0.03143 ( 460) hydrogen bonds : angle 5.47923 ( 1455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4347.22 seconds wall clock time: 74 minutes 54.28 seconds (4494.28 seconds total)