Starting phenix.real_space_refine on Thu Jul 2 14:31:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bg4_12170/07_2026/7bg4_12170.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bg4_12170/07_2026/7bg4_12170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bg4_12170/07_2026/7bg4_12170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bg4_12170/07_2026/7bg4_12170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bg4_12170/07_2026/7bg4_12170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bg4_12170/07_2026/7bg4_12170.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bg4_12170/07_2026/7bg4_12170.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bg4_12170/07_2026/7bg4_12170.cif" } resolution = 4.2 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= 0.010 sd= 0.058 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 5724 2.51 5 N 1483 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 8927 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4405 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Chain breaks: 1 Chain: "B" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4392 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 17, 'TRANS': 551} Chain breaks: 1 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {' MG': 1, 'ATP': 2, 'RHQ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {' MG': 1, 'RHQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.70, per 1000 atoms: 0.19 Number of scatterers: 8927 At special positions: 0 Unit cell: (75.26, 90.1, 137.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 6 15.00 Mg 2 11.99 O 1677 8.00 N 1483 7.00 C 5724 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 203.2 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 4 sheets defined 66.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.527A pdb=" N PHE A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 28 through 56 Proline residue: A 47 - end of helix removed outlier: 4.183A pdb=" N LYS A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.785A pdb=" N THR A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 107 removed outlier: 3.507A pdb=" N ALA A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.921A pdb=" N PHE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.694A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 124' Processing helix chain 'A' and resid 124 through 157 removed outlier: 3.716A pdb=" N THR A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A 136 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ILE A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 166 through 171 removed outlier: 4.102A pdb=" N LEU A 169 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU A 171 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 208 removed outlier: 3.785A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 183 - end of helix removed outlier: 4.315A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 267 removed outlier: 3.768A pdb=" N ALA A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLY A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix removed outlier: 3.854A pdb=" N LEU A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.867A pdb=" N VAL A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 313 removed outlier: 3.575A pdb=" N PHE A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 320 removed outlier: 4.178A pdb=" N GLU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 removed outlier: 3.816A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 444 through 455 removed outlier: 4.182A pdb=" N GLU A 449 " --> pdb=" O ASP A 445 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.526A pdb=" N PHE A 460 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 495 removed outlier: 3.829A pdb=" N ARG A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 removed outlier: 3.778A pdb=" N SER A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 522 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.780A pdb=" N VAL A 541 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.894A pdb=" N ALA A 565 " --> pdb=" O HIS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 4.401A pdb=" N MET A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 4.381A pdb=" N ASN A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 582 through 587' Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.504A pdb=" N PHE B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 58 removed outlier: 3.934A pdb=" N LEU B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA B 30 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N PHE B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.866A pdb=" N GLN B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 79 removed outlier: 4.453A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.621A pdb=" N LYS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.626A pdb=" N THR B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 4.558A pdb=" N SER B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 131 through 140 removed outlier: 3.599A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU B 136 " --> pdb=" O MET B 132 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 159 removed outlier: 3.517A pdb=" N ILE B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 208 removed outlier: 4.149A pdb=" N VAL B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Proline residue: B 175 - end of helix Proline residue: B 183 - end of helix removed outlier: 3.561A pdb=" N ARG B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 220 through 234 removed outlier: 3.878A pdb=" N TYR B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 241 through 268 removed outlier: 3.659A pdb=" N VAL B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLY B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Proline residue: B 252 - end of helix removed outlier: 3.500A pdb=" N LEU B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 removed outlier: 3.713A pdb=" N GLN B 272 " --> pdb=" O GLY B 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 272' Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 293 through 320 removed outlier: 3.629A pdb=" N GLY B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N MET B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 432 through 437 removed outlier: 4.461A pdb=" N TYR B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 456 through 461 removed outlier: 5.656A pdb=" N ASN B 459 " --> pdb=" O TYR B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 495 removed outlier: 3.567A pdb=" N ARG B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 removed outlier: 4.115A pdb=" N SER B 516 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.978A pdb=" N VAL B 541 " --> pdb=" O SER B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 567 removed outlier: 4.224A pdb=" N ALA B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 582 removed outlier: 3.979A pdb=" N GLN B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B 580 " --> pdb=" O GLN B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364 removed outlier: 5.158A pdb=" N VAL A 360 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU A 343 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG A 399 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ARG A 345 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR A 397 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 6.298A pdb=" N THR A 370 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 371 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL A 549 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 364 removed outlier: 5.093A pdb=" N VAL B 360 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 362 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL B 346 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA B 395 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 500 through 502 removed outlier: 5.867A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1239 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: 0.96 Time building geometry restraints manager: 0.79 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: 2855 1.34 - 1.46: 1370 1.46 - 1.58: 4764 1.58 - 1.69: 10 1.69 - 1.81: 68 Bond restraints: 9067 Sorted by residual: bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.43e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.84e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.35e+01 bond pdb=" C5 ATP A 602 " pdb=" C6 ATP A 602 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.21e+01 bond pdb=" C11 RHQ A 604 " pdb=" N1 RHQ A 604 " ideal model delta sigma weight residual 1.437 1.332 0.105 2.00e-02 2.50e+03 2.75e+01 ... (remaining 9062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 12185 4.22 - 8.45: 92 8.45 - 12.67: 5 12.67 - 16.89: 2 16.89 - 21.12: 2 Bond angle restraints: 12286 Sorted by residual: angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 118.75 21.12 1.00e+00 1.00e+00 4.46e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.05 17.82 1.00e+00 1.00e+00 3.17e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 120.08 16.75 1.00e+00 1.00e+00 2.80e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 122.43 14.40 1.00e+00 1.00e+00 2.07e+02 angle pdb=" C5 ATP A 602 " pdb=" C4 ATP A 602 " pdb=" N3 ATP A 602 " ideal model delta sigma weight residual 126.80 118.50 8.30 1.00e+00 1.00e+00 6.90e+01 ... (remaining 12281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4852 18.00 - 36.00: 476 36.00 - 54.00: 74 54.00 - 71.99: 18 71.99 - 89.99: 14 Dihedral angle restraints: 5434 sinusoidal: 2163 harmonic: 3271 Sorted by residual: dihedral pdb=" CA MET A 501 " pdb=" C MET A 501 " pdb=" N LEU A 502 " pdb=" CA LEU A 502 " ideal model delta harmonic sigma weight residual 180.00 152.42 27.58 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA GLU A 323 " pdb=" C GLU A 323 " pdb=" N GLU A 324 " pdb=" CA GLU A 324 " ideal model delta harmonic sigma weight residual 180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLU A 324 " pdb=" C GLU A 324 " pdb=" N GLU A 325 " pdb=" CA GLU A 325 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 5431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1324 0.077 - 0.154: 137 0.154 - 0.231: 4 0.231 - 0.307: 2 0.307 - 0.384: 2 Chirality restraints: 1469 Sorted by residual: chirality pdb=" CB VAL A 540 " pdb=" CA VAL A 540 " pdb=" CG1 VAL A 540 " pdb=" CG2 VAL A 540 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ILE A 533 " pdb=" N ILE A 533 " pdb=" C ILE A 533 " pdb=" CB ILE A 533 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1466 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 RHQ A 604 " -0.051 2.00e-02 2.50e+03 2.84e-01 2.22e+03 pdb=" C2 RHQ A 604 " 0.099 2.00e-02 2.50e+03 pdb=" C21 RHQ A 604 " -0.102 2.00e-02 2.50e+03 pdb=" C24 RHQ A 604 " 0.717 2.00e-02 2.50e+03 pdb=" C3 RHQ A 604 " 0.075 2.00e-02 2.50e+03 pdb=" C4 RHQ A 604 " -0.089 2.00e-02 2.50e+03 pdb=" C5 RHQ A 604 " -0.236 2.00e-02 2.50e+03 pdb=" C6 RHQ A 604 " -0.220 2.00e-02 2.50e+03 pdb=" C9 RHQ A 604 " 0.261 2.00e-02 2.50e+03 pdb=" N2 RHQ A 604 " -0.406 2.00e-02 2.50e+03 pdb=" O1 RHQ A 604 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 RHQ B 602 " 0.051 2.00e-02 2.50e+03 2.84e-01 2.22e+03 pdb=" C2 RHQ B 602 " -0.099 2.00e-02 2.50e+03 pdb=" C21 RHQ B 602 " 0.102 2.00e-02 2.50e+03 pdb=" C24 RHQ B 602 " -0.716 2.00e-02 2.50e+03 pdb=" C3 RHQ B 602 " -0.075 2.00e-02 2.50e+03 pdb=" C4 RHQ B 602 " 0.088 2.00e-02 2.50e+03 pdb=" C5 RHQ B 602 " 0.237 2.00e-02 2.50e+03 pdb=" C6 RHQ B 602 " 0.220 2.00e-02 2.50e+03 pdb=" C9 RHQ B 602 " -0.261 2.00e-02 2.50e+03 pdb=" N2 RHQ B 602 " 0.406 2.00e-02 2.50e+03 pdb=" O1 RHQ B 602 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 251 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO A 252 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " -0.038 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 112 2.53 - 3.12: 7668 3.12 - 3.71: 13774 3.71 - 4.31: 18395 4.31 - 4.90: 28576 Nonbonded interactions: 68525 Sorted by model distance: nonbonded pdb=" O2B ATP A 602 " pdb="MG MG B 601 " model vdw 1.937 2.170 nonbonded pdb=" OG1 THR A 381 " pdb="MG MG A 603 " model vdw 1.978 2.170 nonbonded pdb=" OE1 GLN B 422 " pdb="MG MG B 601 " model vdw 1.999 2.170 nonbonded pdb=" O PRO B 252 " pdb=" OG SER B 255 " model vdw 2.098 3.040 nonbonded pdb=" OG SER A 424 " pdb=" OE1 GLN A 485 " model vdw 2.129 3.040 ... (remaining 68520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 269 or resid 282 through 586 or resid 603 throug \ h 604)) selection = (chain 'B' and (resid 9 through 269 or resid 282 through 602)) } 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 9071 Z= 0.324 Angle : 0.954 21.117 12286 Z= 0.606 Chirality : 0.049 0.384 1469 Planarity : 0.011 0.284 1526 Dihedral : 15.072 89.993 3330 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 0.21 % Allowed : 1.56 % Favored : 98.23 % 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: -2.15 (0.25), residues: 1133 helix: -0.84 (0.22), residues: 589 sheet: -0.23 (0.77), residues: 51 loop : -2.26 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 214 TYR 0.012 0.002 TYR B 570 PHE 0.012 0.002 PHE B 160 TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.32 ( 9067) covalent geometry : angle 0.95399 / 0.61 (12286) hydrogen bonds : bond 0.27704 / 18.27 ( 435) hydrogen bonds : angle 8.87794 / 6.45 ( 1239) Misc. bond : bond 0.00124 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 279 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8594 (tp) cc_final: 0.8224 (tp) REVERT: A 314 THR cc_start: 0.8392 (m) cc_final: 0.7816 (t) REVERT: B 249 LEU cc_start: 0.8948 (tp) cc_final: 0.8739 (tp) REVERT: B 430 THR cc_start: 0.8209 (p) cc_final: 0.6330 (p) outliers start: 2 outliers final: 0 residues processed: 281 average time/residue: 0.0632 time to fit residues: 25.9836 Evaluate side-chains 193 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 HIS B 220 ASN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.080332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.059275 restraints weight = 32565.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.061990 restraints weight = 19096.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.063930 restraints weight = 13011.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.065313 restraints weight = 9778.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066317 restraints weight = 7873.444| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9071 Z= 0.173 Angle : 0.777 7.384 12286 Z= 0.405 Chirality : 0.046 0.176 1469 Planarity : 0.005 0.065 1526 Dihedral : 8.255 59.973 1243 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.31 % Allowed : 6.34 % Favored : 93.35 % 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: -1.39 (0.25), residues: 1133 helix: -0.09 (0.22), residues: 617 sheet: -0.19 (0.77), residues: 44 loop : -2.12 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 475 TYR 0.027 0.002 TYR B 408 PHE 0.013 0.002 PHE A 74 TRP 0.013 0.002 TRP B 413 HIS 0.010 0.002 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 9067) covalent geometry : angle 0.77747 / 0.40 (12286) hydrogen bonds : bond 0.05844 / 3.80 ( 435) hydrogen bonds : angle 5.56738 / 4.00 ( 1239) Misc. bond : bond 0.00088 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 250 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.9619 (m110) cc_final: 0.9139 (m110) REVERT: A 188 MET cc_start: 0.9312 (ttm) cc_final: 0.8860 (ttm) REVERT: A 194 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9330 (mm-30) REVERT: A 208 GLN cc_start: 0.9349 (mt0) cc_final: 0.9005 (mt0) REVERT: A 210 LEU cc_start: 0.9527 (tp) cc_final: 0.9128 (tp) REVERT: A 293 ILE cc_start: 0.9713 (pt) cc_final: 0.9148 (mp) REVERT: A 297 MET cc_start: 0.9438 (mmm) cc_final: 0.9066 (mmm) REVERT: A 305 THR cc_start: 0.9435 (p) cc_final: 0.8726 (p) REVERT: A 417 ILE cc_start: 0.9709 (mp) cc_final: 0.9467 (mp) REVERT: A 460 PHE cc_start: 0.7916 (m-80) cc_final: 0.7137 (m-80) REVERT: A 485 GLN cc_start: 0.9625 (tp40) cc_final: 0.9126 (tp40) REVERT: A 580 MET cc_start: 0.9038 (mmp) cc_final: 0.8512 (mmt) REVERT: B 29 LEU cc_start: 0.9055 (tp) cc_final: 0.8846 (tp) REVERT: B 122 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8296 (mm-30) REVERT: B 136 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 188 MET cc_start: 0.9169 (mmm) cc_final: 0.8888 (mmm) REVERT: B 196 GLN cc_start: 0.9317 (tp40) cc_final: 0.9092 (tp40) REVERT: B 212 GLU cc_start: 0.9092 (mp0) cc_final: 0.8825 (pm20) REVERT: B 243 GLU cc_start: 0.9572 (pp20) cc_final: 0.9252 (pp20) REVERT: B 289 TYR cc_start: 0.8260 (m-80) cc_final: 0.7725 (m-80) REVERT: B 299 GLN cc_start: 0.9197 (tt0) cc_final: 0.8595 (tt0) REVERT: B 358 LYS cc_start: 0.9276 (mptt) cc_final: 0.8934 (mmtm) REVERT: B 391 TYR cc_start: 0.9264 (m-80) cc_final: 0.8890 (m-80) REVERT: B 433 GLU cc_start: 0.9279 (pt0) cc_final: 0.8911 (pp20) outliers start: 3 outliers final: 2 residues processed: 251 average time/residue: 0.0617 time to fit residues: 23.3261 Evaluate side-chains 208 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS B 163 ASN B 196 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.080572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.059369 restraints weight = 32180.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.062070 restraints weight = 18794.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.064019 restraints weight = 12776.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.065355 restraints weight = 9619.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066416 restraints weight = 7746.419| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9071 Z= 0.143 Angle : 0.721 11.641 12286 Z= 0.365 Chirality : 0.045 0.212 1469 Planarity : 0.004 0.047 1526 Dihedral : 7.637 56.971 1243 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.10 % Allowed : 6.03 % Favored : 93.87 % 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: -0.96 (0.26), residues: 1133 helix: 0.27 (0.22), residues: 624 sheet: -0.13 (0.78), residues: 44 loop : -1.94 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 536 TYR 0.019 0.002 TYR A 289 PHE 0.016 0.002 PHE A 74 TRP 0.008 0.001 TRP B 413 HIS 0.006 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9067) covalent geometry : angle 0.72084 / 0.36 (12286) hydrogen bonds : bond 0.04835 / 3.12 ( 435) hydrogen bonds : angle 5.09435 / 3.67 ( 1239) Misc. bond : bond 0.00109 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.9618 (m110) cc_final: 0.9107 (m110) REVERT: A 188 MET cc_start: 0.9296 (ttm) cc_final: 0.8837 (ttm) REVERT: A 203 THR cc_start: 0.9580 (m) cc_final: 0.9344 (p) REVERT: A 208 GLN cc_start: 0.9314 (mt0) cc_final: 0.8258 (tm-30) REVERT: A 210 LEU cc_start: 0.9554 (tp) cc_final: 0.9156 (tp) REVERT: A 293 ILE cc_start: 0.9700 (pt) cc_final: 0.9169 (mp) REVERT: A 297 MET cc_start: 0.9410 (mmm) cc_final: 0.9025 (mmm) REVERT: A 305 THR cc_start: 0.9437 (p) cc_final: 0.8724 (p) REVERT: A 417 ILE cc_start: 0.9708 (mp) cc_final: 0.9303 (mp) REVERT: A 419 TYR cc_start: 0.9379 (t80) cc_final: 0.9096 (t80) REVERT: A 460 PHE cc_start: 0.7697 (m-80) cc_final: 0.7249 (m-80) REVERT: A 468 PHE cc_start: 0.8888 (m-80) cc_final: 0.8374 (t80) REVERT: A 478 MET cc_start: 0.9389 (mmm) cc_final: 0.8864 (mmm) REVERT: B 29 LEU cc_start: 0.9029 (tp) cc_final: 0.8817 (tp) REVERT: B 109 LYS cc_start: 0.9476 (mmmt) cc_final: 0.8948 (ttmt) REVERT: B 122 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8406 (mm-30) REVERT: B 129 ASN cc_start: 0.9586 (m-40) cc_final: 0.9325 (m-40) REVERT: B 130 ASP cc_start: 0.8598 (m-30) cc_final: 0.7833 (m-30) REVERT: B 136 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8334 (tm-30) REVERT: B 188 MET cc_start: 0.9112 (mmm) cc_final: 0.8826 (mmm) REVERT: B 212 GLU cc_start: 0.9043 (mp0) cc_final: 0.8732 (pm20) REVERT: B 243 GLU cc_start: 0.9584 (pp20) cc_final: 0.9275 (pp20) REVERT: B 289 TYR cc_start: 0.8230 (m-80) cc_final: 0.7689 (m-80) REVERT: B 358 LYS cc_start: 0.9263 (mptt) cc_final: 0.8877 (mmtm) REVERT: B 391 TYR cc_start: 0.8904 (m-80) cc_final: 0.8697 (m-80) REVERT: B 408 TYR cc_start: 0.8552 (m-80) cc_final: 0.8158 (m-80) REVERT: B 415 GLU cc_start: 0.9421 (tm-30) cc_final: 0.9199 (tm-30) REVERT: B 430 THR cc_start: 0.9535 (p) cc_final: 0.9190 (t) REVERT: B 431 ILE cc_start: 0.9546 (pt) cc_final: 0.9297 (pt) REVERT: B 433 GLU cc_start: 0.9277 (pt0) cc_final: 0.8903 (pp20) REVERT: B 474 GLU cc_start: 0.8706 (pp20) cc_final: 0.7859 (pp20) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.0537 time to fit residues: 19.5344 Evaluate side-chains 212 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 0.0050 chunk 3 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058407 restraints weight = 32685.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.061051 restraints weight = 19192.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062967 restraints weight = 13110.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.064280 restraints weight = 9907.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.065328 restraints weight = 8034.031| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9071 Z= 0.159 Angle : 0.705 7.947 12286 Z= 0.358 Chirality : 0.044 0.168 1469 Planarity : 0.004 0.042 1526 Dihedral : 7.429 55.211 1243 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.26), residues: 1133 helix: 0.50 (0.22), residues: 619 sheet: -0.05 (0.78), residues: 44 loop : -1.79 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 414 TYR 0.019 0.001 TYR A 289 PHE 0.019 0.001 PHE A 74 TRP 0.007 0.001 TRP A 413 HIS 0.006 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 9067) covalent geometry : angle 0.70540 / 0.36 (12286) hydrogen bonds : bond 0.04322 / 2.81 ( 435) hydrogen bonds : angle 4.94062 / 3.55 ( 1239) Misc. bond : bond 0.00126 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.9612 (m110) cc_final: 0.9111 (m110) REVERT: A 188 MET cc_start: 0.9289 (ttm) cc_final: 0.8850 (ttm) REVERT: A 194 GLU cc_start: 0.9583 (mm-30) cc_final: 0.9360 (mm-30) REVERT: A 203 THR cc_start: 0.9599 (m) cc_final: 0.9345 (p) REVERT: A 208 GLN cc_start: 0.9334 (mt0) cc_final: 0.8371 (tm-30) REVERT: A 210 LEU cc_start: 0.9554 (tp) cc_final: 0.9207 (tp) REVERT: A 293 ILE cc_start: 0.9711 (pt) cc_final: 0.9174 (mp) REVERT: A 297 MET cc_start: 0.9384 (mmm) cc_final: 0.8977 (mmm) REVERT: A 305 THR cc_start: 0.9437 (p) cc_final: 0.8711 (p) REVERT: A 460 PHE cc_start: 0.7806 (m-80) cc_final: 0.7409 (m-80) REVERT: A 468 PHE cc_start: 0.8895 (m-80) cc_final: 0.8453 (t80) REVERT: A 501 MET cc_start: 0.8417 (mpp) cc_final: 0.8068 (mpp) REVERT: A 580 MET cc_start: 0.9146 (mmp) cc_final: 0.8642 (mmt) REVERT: B 29 LEU cc_start: 0.9030 (tp) cc_final: 0.8823 (tp) REVERT: B 89 ASN cc_start: 0.9565 (m-40) cc_final: 0.9110 (m110) REVERT: B 122 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8282 (mm-30) REVERT: B 188 MET cc_start: 0.9112 (mmm) cc_final: 0.8862 (mmm) REVERT: B 197 ASP cc_start: 0.9287 (m-30) cc_final: 0.8831 (p0) REVERT: B 212 GLU cc_start: 0.9249 (mp0) cc_final: 0.8948 (mp0) REVERT: B 243 GLU cc_start: 0.9559 (pp20) cc_final: 0.9273 (pp20) REVERT: B 289 TYR cc_start: 0.8243 (m-80) cc_final: 0.7718 (m-80) REVERT: B 358 LYS cc_start: 0.9285 (mptt) cc_final: 0.8848 (mmtt) REVERT: B 391 TYR cc_start: 0.9251 (m-80) cc_final: 0.8931 (m-80) REVERT: B 408 TYR cc_start: 0.8574 (m-80) cc_final: 0.8166 (m-80) REVERT: B 415 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9185 (tm-30) REVERT: B 466 ASN cc_start: 0.8568 (t0) cc_final: 0.8363 (t0) REVERT: B 469 ASP cc_start: 0.7965 (t0) cc_final: 0.7673 (t70) REVERT: B 471 GLU cc_start: 0.9593 (pm20) cc_final: 0.9350 (pm20) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.0545 time to fit residues: 18.9818 Evaluate side-chains 198 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN A 434 ASN ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059135 restraints weight = 32089.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061795 restraints weight = 18800.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063745 restraints weight = 12824.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.065054 restraints weight = 9607.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.066076 restraints weight = 7750.176| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9071 Z= 0.141 Angle : 0.708 7.944 12286 Z= 0.353 Chirality : 0.045 0.209 1469 Planarity : 0.004 0.039 1526 Dihedral : 7.069 51.202 1243 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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: -0.53 (0.26), residues: 1133 helix: 0.54 (0.22), residues: 633 sheet: -0.12 (0.68), residues: 57 loop : -1.68 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 475 TYR 0.021 0.001 TYR A 289 PHE 0.025 0.002 PHE B 304 TRP 0.008 0.001 TRP A 413 HIS 0.004 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 9067) covalent geometry : angle 0.70802 / 0.35 (12286) hydrogen bonds : bond 0.04095 / 2.64 ( 435) hydrogen bonds : angle 4.77765 / 3.44 ( 1239) Misc. bond : bond 0.00099 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.9605 (m110) cc_final: 0.9088 (m110) REVERT: A 136 GLU cc_start: 0.9465 (tp30) cc_final: 0.9194 (tp30) REVERT: A 188 MET cc_start: 0.9335 (ttm) cc_final: 0.8734 (ttm) REVERT: A 194 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9370 (mm-30) REVERT: A 203 THR cc_start: 0.9572 (m) cc_final: 0.9271 (p) REVERT: A 208 GLN cc_start: 0.9268 (mt0) cc_final: 0.8380 (tm-30) REVERT: A 210 LEU cc_start: 0.9576 (tp) cc_final: 0.9330 (tp) REVERT: A 231 MET cc_start: 0.8988 (tmm) cc_final: 0.8155 (tmm) REVERT: A 293 ILE cc_start: 0.9716 (pt) cc_final: 0.9162 (mp) REVERT: A 297 MET cc_start: 0.9381 (mmm) cc_final: 0.8951 (mmm) REVERT: A 305 THR cc_start: 0.9429 (p) cc_final: 0.8657 (p) REVERT: A 460 PHE cc_start: 0.7905 (m-80) cc_final: 0.7408 (m-80) REVERT: A 468 PHE cc_start: 0.8867 (m-80) cc_final: 0.8386 (t80) REVERT: A 501 MET cc_start: 0.8478 (mpp) cc_final: 0.8059 (mpp) REVERT: A 580 MET cc_start: 0.9154 (mmp) cc_final: 0.8653 (mmt) REVERT: B 29 LEU cc_start: 0.8946 (tp) cc_final: 0.8739 (tp) REVERT: B 89 ASN cc_start: 0.9571 (m-40) cc_final: 0.9122 (m110) REVERT: B 109 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9115 (mtpp) REVERT: B 122 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 129 ASN cc_start: 0.9634 (m-40) cc_final: 0.9313 (m-40) REVERT: B 130 ASP cc_start: 0.8559 (m-30) cc_final: 0.8023 (m-30) REVERT: B 136 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8479 (tm-30) REVERT: B 212 GLU cc_start: 0.9191 (mp0) cc_final: 0.8892 (mp0) REVERT: B 243 GLU cc_start: 0.9547 (pp20) cc_final: 0.9268 (pp20) REVERT: B 289 TYR cc_start: 0.8259 (m-80) cc_final: 0.7681 (m-80) REVERT: B 319 GLU cc_start: 0.9457 (tp30) cc_final: 0.9214 (tp30) REVERT: B 415 GLU cc_start: 0.9447 (tm-30) cc_final: 0.9162 (tm-30) REVERT: B 441 ARG cc_start: 0.8716 (ptp90) cc_final: 0.8513 (mtm110) REVERT: B 469 ASP cc_start: 0.8008 (t0) cc_final: 0.7600 (t70) REVERT: B 471 GLU cc_start: 0.9600 (pm20) cc_final: 0.9293 (pm20) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.0549 time to fit residues: 19.2217 Evaluate side-chains 195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 HIS B 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.077689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.056962 restraints weight = 33316.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059551 restraints weight = 19601.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.061363 restraints weight = 13453.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062753 restraints weight = 10231.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.063686 restraints weight = 8242.883| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9071 Z= 0.175 Angle : 0.714 6.988 12286 Z= 0.361 Chirality : 0.044 0.159 1469 Planarity : 0.004 0.045 1526 Dihedral : 6.755 49.345 1243 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % 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: -0.54 (0.26), residues: 1133 helix: 0.53 (0.22), residues: 638 sheet: -0.17 (0.69), residues: 57 loop : -1.70 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 414 TYR 0.019 0.002 TYR A 289 PHE 0.031 0.002 PHE B 384 TRP 0.005 0.001 TRP B 104 HIS 0.005 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 9067) covalent geometry : angle 0.71433 / 0.36 (12286) hydrogen bonds : bond 0.03985 / 2.59 ( 435) hydrogen bonds : angle 4.79941 / 3.45 ( 1239) Misc. bond : bond 0.00105 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.9596 (m110) cc_final: 0.9063 (m110) REVERT: A 136 GLU cc_start: 0.9439 (tp30) cc_final: 0.9143 (tp30) REVERT: A 188 MET cc_start: 0.9289 (ttm) cc_final: 0.8699 (ttm) REVERT: A 208 GLN cc_start: 0.9311 (mt0) cc_final: 0.8207 (tm-30) REVERT: A 210 LEU cc_start: 0.9612 (tp) cc_final: 0.9359 (tp) REVERT: A 231 MET cc_start: 0.8976 (tmm) cc_final: 0.8285 (tmm) REVERT: A 236 LEU cc_start: 0.8863 (mp) cc_final: 0.8628 (mp) REVERT: A 293 ILE cc_start: 0.9725 (pt) cc_final: 0.9181 (mp) REVERT: A 297 MET cc_start: 0.9386 (mmm) cc_final: 0.9000 (mmm) REVERT: A 305 THR cc_start: 0.9438 (p) cc_final: 0.8674 (p) REVERT: A 460 PHE cc_start: 0.7770 (m-80) cc_final: 0.7407 (m-80) REVERT: A 468 PHE cc_start: 0.8884 (m-80) cc_final: 0.8428 (t80) REVERT: A 501 MET cc_start: 0.8514 (mpp) cc_final: 0.7998 (mpp) REVERT: B 29 LEU cc_start: 0.9056 (tp) cc_final: 0.8846 (tp) REVERT: B 89 ASN cc_start: 0.9586 (m-40) cc_final: 0.9154 (m110) REVERT: B 109 LYS cc_start: 0.9451 (mmmt) cc_final: 0.9118 (mtpp) REVERT: B 110 LEU cc_start: 0.9068 (pp) cc_final: 0.8762 (pp) REVERT: B 122 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8246 (mm-30) REVERT: B 188 MET cc_start: 0.9088 (mmp) cc_final: 0.8825 (mmp) REVERT: B 197 ASP cc_start: 0.9111 (m-30) cc_final: 0.8718 (p0) REVERT: B 212 GLU cc_start: 0.9189 (mp0) cc_final: 0.8889 (mp0) REVERT: B 243 GLU cc_start: 0.9540 (pp20) cc_final: 0.9292 (pp20) REVERT: B 249 LEU cc_start: 0.9362 (tp) cc_final: 0.9118 (tp) REVERT: B 289 TYR cc_start: 0.8225 (m-80) cc_final: 0.7688 (m-80) REVERT: B 319 GLU cc_start: 0.9477 (tp30) cc_final: 0.9223 (tp30) REVERT: B 358 LYS cc_start: 0.8825 (mppt) cc_final: 0.8321 (mmtt) REVERT: B 408 TYR cc_start: 0.9066 (m-80) cc_final: 0.8291 (m-80) REVERT: B 415 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9182 (tm-30) REVERT: B 469 ASP cc_start: 0.8008 (t0) cc_final: 0.7708 (t70) REVERT: B 471 GLU cc_start: 0.9639 (pm20) cc_final: 0.9260 (pm20) REVERT: B 531 ILE cc_start: 0.9669 (mt) cc_final: 0.9390 (pt) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.0509 time to fit residues: 17.0164 Evaluate side-chains 189 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.080208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.059143 restraints weight = 32435.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061852 restraints weight = 18967.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.063837 restraints weight = 12921.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065215 restraints weight = 9662.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.066261 restraints weight = 7750.818| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9071 Z= 0.133 Angle : 0.724 8.653 12286 Z= 0.356 Chirality : 0.044 0.172 1469 Planarity : 0.004 0.040 1526 Dihedral : 6.455 47.308 1243 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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 (0.26), residues: 1133 helix: 0.52 (0.21), residues: 646 sheet: -0.12 (0.68), residues: 57 loop : -1.59 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 214 TYR 0.021 0.001 TYR A 289 PHE 0.027 0.002 PHE B 384 TRP 0.006 0.001 TRP B 104 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9067) covalent geometry : angle 0.72432 / 0.36 (12286) hydrogen bonds : bond 0.03806 / 2.45 ( 435) hydrogen bonds : angle 4.64806 / 3.35 ( 1239) Misc. bond : bond 0.00103 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 GLU cc_start: 0.8726 (pm20) cc_final: 0.8497 (pm20) REVERT: A 129 ASN cc_start: 0.9606 (m110) cc_final: 0.9078 (m110) REVERT: A 136 GLU cc_start: 0.9458 (tp30) cc_final: 0.9153 (tp30) REVERT: A 188 MET cc_start: 0.9283 (ttm) cc_final: 0.8634 (ttm) REVERT: A 197 ASP cc_start: 0.9113 (t70) cc_final: 0.8628 (m-30) REVERT: A 203 THR cc_start: 0.9582 (m) cc_final: 0.9299 (p) REVERT: A 205 LEU cc_start: 0.9407 (tt) cc_final: 0.9186 (tt) REVERT: A 208 GLN cc_start: 0.9212 (mt0) cc_final: 0.8994 (mt0) REVERT: A 210 LEU cc_start: 0.9567 (tp) cc_final: 0.9229 (tp) REVERT: A 231 MET cc_start: 0.8902 (tmm) cc_final: 0.8225 (tmm) REVERT: A 247 GLN cc_start: 0.9605 (tm-30) cc_final: 0.9095 (tp-100) REVERT: A 293 ILE cc_start: 0.9723 (pt) cc_final: 0.9170 (mp) REVERT: A 297 MET cc_start: 0.9378 (mmm) cc_final: 0.8962 (mmm) REVERT: A 305 THR cc_start: 0.9424 (p) cc_final: 0.8612 (p) REVERT: A 326 GLU cc_start: 0.8689 (pp20) cc_final: 0.8394 (pp20) REVERT: A 408 TYR cc_start: 0.8525 (m-10) cc_final: 0.8084 (m-80) REVERT: A 460 PHE cc_start: 0.7820 (m-80) cc_final: 0.7427 (m-80) REVERT: A 468 PHE cc_start: 0.8911 (m-80) cc_final: 0.8362 (t80) REVERT: A 478 MET cc_start: 0.9295 (mmm) cc_final: 0.8931 (mmm) REVERT: A 501 MET cc_start: 0.8373 (mpp) cc_final: 0.7889 (mpp) REVERT: A 567 HIS cc_start: 0.8629 (t70) cc_final: 0.8414 (t-90) REVERT: A 580 MET cc_start: 0.9181 (mmp) cc_final: 0.8678 (mmt) REVERT: B 29 LEU cc_start: 0.8995 (tp) cc_final: 0.8789 (tp) REVERT: B 89 ASN cc_start: 0.9550 (m-40) cc_final: 0.9091 (m110) REVERT: B 107 LEU cc_start: 0.9759 (tt) cc_final: 0.9556 (pp) REVERT: B 109 LYS cc_start: 0.9346 (mmmt) cc_final: 0.8927 (ttmt) REVERT: B 122 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8348 (mm-30) REVERT: B 129 ASN cc_start: 0.9629 (m-40) cc_final: 0.9261 (m-40) REVERT: B 130 ASP cc_start: 0.8437 (m-30) cc_final: 0.7544 (m-30) REVERT: B 136 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 188 MET cc_start: 0.9155 (mmp) cc_final: 0.8895 (mmm) REVERT: B 197 ASP cc_start: 0.9142 (m-30) cc_final: 0.8773 (p0) REVERT: B 212 GLU cc_start: 0.9144 (mp0) cc_final: 0.8823 (mp0) REVERT: B 243 GLU cc_start: 0.9527 (pp20) cc_final: 0.9326 (pp20) REVERT: B 249 LEU cc_start: 0.9366 (tp) cc_final: 0.9150 (tp) REVERT: B 289 TYR cc_start: 0.8221 (m-80) cc_final: 0.7617 (m-80) REVERT: B 324 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8922 (tp30) REVERT: B 357 LEU cc_start: 0.8910 (mt) cc_final: 0.8628 (mp) REVERT: B 408 TYR cc_start: 0.9082 (m-80) cc_final: 0.8139 (m-80) REVERT: B 415 GLU cc_start: 0.9491 (tm-30) cc_final: 0.9173 (tm-30) REVERT: B 471 GLU cc_start: 0.9621 (pm20) cc_final: 0.9262 (pm20) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.0530 time to fit residues: 17.4411 Evaluate side-chains 195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 112 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.057682 restraints weight = 32864.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.060300 restraints weight = 19448.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.062236 restraints weight = 13322.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.063632 restraints weight = 10009.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064562 restraints weight = 8074.580| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9071 Z= 0.167 Angle : 0.718 7.521 12286 Z= 0.362 Chirality : 0.044 0.280 1469 Planarity : 0.004 0.053 1526 Dihedral : 6.414 48.761 1243 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: -0.36 (0.26), residues: 1133 helix: 0.60 (0.22), residues: 647 sheet: -0.38 (0.64), residues: 63 loop : -1.49 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 214 TYR 0.018 0.001 TYR A 289 PHE 0.024 0.002 PHE B 384 TRP 0.010 0.001 TRP A 413 HIS 0.005 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 9067) covalent geometry : angle 0.71791 / 0.36 (12286) hydrogen bonds : bond 0.03791 / 2.43 ( 435) hydrogen bonds : angle 4.67510 / 3.36 ( 1239) Misc. bond : bond 0.00122 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.9605 (m110) cc_final: 0.9069 (m110) REVERT: A 136 GLU cc_start: 0.9437 (tp30) cc_final: 0.9091 (tp30) REVERT: A 188 MET cc_start: 0.9286 (ttm) cc_final: 0.8694 (ttm) REVERT: A 208 GLN cc_start: 0.9256 (mt0) cc_final: 0.9033 (mt0) REVERT: A 210 LEU cc_start: 0.9625 (tp) cc_final: 0.9282 (tp) REVERT: A 222 GLU cc_start: 0.9113 (pm20) cc_final: 0.8907 (pm20) REVERT: A 231 MET cc_start: 0.8940 (tmm) cc_final: 0.8245 (tmm) REVERT: A 293 ILE cc_start: 0.9733 (pt) cc_final: 0.9180 (mp) REVERT: A 297 MET cc_start: 0.9369 (mmm) cc_final: 0.9034 (mmm) REVERT: A 305 THR cc_start: 0.9455 (p) cc_final: 0.8674 (p) REVERT: A 317 MET cc_start: 0.9369 (ptp) cc_final: 0.8804 (ptp) REVERT: A 408 TYR cc_start: 0.8619 (m-10) cc_final: 0.8217 (m-80) REVERT: A 417 ILE cc_start: 0.9283 (mp) cc_final: 0.9070 (mm) REVERT: A 454 MET cc_start: 0.9335 (mtp) cc_final: 0.9113 (mtp) REVERT: A 460 PHE cc_start: 0.7972 (m-80) cc_final: 0.7467 (m-80) REVERT: A 468 PHE cc_start: 0.8952 (m-80) cc_final: 0.8434 (t80) REVERT: A 478 MET cc_start: 0.9323 (mmm) cc_final: 0.8895 (mmm) REVERT: A 501 MET cc_start: 0.8610 (mpp) cc_final: 0.7995 (mpp) REVERT: A 580 MET cc_start: 0.9174 (mmp) cc_final: 0.8683 (mmt) REVERT: B 59 MET cc_start: 0.9600 (ppp) cc_final: 0.9246 (ppp) REVERT: B 89 ASN cc_start: 0.9555 (m-40) cc_final: 0.9101 (m110) REVERT: B 109 LYS cc_start: 0.9408 (mmmt) cc_final: 0.8958 (ttmt) REVERT: B 122 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8291 (mm-30) REVERT: B 129 ASN cc_start: 0.9595 (m-40) cc_final: 0.9373 (m-40) REVERT: B 136 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8538 (tm-30) REVERT: B 188 MET cc_start: 0.9153 (mmp) cc_final: 0.8950 (mmm) REVERT: B 197 ASP cc_start: 0.9257 (m-30) cc_final: 0.8832 (p0) REVERT: B 212 GLU cc_start: 0.9128 (mp0) cc_final: 0.8807 (mp0) REVERT: B 249 LEU cc_start: 0.9356 (tp) cc_final: 0.9134 (tp) REVERT: B 289 TYR cc_start: 0.8243 (m-80) cc_final: 0.7653 (m-80) REVERT: B 324 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8956 (tp30) REVERT: B 357 LEU cc_start: 0.8913 (mt) cc_final: 0.8691 (mt) REVERT: B 408 TYR cc_start: 0.9162 (m-80) cc_final: 0.8177 (m-80) REVERT: B 415 GLU cc_start: 0.9510 (tm-30) cc_final: 0.9229 (tm-30) REVERT: B 471 GLU cc_start: 0.9622 (pm20) cc_final: 0.9205 (pm20) REVERT: B 531 ILE cc_start: 0.9667 (mt) cc_final: 0.9422 (pt) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.0539 time to fit residues: 17.4331 Evaluate side-chains 186 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.0020 chunk 60 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.080280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059093 restraints weight = 31939.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.061809 restraints weight = 18822.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063764 restraints weight = 12891.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.065283 restraints weight = 9724.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.066263 restraints weight = 7782.644| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9071 Z= 0.129 Angle : 0.730 9.034 12286 Z= 0.356 Chirality : 0.044 0.261 1469 Planarity : 0.004 0.045 1526 Dihedral : 6.259 46.751 1243 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: -0.37 (0.26), residues: 1133 helix: 0.53 (0.21), residues: 660 sheet: -0.24 (0.65), residues: 57 loop : -1.44 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.020 0.001 TYR A 289 PHE 0.027 0.002 PHE A 286 TRP 0.009 0.001 TRP B 104 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9067) covalent geometry : angle 0.73019 / 0.36 (12286) hydrogen bonds : bond 0.03635 / 2.33 ( 435) hydrogen bonds : angle 4.50828 / 3.24 ( 1239) Misc. bond : bond 0.00089 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.9595 (m110) cc_final: 0.9059 (m110) REVERT: A 136 GLU cc_start: 0.9438 (tp30) cc_final: 0.9074 (tp30) REVERT: A 188 MET cc_start: 0.9264 (ttm) cc_final: 0.8661 (ttm) REVERT: A 197 ASP cc_start: 0.9141 (t70) cc_final: 0.8644 (m-30) REVERT: A 208 GLN cc_start: 0.9196 (mt0) cc_final: 0.8107 (tm-30) REVERT: A 210 LEU cc_start: 0.9543 (tp) cc_final: 0.9198 (tp) REVERT: A 222 GLU cc_start: 0.9109 (pm20) cc_final: 0.8876 (pm20) REVERT: A 231 MET cc_start: 0.8896 (tmm) cc_final: 0.8222 (tmm) REVERT: A 247 GLN cc_start: 0.9583 (tm-30) cc_final: 0.9223 (tm-30) REVERT: A 293 ILE cc_start: 0.9726 (pt) cc_final: 0.9174 (mp) REVERT: A 297 MET cc_start: 0.9419 (mmm) cc_final: 0.9018 (mmm) REVERT: A 305 THR cc_start: 0.9431 (p) cc_final: 0.8579 (p) REVERT: A 317 MET cc_start: 0.9302 (ptp) cc_final: 0.8874 (ptp) REVERT: A 408 TYR cc_start: 0.8605 (m-10) cc_final: 0.8087 (m-80) REVERT: A 417 ILE cc_start: 0.9243 (mp) cc_final: 0.9029 (mm) REVERT: A 428 SER cc_start: 0.8993 (p) cc_final: 0.8760 (m) REVERT: A 454 MET cc_start: 0.9330 (mtp) cc_final: 0.9120 (mtp) REVERT: A 460 PHE cc_start: 0.7691 (m-80) cc_final: 0.7451 (m-80) REVERT: A 468 PHE cc_start: 0.8930 (m-80) cc_final: 0.8396 (t80) REVERT: A 501 MET cc_start: 0.8644 (mpp) cc_final: 0.8011 (mpp) REVERT: A 514 GLU cc_start: 0.9535 (pp20) cc_final: 0.9290 (pp20) REVERT: A 580 MET cc_start: 0.9165 (mmp) cc_final: 0.8672 (mmt) REVERT: B 59 MET cc_start: 0.9604 (ppp) cc_final: 0.9278 (ppp) REVERT: B 89 ASN cc_start: 0.9534 (m-40) cc_final: 0.9069 (m110) REVERT: B 109 LYS cc_start: 0.9368 (mmmt) cc_final: 0.8941 (ttmt) REVERT: B 122 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8378 (mm-30) REVERT: B 129 ASN cc_start: 0.9599 (m-40) cc_final: 0.9341 (m-40) REVERT: B 136 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8495 (tm-30) REVERT: B 149 ILE cc_start: 0.9374 (tp) cc_final: 0.9152 (pt) REVERT: B 197 ASP cc_start: 0.9225 (m-30) cc_final: 0.8773 (p0) REVERT: B 198 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9210 (mm-30) REVERT: B 212 GLU cc_start: 0.9232 (mp0) cc_final: 0.8871 (mp0) REVERT: B 243 GLU cc_start: 0.9546 (pp20) cc_final: 0.9070 (pp20) REVERT: B 249 LEU cc_start: 0.9332 (tp) cc_final: 0.9100 (tp) REVERT: B 289 TYR cc_start: 0.8197 (m-80) cc_final: 0.7616 (m-80) REVERT: B 357 LEU cc_start: 0.8865 (mt) cc_final: 0.8606 (mt) REVERT: B 391 TYR cc_start: 0.9185 (m-10) cc_final: 0.8742 (m-10) REVERT: B 408 TYR cc_start: 0.9011 (m-80) cc_final: 0.7987 (m-80) REVERT: B 413 TRP cc_start: 0.9057 (t60) cc_final: 0.8359 (t60) REVERT: B 471 GLU cc_start: 0.9625 (pm20) cc_final: 0.9186 (pm20) REVERT: B 531 ILE cc_start: 0.9632 (mt) cc_final: 0.9400 (pt) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.0514 time to fit residues: 17.4442 Evaluate side-chains 194 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 104 optimal weight: 0.0040 chunk 37 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.1774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.058618 restraints weight = 31993.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.061306 restraints weight = 19178.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063261 restraints weight = 13245.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.064598 restraints weight = 10025.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065754 restraints weight = 8139.596| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9071 Z= 0.129 Angle : 0.727 9.444 12286 Z= 0.356 Chirality : 0.044 0.254 1469 Planarity : 0.004 0.046 1526 Dihedral : 6.200 45.806 1243 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.26), residues: 1133 helix: 0.58 (0.21), residues: 660 sheet: -0.28 (0.64), residues: 57 loop : -1.43 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.020 0.001 TYR A 289 PHE 0.021 0.002 PHE A 74 TRP 0.013 0.002 TRP A 413 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9067) covalent geometry : angle 0.72701 / 0.36 (12286) hydrogen bonds : bond 0.03599 / 2.33 ( 435) hydrogen bonds : angle 4.47710 / 3.23 ( 1239) Misc. bond : bond 0.00093 / 0.05 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASN cc_start: 0.9573 (m110) cc_final: 0.9033 (m110) REVERT: A 136 GLU cc_start: 0.9431 (tp30) cc_final: 0.9080 (tp30) REVERT: A 188 MET cc_start: 0.9238 (ttm) cc_final: 0.8639 (ttm) REVERT: A 196 GLN cc_start: 0.9340 (mm110) cc_final: 0.8930 (mm110) REVERT: A 197 ASP cc_start: 0.9163 (t70) cc_final: 0.8636 (m-30) REVERT: A 208 GLN cc_start: 0.9212 (mt0) cc_final: 0.8120 (tm-30) REVERT: A 210 LEU cc_start: 0.9546 (tp) cc_final: 0.9196 (tp) REVERT: A 222 GLU cc_start: 0.9100 (pm20) cc_final: 0.8878 (pm20) REVERT: A 231 MET cc_start: 0.8843 (tmm) cc_final: 0.8188 (tmm) REVERT: A 247 GLN cc_start: 0.9561 (tm-30) cc_final: 0.9195 (tm-30) REVERT: A 259 MET cc_start: 0.9062 (tmm) cc_final: 0.8855 (tmm) REVERT: A 293 ILE cc_start: 0.9717 (pt) cc_final: 0.9167 (mp) REVERT: A 297 MET cc_start: 0.9434 (mmm) cc_final: 0.9030 (mmm) REVERT: A 305 THR cc_start: 0.9423 (p) cc_final: 0.8572 (p) REVERT: A 317 MET cc_start: 0.9321 (ptp) cc_final: 0.8875 (ptp) REVERT: A 408 TYR cc_start: 0.8684 (m-10) cc_final: 0.8180 (m-80) REVERT: A 417 ILE cc_start: 0.9282 (mp) cc_final: 0.9058 (mm) REVERT: A 454 MET cc_start: 0.9315 (mtp) cc_final: 0.9097 (mtp) REVERT: A 460 PHE cc_start: 0.7969 (m-80) cc_final: 0.7460 (m-80) REVERT: A 468 PHE cc_start: 0.8925 (m-80) cc_final: 0.8369 (t80) REVERT: A 501 MET cc_start: 0.8619 (mpp) cc_final: 0.7964 (mpp) REVERT: A 514 GLU cc_start: 0.9551 (pp20) cc_final: 0.9284 (pp20) REVERT: A 580 MET cc_start: 0.9162 (mmp) cc_final: 0.8679 (mmt) REVERT: B 59 MET cc_start: 0.9596 (ppp) cc_final: 0.9309 (ppp) REVERT: B 89 ASN cc_start: 0.9535 (m-40) cc_final: 0.9073 (m110) REVERT: B 102 LEU cc_start: 0.9450 (tp) cc_final: 0.9241 (tt) REVERT: B 109 LYS cc_start: 0.9382 (mmmt) cc_final: 0.8954 (ttmt) REVERT: B 122 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8398 (mm-30) REVERT: B 129 ASN cc_start: 0.9586 (m-40) cc_final: 0.9365 (m-40) REVERT: B 136 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8505 (tm-30) REVERT: B 149 ILE cc_start: 0.9370 (tp) cc_final: 0.9130 (pt) REVERT: B 197 ASP cc_start: 0.9219 (m-30) cc_final: 0.8776 (p0) REVERT: B 198 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9201 (mm-30) REVERT: B 207 ASN cc_start: 0.9278 (t0) cc_final: 0.8869 (t0) REVERT: B 212 GLU cc_start: 0.9195 (mp0) cc_final: 0.8850 (mp0) REVERT: B 243 GLU cc_start: 0.9535 (pp20) cc_final: 0.9079 (pp20) REVERT: B 249 LEU cc_start: 0.9333 (tp) cc_final: 0.9105 (tp) REVERT: B 289 TYR cc_start: 0.8222 (m-80) cc_final: 0.7610 (m-80) REVERT: B 319 GLU cc_start: 0.9422 (tp30) cc_final: 0.8897 (tp30) REVERT: B 357 LEU cc_start: 0.8855 (mt) cc_final: 0.8624 (mt) REVERT: B 408 TYR cc_start: 0.8995 (m-80) cc_final: 0.8035 (m-80) REVERT: B 413 TRP cc_start: 0.9096 (t60) cc_final: 0.8369 (t60) REVERT: B 471 GLU cc_start: 0.9618 (pm20) cc_final: 0.9311 (pm20) REVERT: B 525 MET cc_start: 0.9197 (mmp) cc_final: 0.8829 (mmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.0548 time to fit residues: 18.1849 Evaluate side-chains 192 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.0370 chunk 1 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.058089 restraints weight = 32363.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.060719 restraints weight = 19455.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.062698 restraints weight = 13513.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.064071 restraints weight = 10224.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065079 restraints weight = 8304.014| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9071 Z= 0.130 Angle : 0.724 9.686 12286 Z= 0.355 Chirality : 0.044 0.248 1469 Planarity : 0.004 0.047 1526 Dihedral : 6.126 45.633 1243 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -0.27 (0.27), residues: 1133 helix: 0.61 (0.21), residues: 666 sheet: -0.35 (0.64), residues: 57 loop : -1.40 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 214 TYR 0.019 0.001 TYR A 289 PHE 0.022 0.002 PHE B 384 TRP 0.011 0.002 TRP A 413 HIS 0.006 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9067) covalent geometry : angle 0.72420 / 0.35 (12286) hydrogen bonds : bond 0.03569 / 2.30 ( 435) hydrogen bonds : angle 4.44545 / 3.20 ( 1239) Misc. bond : bond 0.00084 / 0.04 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1166.96 seconds wall clock time: 20 minutes 53.50 seconds (1253.50 seconds total)