Starting phenix.real_space_refine on Sat Jul 4 03:54:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ipt_35643/07_2026/8ipt_35643.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ipt_35643/07_2026/8ipt_35643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ipt_35643/07_2026/8ipt_35643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ipt_35643/07_2026/8ipt_35643.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ipt_35643/07_2026/8ipt_35643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ipt_35643/07_2026/8ipt_35643.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ipt_35643/07_2026/8ipt_35643.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ipt_35643/07_2026/8ipt_35643.cif" } resolution = 3.5 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= 0.003 sd= 0.056 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 11618 2.51 5 N 3198 2.21 5 O 3290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18178 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "A" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4594 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "D" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "E" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4594 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.15 Number of scatterers: 18178 At special positions: 0 Unit cell: (90.24, 106.56, 229.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 12 15.00 O 3290 8.00 N 3198 7.00 C 11618 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: 1.47 Conformation dependent library (CDL) restraints added in 561.9 milliseconds 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 10 sheets defined 64.6% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'C' and resid 1 through 3 No H-bonds generated for 'chain 'C' and resid 1 through 3' Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 14 through 49 removed outlier: 3.570A pdb=" N GLY C 21 " --> pdb=" O MET C 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 60 through 104 removed outlier: 3.660A pdb=" N GLY C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 125 removed outlier: 4.215A pdb=" N LEU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 138 through 156 Processing helix chain 'C' and resid 159 through 207 removed outlier: 3.716A pdb=" N ALA C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 4.614A pdb=" N ARG C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 219 through 266 removed outlier: 4.010A pdb=" N GLN C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.510A pdb=" N ALA C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 294 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 removed outlier: 3.874A pdb=" N ALA C 300 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 removed outlier: 3.931A pdb=" N VAL C 307 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 386 removed outlier: 3.688A pdb=" N LEU C 382 " --> pdb=" O GLY C 378 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.523A pdb=" N ARG C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.691A pdb=" N VAL C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 487 Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 566 through 572 removed outlier: 3.942A pdb=" N LYS C 570 " --> pdb=" O TYR C 566 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 572 " --> pdb=" O GLN C 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 566 through 572' Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.962A pdb=" N GLN A 16 " --> pdb=" O TRP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 55 removed outlier: 3.820A pdb=" N ILE A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 55 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 removed outlier: 3.515A pdb=" N ALA A 61 " --> pdb=" O PRO A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 62 through 110 removed outlier: 4.360A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.504A pdb=" N ILE A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 115' Processing helix chain 'A' and resid 118 through 132 removed outlier: 3.785A pdb=" N GLN A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 139 through 159 removed outlier: 4.458A pdb=" N ALA A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 162 through 173 removed outlier: 3.943A pdb=" N ALA A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 4.380A pdb=" N LEU A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.836A pdb=" N ARG A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.680A pdb=" N LEU A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 273 removed outlier: 3.595A pdb=" N ARG A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 328 removed outlier: 3.570A pdb=" N GLY A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Proline residue: A 298 - end of helix Proline residue: A 303 - end of helix removed outlier: 4.079A pdb=" N HIS A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 398 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.681A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 416 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.651A pdb=" N VAL A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.797A pdb=" N GLN A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.557A pdb=" N LEU A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 500 removed outlier: 3.834A pdb=" N GLN A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 533 Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 575 through 588 removed outlier: 3.516A pdb=" N ILE A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 3 No H-bonds generated for 'chain 'D' and resid 1 through 3' Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 14 through 49 removed outlier: 3.570A pdb=" N GLY D 21 " --> pdb=" O MET D 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 60 through 104 removed outlier: 3.660A pdb=" N GLY D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 removed outlier: 4.215A pdb=" N LEU D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN D 121 " --> pdb=" O GLY D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 136 Processing helix chain 'D' and resid 138 through 156 Processing helix chain 'D' and resid 159 through 207 removed outlier: 3.716A pdb=" N ALA D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.614A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 207 " --> pdb=" O LEU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 266 removed outlier: 4.010A pdb=" N GLN D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.510A pdb=" N ALA D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 303 removed outlier: 3.874A pdb=" N ALA D 300 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS D 303 " --> pdb=" O GLY D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.931A pdb=" N VAL D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 3.688A pdb=" N LEU D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 removed outlier: 3.523A pdb=" N ARG D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 435 Processing helix chain 'D' and resid 444 through 453 removed outlier: 3.692A pdb=" N VAL D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 487 Processing helix chain 'D' and resid 506 through 521 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 566 through 572 removed outlier: 3.941A pdb=" N LYS D 570 " --> pdb=" O TYR D 566 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN D 571 " --> pdb=" O TYR D 567 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 572 " --> pdb=" O GLN D 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 566 through 572' Processing helix chain 'E' and resid 2 through 16 removed outlier: 3.962A pdb=" N GLN E 16 " --> pdb=" O TRP E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 55 removed outlier: 3.821A pdb=" N ILE E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU E 55 " --> pdb=" O HIS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 61 removed outlier: 3.515A pdb=" N ALA E 61 " --> pdb=" O PRO E 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 58 through 61' Processing helix chain 'E' and resid 62 through 110 removed outlier: 4.361A pdb=" N PHE E 66 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 removed outlier: 3.503A pdb=" N ILE E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 110 through 115' Processing helix chain 'E' and resid 118 through 132 removed outlier: 3.785A pdb=" N GLN E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 139 Processing helix chain 'E' and resid 139 through 159 removed outlier: 4.459A pdb=" N ALA E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL E 148 " --> pdb=" O MET E 144 " (cutoff:3.500A) Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 162 through 173 removed outlier: 3.943A pdb=" N ALA E 166 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.380A pdb=" N LEU E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 211 removed outlier: 3.835A pdb=" N ARG E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY E 211 " --> pdb=" O ASP E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 219 removed outlier: 3.680A pdb=" N LEU E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 273 removed outlier: 3.595A pdb=" N ARG E 238 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR E 272 " --> pdb=" O PHE E 268 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU E 273 " --> pdb=" O GLY E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 328 removed outlier: 3.570A pdb=" N GLY E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) Proline residue: E 298 - end of helix Proline residue: E 303 - end of helix removed outlier: 4.079A pdb=" N HIS E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA E 313 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER E 323 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU E 324 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 398 Processing helix chain 'E' and resid 412 through 416 removed outlier: 3.681A pdb=" N ASP E 415 " --> pdb=" O GLU E 412 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU E 416 " --> pdb=" O LEU E 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 412 through 416' Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 423 through 425 No H-bonds generated for 'chain 'E' and resid 423 through 425' Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.650A pdb=" N VAL E 443 " --> pdb=" O LEU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 461 removed outlier: 3.796A pdb=" N GLN E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 471 removed outlier: 3.557A pdb=" N LEU E 471 " --> pdb=" O LEU E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 500 removed outlier: 3.834A pdb=" N GLN E 492 " --> pdb=" O VAL E 488 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG E 493 " --> pdb=" O GLY E 489 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL E 494 " --> pdb=" O GLN E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 533 Processing helix chain 'E' and resid 566 through 571 Processing helix chain 'E' and resid 575 through 588 removed outlier: 3.516A pdb=" N ILE E 588 " --> pdb=" O ARG E 584 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 361 through 363 removed outlier: 3.645A pdb=" N THR C 340 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 342 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU C 396 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL C 344 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN C 394 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 417 through 419 removed outlier: 3.655A pdb=" N LEU C 527 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 498 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS C 368 " --> pdb=" O GLN C 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE C 542 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA C 370 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL C 544 " --> pdb=" O ALA C 370 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 372 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 541 " --> pdb=" O GLU C 552 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLU C 552 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE C 543 " --> pdb=" O ILE C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 369 through 372 removed outlier: 5.646A pdb=" N LEU A 369 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.612A pdb=" N VAL A 380 " --> pdb=" O TRP A 554 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N MET A 556 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL A 382 " --> pdb=" O MET A 556 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 563 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN A 557 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ILE A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 509 removed outlier: 6.591A pdb=" N LEU A 507 " --> pdb=" O LEU A 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 361 through 363 removed outlier: 3.645A pdb=" N THR D 340 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 342 " --> pdb=" O GLU D 396 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU D 396 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL D 344 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN D 394 " --> pdb=" O VAL D 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 417 through 419 removed outlier: 3.656A pdb=" N LEU D 527 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 498 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE D 369 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS D 368 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE D 542 " --> pdb=" O HIS D 368 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA D 370 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL D 544 " --> pdb=" O ALA D 370 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 372 " --> pdb=" O VAL D 544 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN D 541 " --> pdb=" O GLU D 552 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU D 552 " --> pdb=" O GLN D 541 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE D 543 " --> pdb=" O ILE D 550 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 369 through 372 removed outlier: 5.646A pdb=" N LEU E 369 " --> pdb=" O ASP E 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 380 through 382 removed outlier: 6.611A pdb=" N VAL E 380 " --> pdb=" O TRP E 554 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N MET E 556 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL E 382 " --> pdb=" O MET E 556 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU E 563 " --> pdb=" O VAL E 555 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN E 557 " --> pdb=" O ILE E 561 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ILE E 561 " --> pdb=" O GLN E 557 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 507 through 509 removed outlier: 6.592A pdb=" N LEU E 507 " --> pdb=" O LEU E 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 960 hydrogen bonds defined for protein. 2844 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5322 1.34 - 1.45: 2719 1.45 - 1.57: 10367 1.57 - 1.69: 20 1.69 - 1.81: 114 Bond restraints: 18542 Sorted by residual: bond pdb=" N PHE E 159 " pdb=" CA PHE E 159 " ideal model delta sigma weight residual 1.462 1.489 -0.027 8.50e-03 1.38e+04 1.02e+01 bond pdb=" N ILE A 158 " pdb=" CA ILE A 158 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.58e+00 bond pdb=" N ILE A 357 " pdb=" CA ILE A 357 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.37e+00 bond pdb=" N ILE E 357 " pdb=" CA ILE E 357 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 8.06e+00 bond pdb=" N ILE E 158 " pdb=" CA ILE E 158 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.33e-02 5.65e+03 7.47e+00 ... (remaining 18537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 24704 2.00 - 3.99: 391 3.99 - 5.99: 100 5.99 - 7.99: 15 7.99 - 9.98: 6 Bond angle restraints: 25216 Sorted by residual: angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 129.89 9.98 1.00e+00 1.00e+00 9.96e+01 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 129.90 9.97 1.00e+00 1.00e+00 9.95e+01 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 130.25 9.62 1.00e+00 1.00e+00 9.26e+01 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 130.26 9.61 1.00e+00 1.00e+00 9.23e+01 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 129.59 7.24 1.00e+00 1.00e+00 5.24e+01 ... (remaining 25211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 9223 17.88 - 35.76: 1387 35.76 - 53.64: 321 53.64 - 71.52: 45 71.52 - 89.40: 36 Dihedral angle restraints: 11012 sinusoidal: 4350 harmonic: 6662 Sorted by residual: dihedral pdb=" CA ASN C 58 " pdb=" C ASN C 58 " pdb=" N TYR C 59 " pdb=" CA TYR C 59 " ideal model delta harmonic sigma weight residual -180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN D 58 " pdb=" C ASN D 58 " pdb=" N TYR D 59 " pdb=" CA TYR D 59 " ideal model delta harmonic sigma weight residual -180.00 -158.67 -21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PHE C 57 " pdb=" C PHE C 57 " pdb=" N ASN C 58 " pdb=" CA ASN C 58 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 11009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2139 0.038 - 0.076: 613 0.076 - 0.114: 147 0.114 - 0.152: 23 0.152 - 0.190: 6 Chirality restraints: 2928 Sorted by residual: chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA ILE E 357 " pdb=" N ILE E 357 " pdb=" C ILE E 357 " pdb=" CB ILE E 357 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA ILE A 158 " pdb=" N ILE A 158 " pdb=" C ILE A 158 " pdb=" CB ILE A 158 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 2925 not shown) Planarity restraints: 3206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 273 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ASN D 273 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN D 273 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA D 274 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 273 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C ASN C 273 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN C 273 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA C 274 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO E 151 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.025 5.00e-02 4.00e+02 ... (remaining 3203 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1371 2.74 - 3.28: 18002 3.28 - 3.82: 28524 3.82 - 4.36: 31212 4.36 - 4.90: 56484 Nonbonded interactions: 135593 Sorted by model distance: nonbonded pdb=" NE2 GLN C 553 " pdb=" CG2 THR C 555 " model vdw 2.200 3.540 nonbonded pdb=" NE2 GLN D 553 " pdb=" CG2 THR D 555 " model vdw 2.200 3.540 nonbonded pdb=" NH2 ARG A 99 " pdb=" OD1 ASP A 131 " model vdw 2.269 3.120 nonbonded pdb=" NH2 ARG E 99 " pdb=" OD1 ASP E 131 " model vdw 2.269 3.120 nonbonded pdb=" CG2 THR C 555 " pdb=" OE1 GLU C 558 " model vdw 2.295 3.460 ... (remaining 135588 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'E' } 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 group one per residue 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: 2.430 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.710 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 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 : 0.003 0.042 18542 Z= 0.181 Angle : 0.672 9.982 25216 Z= 0.383 Chirality : 0.039 0.190 2928 Planarity : 0.004 0.045 3206 Dihedral : 17.954 89.402 6716 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.95 % Favored : 91.88 % Rotamer: Outliers : 0.32 % Allowed : 31.97 % Favored : 67.71 % 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: -0.06 (0.19), residues: 2314 helix: 1.91 (0.15), residues: 1294 sheet: -1.68 (0.50), residues: 108 loop : -2.93 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 220 TYR 0.012 0.001 TYR A 88 PHE 0.012 0.001 PHE C 145 TRP 0.011 0.001 TRP E 550 HIS 0.004 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.18 (18542) covalent geometry : angle 0.67189 / 0.38 (25216) hydrogen bonds : bond 0.14672 / 9.52 ( 960) hydrogen bonds : angle 5.45333 / 3.86 ( 2844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8344 (mmm) cc_final: 0.8115 (mtp) REVERT: E 159 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8086 (t80) outliers start: 6 outliers final: 2 residues processed: 265 average time/residue: 0.1653 time to fit residues: 63.9426 Evaluate side-chains 153 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 416 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN A 394 ASN ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.126685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094631 restraints weight = 34717.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.097404 restraints weight = 18309.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099295 restraints weight = 11816.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100511 restraints weight = 8817.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.101309 restraints weight = 7242.418| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18542 Z= 0.186 Angle : 0.648 9.208 25216 Z= 0.333 Chirality : 0.042 0.202 2928 Planarity : 0.005 0.078 3206 Dihedral : 5.185 57.522 2548 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.38 % Favored : 90.54 % Rotamer: Outliers : 3.87 % Allowed : 30.17 % Favored : 65.96 % 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: -0.09 (0.19), residues: 2314 helix: 1.87 (0.15), residues: 1336 sheet: -1.54 (0.52), residues: 108 loop : -3.18 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 374 TYR 0.015 0.001 TYR C 7 PHE 0.012 0.001 PHE A 278 TRP 0.019 0.001 TRP A 550 HIS 0.008 0.001 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (18542) covalent geometry : angle 0.64827 / 0.33 (25216) hydrogen bonds : bond 0.07885 / 5.29 ( 960) hydrogen bonds : angle 4.31535 / 3.09 ( 2844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 162 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: C 80 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7644 (tm-30) REVERT: C 301 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: C 541 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7443 (mm-40) REVERT: C 567 TYR cc_start: 0.7559 (t80) cc_final: 0.7231 (t80) REVERT: A 240 MET cc_start: 0.7663 (mmm) cc_final: 0.7449 (mtp) REVERT: A 361 GLU cc_start: 0.7768 (tt0) cc_final: 0.6728 (pp20) REVERT: A 525 MET cc_start: 0.8412 (mmt) cc_final: 0.8125 (mmm) REVERT: A 529 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8145 (m-40) REVERT: A 556 MET cc_start: 0.7376 (ttt) cc_final: 0.6070 (tmm) REVERT: E 54 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7061 (mtm) REVERT: E 344 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7107 (mt) outliers start: 73 outliers final: 36 residues processed: 225 average time/residue: 0.1439 time to fit residues: 49.5744 Evaluate side-chains 170 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 510 ASP Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 12 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 144 optimal weight: 0.1980 chunk 163 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 302 GLN C 547 ASN A 394 ASN A 461 ASN A 543 GLN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.129128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.097516 restraints weight = 34903.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100367 restraints weight = 18176.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102277 restraints weight = 11658.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.103550 restraints weight = 8637.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104272 restraints weight = 7084.487| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18542 Z= 0.136 Angle : 0.575 8.838 25216 Z= 0.293 Chirality : 0.039 0.175 2928 Planarity : 0.004 0.050 3206 Dihedral : 4.861 57.521 2544 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.43 % Favored : 91.49 % Rotamer: Outliers : 3.92 % Allowed : 30.06 % Favored : 66.01 % 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: 0.19 (0.19), residues: 2314 helix: 2.13 (0.15), residues: 1334 sheet: -1.56 (0.51), residues: 108 loop : -3.08 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 584 TYR 0.012 0.001 TYR C 7 PHE 0.012 0.001 PHE C 57 TRP 0.010 0.001 TRP A 550 HIS 0.003 0.001 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (18542) covalent geometry : angle 0.57461 / 0.29 (25216) hydrogen bonds : bond 0.06887 / 4.62 ( 960) hydrogen bonds : angle 4.02620 / 2.89 ( 2844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 143 time to evaluate : 0.665 Fit side-chains REVERT: C 80 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7510 (tm-30) REVERT: C 301 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: C 407 LEU cc_start: 0.8787 (mt) cc_final: 0.8488 (mt) REVERT: C 434 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7299 (tt) REVERT: C 567 TYR cc_start: 0.7617 (t80) cc_final: 0.7348 (t80) REVERT: A 16 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.6401 (mp10) REVERT: A 240 MET cc_start: 0.7598 (mmm) cc_final: 0.7329 (mtp) REVERT: A 361 GLU cc_start: 0.7748 (tt0) cc_final: 0.6720 (pp20) REVERT: A 456 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8147 (mp10) REVERT: A 533 LEU cc_start: 0.8360 (mm) cc_final: 0.8092 (mm) REVERT: A 539 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7085 (ttp) REVERT: A 556 MET cc_start: 0.7625 (ttt) cc_final: 0.6228 (tmm) outliers start: 74 outliers final: 42 residues processed: 207 average time/residue: 0.1361 time to fit residues: 44.2178 Evaluate side-chains 179 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 532 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 19 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 55 optimal weight: 30.0000 chunk 226 optimal weight: 6.9990 chunk 216 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 151 optimal weight: 0.0270 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 547 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.130297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099026 restraints weight = 34788.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.101907 restraints weight = 17980.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103841 restraints weight = 11470.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.105168 restraints weight = 8442.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.105964 restraints weight = 6861.286| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18542 Z= 0.127 Angle : 0.558 9.606 25216 Z= 0.281 Chirality : 0.038 0.137 2928 Planarity : 0.004 0.046 3206 Dihedral : 4.599 56.413 2544 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.73 % Favored : 91.18 % Rotamer: Outliers : 4.35 % Allowed : 29.43 % Favored : 66.22 % 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: 2314 helix: 2.31 (0.15), residues: 1326 sheet: -1.47 (0.51), residues: 108 loop : -3.11 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 220 TYR 0.013 0.001 TYR E 88 PHE 0.012 0.001 PHE D 57 TRP 0.008 0.001 TRP E 427 HIS 0.005 0.000 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (18542) covalent geometry : angle 0.55806 / 0.28 (25216) hydrogen bonds : bond 0.06276 / 4.21 ( 960) hydrogen bonds : angle 3.83499 / 2.75 ( 2844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 151 time to evaluate : 0.740 Fit side-chains REVERT: C 80 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7455 (tm-30) REVERT: C 407 LEU cc_start: 0.8804 (mt) cc_final: 0.8514 (mt) REVERT: C 434 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7318 (tt) REVERT: C 524 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.6045 (mmtp) REVERT: C 567 TYR cc_start: 0.7601 (t80) cc_final: 0.7353 (t80) REVERT: A 16 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.6407 (mp10) REVERT: A 240 MET cc_start: 0.7539 (mmm) cc_final: 0.7252 (mtp) REVERT: A 361 GLU cc_start: 0.7788 (tt0) cc_final: 0.6764 (pp20) REVERT: A 456 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8146 (mp10) REVERT: A 525 MET cc_start: 0.8946 (mmm) cc_final: 0.8577 (mmt) REVERT: A 533 LEU cc_start: 0.8360 (mm) cc_final: 0.8027 (mm) REVERT: A 539 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7215 (mtp) REVERT: A 550 TRP cc_start: 0.6053 (m100) cc_final: 0.5571 (m100) REVERT: A 556 MET cc_start: 0.7618 (ttt) cc_final: 0.6325 (tmm) REVERT: E 384 ARG cc_start: 0.7829 (tpp80) cc_final: 0.7572 (mtp85) outliers start: 82 outliers final: 49 residues processed: 221 average time/residue: 0.1416 time to fit residues: 48.7923 Evaluate side-chains 185 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 66 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 229 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 190 GLN C 547 ASN A 394 ASN D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.129625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.098586 restraints weight = 34669.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101446 restraints weight = 17993.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103392 restraints weight = 11480.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.104497 restraints weight = 8454.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.105412 restraints weight = 6966.358| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18542 Z= 0.128 Angle : 0.553 9.786 25216 Z= 0.281 Chirality : 0.038 0.136 2928 Planarity : 0.004 0.044 3206 Dihedral : 4.451 49.958 2544 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.30 % Favored : 91.62 % Rotamer: Outliers : 4.24 % Allowed : 29.85 % Favored : 65.91 % 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: 0.38 (0.19), residues: 2314 helix: 2.27 (0.15), residues: 1342 sheet: -1.35 (0.52), residues: 108 loop : -3.06 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 220 TYR 0.013 0.001 TYR E 88 PHE 0.017 0.001 PHE D 145 TRP 0.011 0.001 TRP A 550 HIS 0.002 0.000 HIS E 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (18542) covalent geometry : angle 0.55319 / 0.28 (25216) hydrogen bonds : bond 0.06301 / 4.23 ( 960) hydrogen bonds : angle 3.78001 / 2.72 ( 2844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 137 time to evaluate : 0.877 Fit side-chains REVERT: C 80 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 407 LEU cc_start: 0.8796 (mt) cc_final: 0.8498 (mt) REVERT: C 430 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7993 (tt) REVERT: C 434 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7323 (tt) REVERT: C 524 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5870 (mmtp) REVERT: C 567 TYR cc_start: 0.7617 (t80) cc_final: 0.7403 (t80) REVERT: A 16 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.6225 (mp10) REVERT: A 240 MET cc_start: 0.7534 (mmm) cc_final: 0.7252 (mtp) REVERT: A 361 GLU cc_start: 0.7818 (tt0) cc_final: 0.6768 (pp20) REVERT: A 456 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8154 (mp10) REVERT: A 533 LEU cc_start: 0.8375 (mm) cc_final: 0.8081 (mm) REVERT: A 539 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7114 (mtp) REVERT: A 550 TRP cc_start: 0.6179 (m100) cc_final: 0.5921 (m100) REVERT: A 556 MET cc_start: 0.7682 (ttt) cc_final: 0.6402 (tmm) REVERT: A 558 ASP cc_start: 0.7223 (t70) cc_final: 0.6823 (t70) outliers start: 80 outliers final: 54 residues processed: 208 average time/residue: 0.1323 time to fit residues: 43.5724 Evaluate side-chains 187 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 0.0870 chunk 85 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.128754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.097650 restraints weight = 34593.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100500 restraints weight = 18035.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102434 restraints weight = 11510.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.103664 restraints weight = 8517.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104516 restraints weight = 6995.629| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18542 Z= 0.130 Angle : 0.559 14.395 25216 Z= 0.281 Chirality : 0.039 0.154 2928 Planarity : 0.004 0.042 3206 Dihedral : 4.292 44.716 2544 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.47 % Favored : 91.44 % Rotamer: Outliers : 4.72 % Allowed : 29.53 % Favored : 65.75 % 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: 0.43 (0.19), residues: 2314 helix: 2.33 (0.15), residues: 1328 sheet: -1.40 (0.50), residues: 114 loop : -2.99 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 220 TYR 0.012 0.001 TYR E 88 PHE 0.015 0.001 PHE D 145 TRP 0.012 0.001 TRP A 550 HIS 0.003 0.001 HIS E 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (18542) covalent geometry : angle 0.55868 / 0.28 (25216) hydrogen bonds : bond 0.06408 / 4.30 ( 960) hydrogen bonds : angle 3.75442 / 2.70 ( 2844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 141 time to evaluate : 0.716 Fit side-chains REVERT: C 80 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7537 (tt0) REVERT: C 172 LEU cc_start: 0.7658 (mm) cc_final: 0.7396 (mp) REVERT: C 407 LEU cc_start: 0.8758 (mt) cc_final: 0.8453 (mt) REVERT: C 430 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8040 (tt) REVERT: C 434 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7284 (tt) REVERT: C 524 LYS cc_start: 0.6111 (OUTLIER) cc_final: 0.5781 (mmtp) REVERT: A 16 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.6255 (mp10) REVERT: A 240 MET cc_start: 0.7540 (mmm) cc_final: 0.7266 (mtp) REVERT: A 456 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8141 (mp10) REVERT: A 482 GLN cc_start: 0.7590 (mp10) cc_final: 0.7284 (mp10) REVERT: A 525 MET cc_start: 0.8834 (mmm) cc_final: 0.8448 (mmt) REVERT: A 533 LEU cc_start: 0.8357 (mm) cc_final: 0.8059 (mm) REVERT: A 539 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7129 (mtp) REVERT: A 556 MET cc_start: 0.7699 (ttt) cc_final: 0.6467 (tmm) REVERT: A 558 ASP cc_start: 0.7292 (t70) cc_final: 0.6955 (t70) outliers start: 89 outliers final: 58 residues processed: 219 average time/residue: 0.1368 time to fit residues: 46.7462 Evaluate side-chains 194 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 131 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 43 optimal weight: 8.9990 chunk 100 optimal weight: 0.4980 chunk 175 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.125107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093382 restraints weight = 34991.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096152 restraints weight = 18539.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097975 restraints weight = 12007.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.099231 restraints weight = 8977.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099952 restraints weight = 7390.416| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18542 Z= 0.168 Angle : 0.594 12.339 25216 Z= 0.303 Chirality : 0.040 0.142 2928 Planarity : 0.004 0.045 3206 Dihedral : 4.339 44.095 2544 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.56 % Favored : 91.36 % Rotamer: Outliers : 4.61 % Allowed : 29.64 % Favored : 65.75 % 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: 0.28 (0.19), residues: 2314 helix: 2.18 (0.15), residues: 1326 sheet: -1.34 (0.49), residues: 114 loop : -3.00 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 220 TYR 0.019 0.001 TYR C 567 PHE 0.014 0.001 PHE D 145 TRP 0.020 0.001 TRP E 427 HIS 0.004 0.001 HIS E 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (18542) covalent geometry : angle 0.59390 / 0.30 (25216) hydrogen bonds : bond 0.07533 / 5.06 ( 960) hydrogen bonds : angle 3.98311 / 2.87 ( 2844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 129 time to evaluate : 0.695 Fit side-chains REVERT: C 80 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7623 (tt0) REVERT: C 172 LEU cc_start: 0.7709 (mm) cc_final: 0.7338 (mt) REVERT: C 407 LEU cc_start: 0.8779 (mt) cc_final: 0.8490 (mt) REVERT: C 430 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8122 (tt) REVERT: C 434 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7268 (tt) REVERT: C 524 LYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5778 (mmtp) REVERT: A 16 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.6142 (mp10) REVERT: A 207 ASP cc_start: 0.8400 (t0) cc_final: 0.8168 (t0) REVERT: A 240 MET cc_start: 0.7642 (mmm) cc_final: 0.7304 (mtp) REVERT: A 456 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8155 (mp10) REVERT: A 533 LEU cc_start: 0.8426 (mm) cc_final: 0.8134 (mm) REVERT: A 556 MET cc_start: 0.7710 (ttt) cc_final: 0.6430 (tmm) REVERT: A 558 ASP cc_start: 0.7367 (t70) cc_final: 0.6990 (t70) REVERT: D 60 MET cc_start: 0.8267 (tpp) cc_final: 0.8034 (tmm) REVERT: D 301 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8076 (t80) REVERT: D 417 SER cc_start: 0.7989 (OUTLIER) cc_final: 0.7785 (p) outliers start: 87 outliers final: 60 residues processed: 205 average time/residue: 0.1338 time to fit residues: 43.4961 Evaluate side-chains 188 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 122 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 553 GLN Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 542 HIS Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 154 optimal weight: 0.0970 chunk 217 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.126084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.094636 restraints weight = 34746.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.097384 restraints weight = 18442.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.099218 restraints weight = 11975.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100484 restraints weight = 8946.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101155 restraints weight = 7370.794| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18542 Z= 0.144 Angle : 0.574 14.709 25216 Z= 0.291 Chirality : 0.039 0.142 2928 Planarity : 0.004 0.045 3206 Dihedral : 4.308 46.007 2544 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.43 % Favored : 91.49 % Rotamer: Outliers : 3.87 % Allowed : 30.28 % Favored : 65.85 % 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: 2314 helix: 2.20 (0.15), residues: 1332 sheet: -1.26 (0.49), residues: 114 loop : -2.98 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 220 TYR 0.019 0.001 TYR C 567 PHE 0.014 0.001 PHE D 145 TRP 0.016 0.001 TRP E 427 HIS 0.005 0.001 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (18542) covalent geometry : angle 0.57414 / 0.29 (25216) hydrogen bonds : bond 0.07131 / 4.79 ( 960) hydrogen bonds : angle 3.89886 / 2.81 ( 2844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 130 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: C 80 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7631 (tt0) REVERT: C 172 LEU cc_start: 0.7720 (mm) cc_final: 0.7420 (mp) REVERT: C 407 LEU cc_start: 0.8791 (mt) cc_final: 0.8505 (mt) REVERT: C 430 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8165 (tt) REVERT: C 434 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7301 (tt) REVERT: C 524 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5770 (mmtp) REVERT: A 16 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.6172 (mp10) REVERT: A 207 ASP cc_start: 0.8467 (t0) cc_final: 0.8215 (t0) REVERT: A 240 MET cc_start: 0.7588 (mmm) cc_final: 0.7285 (mtp) REVERT: A 456 GLN cc_start: 0.8874 (mm-40) cc_final: 0.7921 (pt0) REVERT: A 533 LEU cc_start: 0.8418 (mm) cc_final: 0.8123 (mm) REVERT: A 556 MET cc_start: 0.7702 (ttt) cc_final: 0.6439 (tmm) REVERT: A 558 ASP cc_start: 0.7245 (t70) cc_final: 0.6871 (t70) REVERT: D 301 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8030 (t80) REVERT: D 417 SER cc_start: 0.7920 (OUTLIER) cc_final: 0.7710 (p) outliers start: 73 outliers final: 60 residues processed: 194 average time/residue: 0.1391 time to fit residues: 42.3354 Evaluate side-chains 194 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 128 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 553 GLN Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 542 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 26 optimal weight: 7.9990 chunk 173 optimal weight: 0.1980 chunk 113 optimal weight: 7.9990 chunk 29 optimal weight: 0.0270 chunk 223 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 178 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.129119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.098184 restraints weight = 34692.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101032 restraints weight = 18101.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.102924 restraints weight = 11590.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.104001 restraints weight = 8607.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.104898 restraints weight = 7135.589| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 18542 Z= 0.125 Angle : 0.569 15.143 25216 Z= 0.284 Chirality : 0.038 0.183 2928 Planarity : 0.004 0.045 3206 Dihedral : 4.205 49.963 2544 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.30 % Favored : 91.62 % Rotamer: Outliers : 3.39 % Allowed : 30.65 % Favored : 65.96 % 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: 0.47 (0.19), residues: 2314 helix: 2.39 (0.15), residues: 1330 sheet: -1.21 (0.49), residues: 114 loop : -3.04 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 220 TYR 0.015 0.001 TYR A 88 PHE 0.014 0.001 PHE D 145 TRP 0.015 0.001 TRP E 427 HIS 0.003 0.000 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (18542) covalent geometry : angle 0.56914 / 0.28 (25216) hydrogen bonds : bond 0.06171 / 4.14 ( 960) hydrogen bonds : angle 3.73018 / 2.68 ( 2844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 133 time to evaluate : 0.712 Fit side-chains REVERT: C 80 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7593 (tt0) REVERT: C 407 LEU cc_start: 0.8771 (mt) cc_final: 0.8478 (mt) REVERT: C 430 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8106 (tt) REVERT: C 524 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5848 (mmtp) REVERT: A 16 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6213 (mp10) REVERT: A 207 ASP cc_start: 0.8419 (t0) cc_final: 0.8145 (t0) REVERT: A 456 GLN cc_start: 0.8863 (mm-40) cc_final: 0.7912 (pt0) REVERT: A 533 LEU cc_start: 0.8356 (mm) cc_final: 0.8065 (mm) REVERT: A 556 MET cc_start: 0.7688 (ttt) cc_final: 0.6443 (tmm) REVERT: A 558 ASP cc_start: 0.7189 (t70) cc_final: 0.6800 (t70) REVERT: D 301 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7957 (t80) REVERT: D 417 SER cc_start: 0.7771 (OUTLIER) cc_final: 0.7551 (p) REVERT: E 220 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.8199 (mmp80) REVERT: E 384 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7601 (mmm160) outliers start: 64 outliers final: 49 residues processed: 191 average time/residue: 0.1390 time to fit residues: 41.6087 Evaluate side-chains 184 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 553 GLN Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 55 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 63 optimal weight: 0.0000 chunk 58 optimal weight: 0.6980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 302 GLN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.130604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.100013 restraints weight = 34686.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.102888 restraints weight = 17979.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.104812 restraints weight = 11469.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.106060 restraints weight = 8480.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.106843 restraints weight = 6930.777| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18542 Z= 0.120 Angle : 0.565 15.802 25216 Z= 0.279 Chirality : 0.038 0.140 2928 Planarity : 0.003 0.039 3206 Dihedral : 4.070 49.846 2544 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.91 % Favored : 92.01 % Rotamer: Outliers : 2.86 % Allowed : 31.18 % Favored : 65.96 % 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: 0.55 (0.19), residues: 2314 helix: 2.44 (0.15), residues: 1332 sheet: -1.07 (0.49), residues: 114 loop : -3.02 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 220 TYR 0.019 0.001 TYR C 567 PHE 0.013 0.001 PHE D 145 TRP 0.022 0.001 TRP E 427 HIS 0.003 0.000 HIS A 542 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (18542) covalent geometry : angle 0.56498 / 0.28 (25216) hydrogen bonds : bond 0.05754 / 3.86 ( 960) hydrogen bonds : angle 3.63206 / 2.61 ( 2844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 128 time to evaluate : 0.744 Fit side-chains REVERT: C 80 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7544 (tt0) REVERT: C 407 LEU cc_start: 0.8809 (mt) cc_final: 0.8518 (mt) REVERT: C 524 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5634 (mmtp) REVERT: A 16 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6250 (mp10) REVERT: A 207 ASP cc_start: 0.8403 (t0) cc_final: 0.8111 (t0) REVERT: A 533 LEU cc_start: 0.8322 (mm) cc_final: 0.8044 (mm) REVERT: A 556 MET cc_start: 0.7696 (ttt) cc_final: 0.6488 (tmm) REVERT: A 558 ASP cc_start: 0.7160 (t70) cc_final: 0.6796 (t70) REVERT: D 97 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8485 (mp) REVERT: D 301 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7937 (t80) REVERT: D 417 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.7522 (p) REVERT: E 384 ARG cc_start: 0.7952 (mmm160) cc_final: 0.7552 (mmm160) outliers start: 54 outliers final: 45 residues processed: 175 average time/residue: 0.1404 time to fit residues: 38.3493 Evaluate side-chains 174 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 553 GLN Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 49 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 189 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 85 optimal weight: 0.0980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 202 GLN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.124213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.092419 restraints weight = 34852.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.095143 restraints weight = 18585.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096964 restraints weight = 12143.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.098183 restraints weight = 9095.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.098897 restraints weight = 7522.602| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18542 Z= 0.177 Angle : 0.626 15.006 25216 Z= 0.314 Chirality : 0.041 0.139 2928 Planarity : 0.004 0.041 3206 Dihedral : 4.312 45.569 2544 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.03 % Favored : 90.88 % Rotamer: Outliers : 3.29 % Allowed : 31.07 % Favored : 65.64 % 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: 0.19 (0.19), residues: 2314 helix: 2.07 (0.15), residues: 1340 sheet: -1.13 (0.49), residues: 114 loop : -3.09 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 220 TYR 0.015 0.001 TYR E 88 PHE 0.013 0.001 PHE C 89 TRP 0.028 0.001 TRP E 427 HIS 0.005 0.001 HIS E 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (18542) covalent geometry : angle 0.62572 / 0.31 (25216) hydrogen bonds : bond 0.07815 / 5.25 ( 960) hydrogen bonds : angle 4.00490 / 2.89 ( 2844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3193.60 seconds wall clock time: 56 minutes 2.43 seconds (3362.43 seconds total)