Starting phenix.real_space_refine on Sat Jul 4 09:52:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ras_24385/07_2026/7ras_24385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ras_24385/07_2026/7ras_24385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ras_24385/07_2026/7ras_24385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ras_24385/07_2026/7ras_24385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ras_24385/07_2026/7ras_24385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ras_24385/07_2026/7ras_24385.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ras_24385/07_2026/7ras_24385.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ras_24385/07_2026/7ras_24385.cif" } resolution = 3.64 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= 0.026 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 13072 2.51 5 N 3272 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s 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: 20000 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.73, per 1000 atoms: 0.24 Number of scatterers: 20000 At special positions: 0 Unit cell: (136.95, 136.95, 117.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 3540 8.00 N 3272 7.00 C 13072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 703.6 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 65.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.540A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 148 removed outlier: 3.682A pdb=" N ARG A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.528A pdb=" N MET A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.768A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.845A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.776A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.788A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.638A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.756A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.692A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.513A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.124A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 460 removed outlier: 4.278A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 508 removed outlier: 3.648A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 542 removed outlier: 4.133A pdb=" N PHE A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 563 removed outlier: 4.441A pdb=" N ALA A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 570 through 575 removed outlier: 4.268A pdb=" N MET A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 608 removed outlier: 3.510A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.915A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 679 removed outlier: 3.572A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 707 removed outlier: 3.827A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.550A pdb=" N ARG A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.539A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.682A pdb=" N ARG B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 removed outlier: 3.527A pdb=" N MET B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.767A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.845A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.775A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.789A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.637A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.756A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 354 through 362 removed outlier: 3.692A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.512A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 4.124A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 460 removed outlier: 4.278A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYR B 460 " --> pdb=" O THR B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 508 removed outlier: 3.648A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 508 " --> pdb=" O ALA B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 542 removed outlier: 4.132A pdb=" N PHE B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 563 removed outlier: 4.440A pdb=" N ALA B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 566 No H-bonds generated for 'chain 'B' and resid 564 through 566' Processing helix chain 'B' and resid 570 through 575 removed outlier: 4.268A pdb=" N MET B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 608 removed outlier: 3.509A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.915A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 633 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 679 removed outlier: 3.572A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 707 removed outlier: 3.828A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 690 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.549A pdb=" N ARG B 712 " --> pdb=" O PRO B 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.539A pdb=" N LYS C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 148 removed outlier: 3.682A pdb=" N ARG C 148 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 removed outlier: 3.528A pdb=" N MET C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.767A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.846A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.775A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.789A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.638A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.756A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.692A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.513A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.124A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 460 removed outlier: 4.278A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 508 removed outlier: 3.648A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 542 removed outlier: 4.133A pdb=" N PHE C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 563 removed outlier: 4.441A pdb=" N ALA C 549 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 566 No H-bonds generated for 'chain 'C' and resid 564 through 566' Processing helix chain 'C' and resid 570 through 575 removed outlier: 4.268A pdb=" N MET C 574 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 608 removed outlier: 3.509A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.916A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 633 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 679 removed outlier: 3.573A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 707 removed outlier: 3.829A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 690 " --> pdb=" O LYS C 686 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 removed outlier: 3.548A pdb=" N ARG C 712 " --> pdb=" O PRO C 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.540A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.682A pdb=" N ARG D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.528A pdb=" N MET D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.768A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.845A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.775A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 234 " --> pdb=" O ILE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.790A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.638A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.757A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.691A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 408 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.514A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 4.125A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 460 removed outlier: 4.278A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR D 456 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR D 460 " --> pdb=" O THR D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 508 removed outlier: 3.648A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 542 removed outlier: 4.132A pdb=" N PHE D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 563 removed outlier: 4.441A pdb=" N ALA D 549 " --> pdb=" O LYS D 545 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 566 No H-bonds generated for 'chain 'D' and resid 564 through 566' Processing helix chain 'D' and resid 570 through 575 removed outlier: 4.268A pdb=" N MET D 574 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 608 removed outlier: 3.509A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.915A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 633 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 679 removed outlier: 3.572A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 707 removed outlier: 3.828A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 removed outlier: 3.549A pdb=" N ARG D 712 " --> pdb=" O PRO D 708 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 5.318A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 382 removed outlier: 5.317A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 382 removed outlier: 5.317A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 382 removed outlier: 5.317A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) 989 hydrogen bonds defined for protein. 2907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3216 1.32 - 1.44: 5536 1.44 - 1.56: 11468 1.56 - 1.69: 8 1.69 - 1.81: 196 Bond restraints: 20424 Sorted by residual: bond pdb=" C07 A0O C 902 " pdb=" C12 A0O C 902 " ideal model delta sigma weight residual 1.430 1.647 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C07 A0O A 902 " pdb=" C12 A0O A 902 " ideal model delta sigma weight residual 1.430 1.646 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C07 A0O D 902 " pdb=" C12 A0O D 902 " ideal model delta sigma weight residual 1.430 1.646 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C07 A0O B 902 " pdb=" C12 A0O B 902 " ideal model delta sigma weight residual 1.430 1.646 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C07 A0O B 901 " pdb=" C12 A0O B 901 " ideal model delta sigma weight residual 1.430 1.645 -0.215 2.00e-02 2.50e+03 1.16e+02 ... (remaining 20419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.53: 27385 5.53 - 11.06: 211 11.06 - 16.60: 8 16.60 - 22.13: 8 22.13 - 27.66: 8 Bond angle restraints: 27620 Sorted by residual: angle pdb=" C04 A0O D 902 " pdb=" C06 A0O D 902 " pdb=" O01 A0O D 902 " ideal model delta sigma weight residual 117.13 144.79 -27.66 3.00e+00 1.11e-01 8.50e+01 angle pdb=" C04 A0O C 902 " pdb=" C06 A0O C 902 " pdb=" O01 A0O C 902 " ideal model delta sigma weight residual 117.13 144.76 -27.63 3.00e+00 1.11e-01 8.49e+01 angle pdb=" C04 A0O B 902 " pdb=" C06 A0O B 902 " pdb=" O01 A0O B 902 " ideal model delta sigma weight residual 117.13 144.72 -27.59 3.00e+00 1.11e-01 8.46e+01 angle pdb=" C04 A0O B 901 " pdb=" C06 A0O B 901 " pdb=" O01 A0O B 901 " ideal model delta sigma weight residual 117.13 144.72 -27.59 3.00e+00 1.11e-01 8.46e+01 angle pdb=" C04 A0O A 902 " pdb=" C06 A0O A 902 " pdb=" O01 A0O A 902 " ideal model delta sigma weight residual 117.13 144.69 -27.56 3.00e+00 1.11e-01 8.44e+01 ... (remaining 27615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 11136 15.14 - 30.29: 731 30.29 - 45.43: 217 45.43 - 60.57: 24 60.57 - 75.72: 16 Dihedral angle restraints: 12124 sinusoidal: 4948 harmonic: 7176 Sorted by residual: dihedral pdb=" CA ASP B 414 " pdb=" C ASP B 414 " pdb=" N ASN B 415 " pdb=" CA ASN B 415 " ideal model delta harmonic sigma weight residual 180.00 137.79 42.21 0 5.00e+00 4.00e-02 7.13e+01 dihedral pdb=" CA ASP C 414 " pdb=" C ASP C 414 " pdb=" N ASN C 415 " pdb=" CA ASN C 415 " ideal model delta harmonic sigma weight residual 180.00 137.79 42.21 0 5.00e+00 4.00e-02 7.13e+01 dihedral pdb=" CA ASP D 414 " pdb=" C ASP D 414 " pdb=" N ASN D 415 " pdb=" CA ASN D 415 " ideal model delta harmonic sigma weight residual 180.00 137.83 42.17 0 5.00e+00 4.00e-02 7.11e+01 ... (remaining 12121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2011 0.040 - 0.080: 899 0.080 - 0.119: 168 0.119 - 0.159: 46 0.159 - 0.199: 28 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CA GLU B 423 " pdb=" N GLU B 423 " pdb=" C GLU B 423 " pdb=" CB GLU B 423 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA VAL D 154 " pdb=" N VAL D 154 " pdb=" C VAL D 154 " pdb=" CB VAL D 154 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA VAL C 154 " pdb=" N VAL C 154 " pdb=" C VAL C 154 " pdb=" CB VAL C 154 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 3149 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 752 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.28e+00 pdb=" N PRO D 753 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 753 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 753 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 752 " 0.044 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO A 753 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 753 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 753 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 752 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO C 753 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 753 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 753 " -0.037 5.00e-02 4.00e+02 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5827 2.81 - 3.33: 18509 3.33 - 3.85: 31234 3.85 - 4.38: 37045 4.38 - 4.90: 61921 Nonbonded interactions: 154536 Sorted by model distance: nonbonded pdb=" OG1 THR A 399 " pdb=" O ASN A 401 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR D 399 " pdb=" O ASN D 401 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR C 399 " pdb=" O ASN C 401 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 399 " pdb=" O ASN B 401 " model vdw 2.284 3.040 nonbonded pdb=" OD1 ASP C 322 " pdb=" OH TYR C 359 " model vdw 2.285 3.040 ... (remaining 154531 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.490 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.010 0.217 20424 Z= 0.477 Angle : 1.327 27.659 27620 Z= 0.639 Chirality : 0.048 0.199 3152 Planarity : 0.006 0.067 3420 Dihedral : 11.678 75.715 7460 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.31 % Favored : 93.19 % Rotamer: Outliers : 1.11 % Allowed : 7.41 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -6.09 (0.09), residues: 2408 helix: -4.23 (0.05), residues: 1464 sheet: -1.41 (0.43), residues: 92 loop : -3.61 (0.15), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 696 TYR 0.020 0.003 TYR A 565 PHE 0.021 0.002 PHE D 261 TRP 0.024 0.003 TRP A 692 HIS 0.011 0.002 HIS A 417 Details of bonding type rmsd/Z covalent geometry : bond 0.01015 / 0.48 (20424) covalent geometry : angle 1.32722 / 0.64 (27620) hydrogen bonds : bond 0.31532 / 20.78 ( 989) hydrogen bonds : angle 9.67565 / 6.63 ( 2907) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 466 time to evaluate : 0.624 Fit side-chains REVERT: A 404 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7567 (mt) REVERT: A 418 GLU cc_start: 0.8162 (tp30) cc_final: 0.7841 (tp30) REVERT: A 436 PHE cc_start: 0.7828 (m-10) cc_final: 0.7588 (m-10) REVERT: A 449 PHE cc_start: 0.8080 (t80) cc_final: 0.7834 (t80) REVERT: A 489 PHE cc_start: 0.8454 (t80) cc_final: 0.8179 (t80) REVERT: A 650 TYR cc_start: 0.6730 (m-80) cc_final: 0.6450 (m-80) REVERT: A 695 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8195 (mm-40) REVERT: B 205 ASN cc_start: 0.8430 (m-40) cc_final: 0.7884 (t0) REVERT: B 404 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7714 (mt) REVERT: B 418 GLU cc_start: 0.8065 (tp30) cc_final: 0.7747 (tp30) REVERT: B 449 PHE cc_start: 0.8045 (t80) cc_final: 0.7838 (t80) REVERT: B 489 PHE cc_start: 0.8547 (t80) cc_final: 0.8260 (t80) REVERT: B 550 CYS cc_start: 0.8448 (m) cc_final: 0.7616 (m) REVERT: B 650 TYR cc_start: 0.6843 (m-80) cc_final: 0.6503 (m-80) REVERT: B 669 LEU cc_start: 0.9544 (tp) cc_final: 0.9341 (tt) REVERT: B 695 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8263 (tp40) REVERT: C 404 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7628 (mt) REVERT: C 418 GLU cc_start: 0.8169 (tp30) cc_final: 0.7868 (tp30) REVERT: C 449 PHE cc_start: 0.8094 (t80) cc_final: 0.7834 (t80) REVERT: C 650 TYR cc_start: 0.6653 (m-80) cc_final: 0.6388 (m-80) REVERT: C 695 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8215 (tp40) REVERT: D 404 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7611 (mt) REVERT: D 418 GLU cc_start: 0.8144 (tp30) cc_final: 0.7807 (tp30) REVERT: D 436 PHE cc_start: 0.7808 (m-10) cc_final: 0.7575 (m-10) REVERT: D 449 PHE cc_start: 0.8093 (t80) cc_final: 0.7826 (t80) REVERT: D 489 PHE cc_start: 0.8471 (t80) cc_final: 0.8222 (t80) REVERT: D 550 CYS cc_start: 0.8395 (m) cc_final: 0.7713 (m) REVERT: D 650 TYR cc_start: 0.6776 (m-80) cc_final: 0.6476 (m-80) REVERT: D 695 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8216 (tp40) outliers start: 24 outliers final: 8 residues processed: 490 average time/residue: 0.1224 time to fit residues: 93.5108 Evaluate side-chains 259 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 247 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 404 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS A 645 GLN A 671 ASN B 178 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 645 GLN B 671 ASN C 178 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 GLN C 671 ASN D 178 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN D 671 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.133997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096331 restraints weight = 40481.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099770 restraints weight = 20382.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102037 restraints weight = 13526.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103409 restraints weight = 10551.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104197 restraints weight = 9101.854| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20424 Z= 0.143 Angle : 0.715 12.988 27620 Z= 0.354 Chirality : 0.040 0.212 3152 Planarity : 0.005 0.048 3420 Dihedral : 6.402 45.952 2716 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.10 % Allowed : 12.78 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.32 (0.14), residues: 2408 helix: -1.62 (0.11), residues: 1552 sheet: -0.74 (0.46), residues: 92 loop : -3.40 (0.17), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 371 TYR 0.013 0.001 TYR C 321 PHE 0.013 0.001 PHE C 633 TRP 0.026 0.002 TRP A 493 HIS 0.005 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (20424) covalent geometry : angle 0.71544 / 0.35 (27620) hydrogen bonds : bond 0.05032 / 3.30 ( 989) hydrogen bonds : angle 4.64259 / 3.22 ( 2907) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 346 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8024 (tt0) cc_final: 0.7743 (tp30) REVERT: A 404 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 411 THR cc_start: 0.8601 (p) cc_final: 0.8364 (t) REVERT: A 418 GLU cc_start: 0.8080 (tp30) cc_final: 0.7729 (tp30) REVERT: A 430 HIS cc_start: 0.7616 (t70) cc_final: 0.7070 (t70) REVERT: A 479 MET cc_start: 0.6200 (mpp) cc_final: 0.5712 (mpp) REVERT: A 493 TRP cc_start: 0.8058 (t-100) cc_final: 0.7703 (t-100) REVERT: A 521 TRP cc_start: 0.7477 (t60) cc_final: 0.6492 (t60) REVERT: A 532 LEU cc_start: 0.8917 (tp) cc_final: 0.8684 (tp) REVERT: A 550 CYS cc_start: 0.7770 (m) cc_final: 0.7425 (m) REVERT: A 574 MET cc_start: 0.8242 (tpp) cc_final: 0.7906 (tpp) REVERT: A 741 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: B 160 HIS cc_start: 0.8219 (m-70) cc_final: 0.7891 (m-70) REVERT: B 221 ILE cc_start: 0.8747 (mm) cc_final: 0.8426 (mt) REVERT: B 334 GLU cc_start: 0.8097 (tt0) cc_final: 0.7729 (tp30) REVERT: B 404 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7668 (mt) REVERT: B 411 THR cc_start: 0.8667 (p) cc_final: 0.8435 (t) REVERT: B 418 GLU cc_start: 0.8050 (tp30) cc_final: 0.7669 (tp30) REVERT: B 430 HIS cc_start: 0.7613 (t70) cc_final: 0.7088 (t70) REVERT: B 449 PHE cc_start: 0.8042 (t80) cc_final: 0.7820 (t80) REVERT: B 461 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.7093 (t80) REVERT: B 479 MET cc_start: 0.6096 (mpp) cc_final: 0.5583 (mpp) REVERT: B 493 TRP cc_start: 0.8123 (t-100) cc_final: 0.7899 (t-100) REVERT: B 521 TRP cc_start: 0.7565 (t60) cc_final: 0.6631 (t60) REVERT: B 550 CYS cc_start: 0.7803 (m) cc_final: 0.7578 (m) REVERT: B 562 MET cc_start: 0.8637 (tpp) cc_final: 0.8360 (tpt) REVERT: B 574 MET cc_start: 0.8213 (tpp) cc_final: 0.7874 (tpp) REVERT: B 741 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: C 404 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7687 (mt) REVERT: C 411 THR cc_start: 0.8629 (p) cc_final: 0.8388 (t) REVERT: C 418 GLU cc_start: 0.8077 (tp30) cc_final: 0.7730 (tp30) REVERT: C 430 HIS cc_start: 0.7584 (t70) cc_final: 0.7048 (t70) REVERT: C 479 MET cc_start: 0.6311 (mpp) cc_final: 0.5822 (mpp) REVERT: C 521 TRP cc_start: 0.7483 (t60) cc_final: 0.6492 (t60) REVERT: C 532 LEU cc_start: 0.8967 (tp) cc_final: 0.8753 (tp) REVERT: C 550 CYS cc_start: 0.7701 (m) cc_final: 0.7356 (m) REVERT: C 574 MET cc_start: 0.8226 (tpp) cc_final: 0.7912 (tpp) REVERT: D 404 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7661 (mt) REVERT: D 411 THR cc_start: 0.8630 (p) cc_final: 0.8394 (t) REVERT: D 418 GLU cc_start: 0.8082 (tp30) cc_final: 0.7724 (tp30) REVERT: D 430 HIS cc_start: 0.7634 (t70) cc_final: 0.7089 (t70) REVERT: D 449 PHE cc_start: 0.8078 (t80) cc_final: 0.7875 (t80) REVERT: D 479 MET cc_start: 0.6208 (mpp) cc_final: 0.5721 (mpp) REVERT: D 493 TRP cc_start: 0.8118 (t-100) cc_final: 0.7910 (t-100) REVERT: D 521 TRP cc_start: 0.7486 (t60) cc_final: 0.6497 (t60) REVERT: D 532 LEU cc_start: 0.8953 (tp) cc_final: 0.8742 (tp) REVERT: D 550 CYS cc_start: 0.7785 (m) cc_final: 0.7441 (m) REVERT: D 555 MET cc_start: 0.8671 (ptp) cc_final: 0.8325 (ptp) REVERT: D 574 MET cc_start: 0.8196 (tpp) cc_final: 0.7864 (tpp) REVERT: D 741 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7749 (pm20) outliers start: 67 outliers final: 10 residues processed: 406 average time/residue: 0.1169 time to fit residues: 75.8711 Evaluate side-chains 265 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 113 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 38 optimal weight: 0.3980 chunk 160 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN A 197 ASN A 216 GLN A 410 ASN A 452 ASN A 529 GLN A 735 ASN B 143 GLN B 197 ASN B 216 GLN B 410 ASN B 523 HIS B 529 GLN B 735 ASN C 143 GLN C 197 ASN C 216 GLN C 410 ASN C 452 ASN C 529 GLN C 735 ASN D 143 GLN D 197 ASN D 216 GLN D 410 ASN D 529 GLN D 735 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.132236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.094205 restraints weight = 41032.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097595 restraints weight = 21085.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.099834 restraints weight = 14169.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101229 restraints weight = 11087.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.102117 restraints weight = 9555.889| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20424 Z= 0.144 Angle : 0.672 12.794 27620 Z= 0.329 Chirality : 0.041 0.233 3152 Planarity : 0.004 0.043 3420 Dihedral : 5.871 46.946 2704 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.86 % Favored : 96.01 % Rotamer: Outliers : 3.01 % Allowed : 15.51 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.80 (0.16), residues: 2408 helix: -0.24 (0.12), residues: 1560 sheet: -0.45 (0.45), residues: 92 loop : -3.30 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 371 TYR 0.016 0.001 TYR C 321 PHE 0.026 0.001 PHE A 489 TRP 0.023 0.002 TRP A 493 HIS 0.004 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (20424) covalent geometry : angle 0.67188 / 0.33 (27620) hydrogen bonds : bond 0.04061 / 2.65 ( 989) hydrogen bonds : angle 4.13305 / 2.87 ( 2907) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 261 time to evaluate : 0.697 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: A 404 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7569 (mt) REVERT: A 418 GLU cc_start: 0.8169 (tp30) cc_final: 0.7895 (tp30) REVERT: A 430 HIS cc_start: 0.7692 (t70) cc_final: 0.7141 (t70) REVERT: A 479 MET cc_start: 0.6116 (mpp) cc_final: 0.5577 (mpp) REVERT: A 521 TRP cc_start: 0.7409 (t60) cc_final: 0.6674 (t60) REVERT: A 532 LEU cc_start: 0.9003 (tp) cc_final: 0.8782 (tp) REVERT: A 550 CYS cc_start: 0.7771 (m) cc_final: 0.7357 (m) REVERT: A 574 MET cc_start: 0.8244 (tpp) cc_final: 0.7906 (tpp) REVERT: A 581 LYS cc_start: 0.9082 (ttpm) cc_final: 0.8241 (tptt) REVERT: A 741 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: B 322 ASP cc_start: 0.8808 (t70) cc_final: 0.8507 (t0) REVERT: B 404 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7607 (mt) REVERT: B 418 GLU cc_start: 0.8147 (tp30) cc_final: 0.7838 (tp30) REVERT: B 461 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7049 (t80) REVERT: B 521 TRP cc_start: 0.7479 (t60) cc_final: 0.6787 (t60) REVERT: B 562 MET cc_start: 0.8688 (tpp) cc_final: 0.8238 (tpt) REVERT: B 574 MET cc_start: 0.8216 (tpp) cc_final: 0.7888 (tpp) REVERT: B 578 MET cc_start: 0.8618 (tpp) cc_final: 0.8323 (tpp) REVERT: B 741 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: C 404 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7783 (mt) REVERT: C 418 GLU cc_start: 0.8168 (tp30) cc_final: 0.7878 (tp30) REVERT: C 479 MET cc_start: 0.6170 (mpp) cc_final: 0.5637 (mpp) REVERT: C 521 TRP cc_start: 0.7422 (t60) cc_final: 0.6693 (t60) REVERT: C 532 LEU cc_start: 0.9016 (tp) cc_final: 0.8791 (tp) REVERT: C 550 CYS cc_start: 0.7783 (m) cc_final: 0.7358 (m) REVERT: C 574 MET cc_start: 0.8228 (tpp) cc_final: 0.7872 (tpp) REVERT: C 581 LYS cc_start: 0.9075 (ttpm) cc_final: 0.8252 (tptt) REVERT: D 404 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7759 (mt) REVERT: D 418 GLU cc_start: 0.8178 (tp30) cc_final: 0.7896 (tp30) REVERT: D 430 HIS cc_start: 0.7702 (t70) cc_final: 0.7157 (t70) REVERT: D 488 MET cc_start: 0.7440 (tpp) cc_final: 0.7174 (tpp) REVERT: D 521 TRP cc_start: 0.7434 (t60) cc_final: 0.6729 (t60) REVERT: D 550 CYS cc_start: 0.7841 (m) cc_final: 0.7480 (m) REVERT: D 574 MET cc_start: 0.8241 (tpp) cc_final: 0.7894 (tpp) REVERT: D 581 LYS cc_start: 0.9078 (ttpm) cc_final: 0.8253 (tptt) REVERT: D 741 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7755 (pm20) outliers start: 65 outliers final: 23 residues processed: 312 average time/residue: 0.1150 time to fit residues: 58.2733 Evaluate side-chains 262 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 741 GLU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 741 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 147 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 0.0070 chunk 4 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.133139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095217 restraints weight = 40844.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098583 restraints weight = 21019.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100692 restraints weight = 14170.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102147 restraints weight = 11173.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103039 restraints weight = 9643.984| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20424 Z= 0.128 Angle : 0.608 10.289 27620 Z= 0.304 Chirality : 0.039 0.190 3152 Planarity : 0.004 0.040 3420 Dihedral : 5.469 50.249 2700 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.01 % Allowed : 15.51 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.06 (0.16), residues: 2408 helix: 0.42 (0.13), residues: 1584 sheet: -0.12 (0.48), residues: 92 loop : -3.34 (0.18), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 147 TYR 0.015 0.001 TYR A 321 PHE 0.019 0.001 PHE D 590 TRP 0.017 0.001 TRP A 493 HIS 0.010 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (20424) covalent geometry : angle 0.60768 / 0.30 (27620) hydrogen bonds : bond 0.03632 / 2.36 ( 989) hydrogen bonds : angle 3.92063 / 2.71 ( 2907) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 259 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8160 (tp30) cc_final: 0.7883 (tp30) REVERT: A 521 TRP cc_start: 0.7276 (t60) cc_final: 0.6535 (t60) REVERT: A 532 LEU cc_start: 0.9046 (tp) cc_final: 0.8807 (tp) REVERT: A 550 CYS cc_start: 0.7822 (m) cc_final: 0.7371 (m) REVERT: A 574 MET cc_start: 0.8181 (tpp) cc_final: 0.7971 (tpp) REVERT: A 581 LYS cc_start: 0.9161 (ttpm) cc_final: 0.8264 (tptt) REVERT: B 322 ASP cc_start: 0.8791 (t70) cc_final: 0.8581 (t0) REVERT: B 418 GLU cc_start: 0.8154 (tp30) cc_final: 0.7870 (tp30) REVERT: B 521 TRP cc_start: 0.7345 (t60) cc_final: 0.6647 (t60) REVERT: B 562 MET cc_start: 0.8589 (tpp) cc_final: 0.8056 (tpt) REVERT: B 578 MET cc_start: 0.8666 (tpp) cc_final: 0.8360 (tpp) REVERT: B 672 MET cc_start: 0.8992 (ttp) cc_final: 0.8444 (ttp) REVERT: B 741 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: C 404 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7884 (mt) REVERT: C 418 GLU cc_start: 0.8153 (tp30) cc_final: 0.7855 (tp30) REVERT: C 521 TRP cc_start: 0.7274 (t60) cc_final: 0.6532 (t60) REVERT: C 532 LEU cc_start: 0.9055 (tp) cc_final: 0.8820 (tp) REVERT: C 550 CYS cc_start: 0.7839 (m) cc_final: 0.7381 (m) REVERT: C 574 MET cc_start: 0.8225 (tpp) cc_final: 0.8015 (tpp) REVERT: C 581 LYS cc_start: 0.9164 (ttpm) cc_final: 0.8266 (tptt) REVERT: D 322 ASP cc_start: 0.8736 (t70) cc_final: 0.8532 (t0) REVERT: D 418 GLU cc_start: 0.8167 (tp30) cc_final: 0.7880 (tp30) REVERT: D 521 TRP cc_start: 0.7326 (t60) cc_final: 0.6639 (t60) REVERT: D 574 MET cc_start: 0.8149 (tpp) cc_final: 0.7939 (tpp) outliers start: 65 outliers final: 30 residues processed: 306 average time/residue: 0.1161 time to fit residues: 58.2666 Evaluate side-chains 252 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 715 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 160 HIS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 741 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 167 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 212 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 194 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN A 255 GLN B 182 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN C 244 HIS C 255 GLN C 580 GLN D 182 ASN D 244 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.133379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095339 restraints weight = 40663.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098752 restraints weight = 20990.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.100964 restraints weight = 14149.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102336 restraints weight = 11117.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.103112 restraints weight = 9595.631| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20424 Z= 0.126 Angle : 0.606 9.737 27620 Z= 0.300 Chirality : 0.039 0.172 3152 Planarity : 0.003 0.040 3420 Dihedral : 5.260 50.059 2694 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.82 % Allowed : 16.25 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.74 (0.17), residues: 2408 helix: 0.71 (0.13), residues: 1576 sheet: -0.13 (0.49), residues: 92 loop : -3.25 (0.18), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 147 TYR 0.017 0.001 TYR A 661 PHE 0.023 0.001 PHE A 590 TRP 0.011 0.001 TRP A 710 HIS 0.009 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (20424) covalent geometry : angle 0.60566 / 0.30 (27620) hydrogen bonds : bond 0.03502 / 2.29 ( 989) hydrogen bonds : angle 3.84829 / 2.66 ( 2907) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 241 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8222 (tp30) cc_final: 0.7928 (tp30) REVERT: A 436 PHE cc_start: 0.8093 (m-10) cc_final: 0.7884 (m-10) REVERT: A 521 TRP cc_start: 0.7225 (t60) cc_final: 0.6461 (t60) REVERT: A 532 LEU cc_start: 0.9085 (tp) cc_final: 0.8853 (tp) REVERT: A 550 CYS cc_start: 0.7796 (m) cc_final: 0.7303 (m) REVERT: A 574 MET cc_start: 0.8195 (tpp) cc_final: 0.7993 (tpp) REVERT: A 715 PHE cc_start: 0.6386 (OUTLIER) cc_final: 0.6169 (m-80) REVERT: B 418 GLU cc_start: 0.8211 (tp30) cc_final: 0.7913 (tp30) REVERT: B 521 TRP cc_start: 0.7266 (t60) cc_final: 0.6553 (t60) REVERT: B 562 MET cc_start: 0.8562 (tpp) cc_final: 0.8011 (tpt) REVERT: B 717 MET cc_start: 0.7142 (tpt) cc_final: 0.6942 (tpt) REVERT: B 741 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: C 418 GLU cc_start: 0.8200 (tp30) cc_final: 0.7883 (tp30) REVERT: C 436 PHE cc_start: 0.8221 (m-10) cc_final: 0.7993 (m-10) REVERT: C 521 TRP cc_start: 0.7207 (t60) cc_final: 0.6433 (t60) REVERT: C 532 LEU cc_start: 0.9078 (tp) cc_final: 0.8839 (tp) REVERT: C 550 CYS cc_start: 0.7780 (m) cc_final: 0.7261 (m) REVERT: C 581 LYS cc_start: 0.9168 (ttpm) cc_final: 0.8302 (tptt) REVERT: D 418 GLU cc_start: 0.8235 (tp30) cc_final: 0.7934 (tp30) REVERT: D 521 TRP cc_start: 0.7254 (t60) cc_final: 0.6506 (t60) outliers start: 61 outliers final: 36 residues processed: 283 average time/residue: 0.1041 time to fit residues: 49.4465 Evaluate side-chains 249 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 715 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 741 GLU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 741 GLU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 228 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 216 GLN B 216 GLN B 244 HIS C 216 GLN D 178 ASN D 216 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.135869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094776 restraints weight = 41953.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.098404 restraints weight = 21004.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100742 restraints weight = 14038.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.102068 restraints weight = 11002.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.103124 restraints weight = 9544.942| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20424 Z= 0.118 Angle : 0.613 14.958 27620 Z= 0.298 Chirality : 0.039 0.195 3152 Planarity : 0.003 0.039 3420 Dihedral : 5.084 51.553 2692 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.01 % Allowed : 16.62 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.59 (0.17), residues: 2408 helix: 0.82 (0.13), residues: 1576 sheet: -0.20 (0.49), residues: 92 loop : -3.18 (0.18), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.016 0.001 TYR A 321 PHE 0.013 0.001 PHE A 590 TRP 0.012 0.001 TRP A 710 HIS 0.008 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (20424) covalent geometry : angle 0.61344 / 0.30 (27620) hydrogen bonds : bond 0.03363 / 2.19 ( 989) hydrogen bonds : angle 3.78440 / 2.62 ( 2907) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 238 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 MET cc_start: 0.5958 (mpp) cc_final: 0.5532 (mpp) REVERT: A 521 TRP cc_start: 0.7192 (t60) cc_final: 0.6438 (t60) REVERT: A 532 LEU cc_start: 0.9090 (tp) cc_final: 0.8850 (tp) REVERT: A 550 CYS cc_start: 0.7730 (m) cc_final: 0.7242 (m) REVERT: B 336 MET cc_start: 0.8626 (ttm) cc_final: 0.8341 (ttp) REVERT: B 479 MET cc_start: 0.5882 (mpp) cc_final: 0.5597 (mpp) REVERT: B 521 TRP cc_start: 0.7207 (t60) cc_final: 0.6468 (t60) REVERT: B 562 MET cc_start: 0.8512 (tpp) cc_final: 0.7921 (tpt) REVERT: C 418 GLU cc_start: 0.8124 (tp30) cc_final: 0.7895 (tp30) REVERT: C 479 MET cc_start: 0.5970 (mpp) cc_final: 0.5549 (mpp) REVERT: C 521 TRP cc_start: 0.7191 (t60) cc_final: 0.6436 (t60) REVERT: C 532 LEU cc_start: 0.9088 (tp) cc_final: 0.8839 (tp) REVERT: C 550 CYS cc_start: 0.7750 (m) cc_final: 0.7238 (m) REVERT: C 578 MET cc_start: 0.8628 (tpp) cc_final: 0.8387 (tpp) REVERT: C 731 CYS cc_start: 0.8609 (m) cc_final: 0.8064 (m) REVERT: C 738 LYS cc_start: 0.8630 (mttt) cc_final: 0.8272 (pttm) REVERT: D 418 GLU cc_start: 0.8124 (tp30) cc_final: 0.7918 (tp30) REVERT: D 521 TRP cc_start: 0.7224 (t60) cc_final: 0.6481 (t60) REVERT: D 578 MET cc_start: 0.8648 (tpp) cc_final: 0.8433 (tpp) REVERT: D 696 ARG cc_start: 0.8671 (tpp80) cc_final: 0.8446 (tpp80) REVERT: D 715 PHE cc_start: 0.6806 (m-80) cc_final: 0.6551 (m-80) outliers start: 65 outliers final: 33 residues processed: 283 average time/residue: 0.1159 time to fit residues: 52.7492 Evaluate side-chains 247 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 155 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN A 452 ASN B 410 ASN C 178 ASN C 410 ASN C 452 ASN C 580 GLN D 255 GLN D 410 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.132662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.093826 restraints weight = 40876.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097181 restraints weight = 21403.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099346 restraints weight = 14594.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.100627 restraints weight = 11549.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101529 restraints weight = 10048.517| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20424 Z= 0.139 Angle : 0.653 15.071 27620 Z= 0.314 Chirality : 0.040 0.179 3152 Planarity : 0.003 0.038 3420 Dihedral : 5.183 50.340 2692 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.87 % Allowed : 18.10 % Favored : 79.03 % 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: -0.57 (0.17), residues: 2408 helix: 0.83 (0.13), residues: 1568 sheet: 0.10 (0.50), residues: 88 loop : -3.15 (0.18), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 696 TYR 0.022 0.001 TYR D 321 PHE 0.013 0.001 PHE C 590 TRP 0.011 0.001 TRP A 710 HIS 0.004 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (20424) covalent geometry : angle 0.65271 / 0.31 (27620) hydrogen bonds : bond 0.03377 / 2.20 ( 989) hydrogen bonds : angle 3.81790 / 2.64 ( 2907) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6702 (t80) REVERT: A 479 MET cc_start: 0.5846 (mpp) cc_final: 0.5411 (mpp) REVERT: A 521 TRP cc_start: 0.7164 (t60) cc_final: 0.6421 (t60) REVERT: A 532 LEU cc_start: 0.9090 (tp) cc_final: 0.8882 (tp) REVERT: A 550 CYS cc_start: 0.7632 (m) cc_final: 0.7204 (m) REVERT: A 731 CYS cc_start: 0.8575 (m) cc_final: 0.7991 (m) REVERT: B 351 MET cc_start: 0.8351 (mtt) cc_final: 0.8150 (mtp) REVERT: B 479 MET cc_start: 0.5820 (mpp) cc_final: 0.5525 (mpp) REVERT: B 521 TRP cc_start: 0.7178 (t60) cc_final: 0.6474 (t60) REVERT: B 562 MET cc_start: 0.8537 (tpp) cc_final: 0.7967 (tpt) REVERT: B 731 CYS cc_start: 0.8618 (m) cc_final: 0.8058 (m) REVERT: C 479 MET cc_start: 0.5839 (mpp) cc_final: 0.5422 (mpp) REVERT: C 521 TRP cc_start: 0.7182 (t60) cc_final: 0.6463 (t60) REVERT: C 532 LEU cc_start: 0.9097 (tp) cc_final: 0.8815 (tp) REVERT: C 550 CYS cc_start: 0.7740 (m) cc_final: 0.7154 (m) REVERT: C 731 CYS cc_start: 0.8627 (m) cc_final: 0.8084 (m) REVERT: C 738 LYS cc_start: 0.8631 (mttt) cc_final: 0.8327 (pttm) REVERT: D 479 MET cc_start: 0.5838 (mpp) cc_final: 0.5566 (mpp) REVERT: D 521 TRP cc_start: 0.7213 (t60) cc_final: 0.6479 (t60) REVERT: D 578 MET cc_start: 0.8583 (tpp) cc_final: 0.8332 (tpp) outliers start: 62 outliers final: 35 residues processed: 267 average time/residue: 0.1235 time to fit residues: 54.1646 Evaluate side-chains 254 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 741 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 404 LEU Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 54 optimal weight: 5.9990 chunk 175 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 chunk 221 optimal weight: 0.3980 chunk 94 optimal weight: 8.9990 chunk 67 optimal weight: 0.0970 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 121 optimal weight: 0.0000 chunk 15 optimal weight: 0.9990 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN B 178 ASN B 279 GLN B 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.138882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098453 restraints weight = 41664.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.102197 restraints weight = 21122.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.104578 restraints weight = 14090.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.106034 restraints weight = 11009.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106753 restraints weight = 9496.953| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20424 Z= 0.107 Angle : 0.637 13.799 27620 Z= 0.303 Chirality : 0.039 0.175 3152 Planarity : 0.003 0.041 3420 Dihedral : 4.863 49.161 2692 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.39 % Allowed : 19.58 % Favored : 79.03 % 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 (0.17), residues: 2408 helix: 0.98 (0.13), residues: 1560 sheet: 0.09 (0.51), residues: 88 loop : -3.01 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 696 TYR 0.021 0.001 TYR D 321 PHE 0.015 0.001 PHE D 590 TRP 0.013 0.001 TRP D 710 HIS 0.004 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (20424) covalent geometry : angle 0.63676 / 0.30 (27620) hydrogen bonds : bond 0.03187 / 2.08 ( 989) hydrogen bonds : angle 3.72775 / 2.58 ( 2907) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.771 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 430 HIS cc_start: 0.7467 (t70) cc_final: 0.7249 (t-90) REVERT: A 461 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6631 (t80) REVERT: A 479 MET cc_start: 0.5719 (mpp) cc_final: 0.5327 (mpp) REVERT: A 521 TRP cc_start: 0.7088 (t60) cc_final: 0.6356 (t60) REVERT: A 532 LEU cc_start: 0.9068 (tp) cc_final: 0.8829 (tp) REVERT: A 550 CYS cc_start: 0.7643 (m) cc_final: 0.7183 (m) REVERT: A 731 CYS cc_start: 0.8455 (m) cc_final: 0.7928 (m) REVERT: B 172 LEU cc_start: 0.8616 (tp) cc_final: 0.8407 (tp) REVERT: B 336 MET cc_start: 0.8716 (ttm) cc_final: 0.8492 (ttp) REVERT: B 479 MET cc_start: 0.5712 (mpp) cc_final: 0.5240 (mpp) REVERT: B 521 TRP cc_start: 0.7134 (t60) cc_final: 0.6443 (t60) REVERT: B 562 MET cc_start: 0.8469 (tpp) cc_final: 0.7838 (tpt) REVERT: B 574 MET cc_start: 0.8305 (tpp) cc_final: 0.7962 (tpt) REVERT: B 731 CYS cc_start: 0.8495 (m) cc_final: 0.7920 (m) REVERT: C 479 MET cc_start: 0.5724 (mpp) cc_final: 0.5335 (mpp) REVERT: C 521 TRP cc_start: 0.7131 (t60) cc_final: 0.6392 (t60) REVERT: C 532 LEU cc_start: 0.9078 (tp) cc_final: 0.8831 (tp) REVERT: C 550 CYS cc_start: 0.7616 (m) cc_final: 0.7181 (m) REVERT: C 581 LYS cc_start: 0.9053 (ttpm) cc_final: 0.8209 (tptt) REVERT: C 731 CYS cc_start: 0.8448 (m) cc_final: 0.7902 (m) REVERT: C 738 LYS cc_start: 0.8628 (mttt) cc_final: 0.8184 (pttm) REVERT: D 479 MET cc_start: 0.5726 (mpp) cc_final: 0.5278 (mpp) REVERT: D 521 TRP cc_start: 0.7149 (t60) cc_final: 0.6437 (t60) REVERT: D 574 MET cc_start: 0.8288 (tpp) cc_final: 0.7981 (tpt) REVERT: D 731 CYS cc_start: 0.8560 (m) cc_final: 0.7982 (m) outliers start: 30 outliers final: 18 residues processed: 283 average time/residue: 0.1291 time to fit residues: 58.3482 Evaluate side-chains 239 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 741 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 694 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 228 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 49 optimal weight: 50.0000 chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.133451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094657 restraints weight = 40606.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097987 restraints weight = 21641.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100162 restraints weight = 14878.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101375 restraints weight = 11819.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102317 restraints weight = 10314.765| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20424 Z= 0.141 Angle : 0.687 13.775 27620 Z= 0.325 Chirality : 0.040 0.263 3152 Planarity : 0.004 0.040 3420 Dihedral : 4.989 47.818 2692 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.81 % Allowed : 19.49 % Favored : 78.70 % 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 (0.17), residues: 2408 helix: 1.08 (0.13), residues: 1540 sheet: 0.30 (0.51), residues: 88 loop : -3.00 (0.18), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 696 TYR 0.022 0.001 TYR D 321 PHE 0.023 0.001 PHE C 715 TRP 0.020 0.001 TRP B 710 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (20424) covalent geometry : angle 0.68711 / 0.32 (27620) hydrogen bonds : bond 0.03285 / 2.14 ( 989) hydrogen bonds : angle 3.80476 / 2.63 ( 2907) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6720 (t80) REVERT: A 479 MET cc_start: 0.5742 (mpp) cc_final: 0.5356 (mpp) REVERT: A 521 TRP cc_start: 0.7129 (t60) cc_final: 0.6374 (t60) REVERT: A 523 HIS cc_start: 0.7042 (m90) cc_final: 0.6790 (m170) REVERT: A 550 CYS cc_start: 0.7854 (m) cc_final: 0.7444 (m) REVERT: A 574 MET cc_start: 0.8328 (tpp) cc_final: 0.8077 (tpt) REVERT: A 665 THR cc_start: 0.8987 (m) cc_final: 0.8677 (p) REVERT: A 672 MET cc_start: 0.8867 (tpp) cc_final: 0.8609 (tpp) REVERT: A 731 CYS cc_start: 0.8548 (m) cc_final: 0.8002 (m) REVERT: B 479 MET cc_start: 0.5768 (mpp) cc_final: 0.5471 (mpp) REVERT: B 521 TRP cc_start: 0.7121 (t60) cc_final: 0.6426 (t60) REVERT: B 545 LYS cc_start: 0.7326 (tptm) cc_final: 0.7057 (ptpt) REVERT: B 562 MET cc_start: 0.8537 (tpp) cc_final: 0.8022 (tpt) REVERT: B 731 CYS cc_start: 0.8652 (m) cc_final: 0.8099 (m) REVERT: C 461 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6688 (t80) REVERT: C 479 MET cc_start: 0.5763 (mpp) cc_final: 0.5450 (mpp) REVERT: C 521 TRP cc_start: 0.7102 (t60) cc_final: 0.6355 (t60) REVERT: C 532 LEU cc_start: 0.9088 (tp) cc_final: 0.8840 (tp) REVERT: C 550 CYS cc_start: 0.7828 (m) cc_final: 0.7308 (m) REVERT: C 731 CYS cc_start: 0.8593 (m) cc_final: 0.8062 (m) REVERT: C 738 LYS cc_start: 0.8629 (mttt) cc_final: 0.8423 (pttm) REVERT: D 479 MET cc_start: 0.5754 (mpp) cc_final: 0.5303 (mpp) REVERT: D 521 TRP cc_start: 0.7114 (t60) cc_final: 0.6361 (t60) REVERT: D 574 MET cc_start: 0.8287 (tpp) cc_final: 0.8068 (tpt) REVERT: D 731 CYS cc_start: 0.8598 (m) cc_final: 0.8034 (m) outliers start: 39 outliers final: 26 residues processed: 246 average time/residue: 0.1287 time to fit residues: 51.2758 Evaluate side-chains 247 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 496 CYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 233 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN B 298 ASN B 410 ASN C 410 ASN C 452 ASN C 523 HIS D 410 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.133063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.094107 restraints weight = 40630.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097430 restraints weight = 21664.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099572 restraints weight = 14902.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100906 restraints weight = 11882.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101667 restraints weight = 10329.988| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20424 Z= 0.142 Angle : 0.688 13.896 27620 Z= 0.327 Chirality : 0.040 0.237 3152 Planarity : 0.003 0.037 3420 Dihedral : 5.036 48.281 2692 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.44 % Allowed : 20.42 % Favored : 78.15 % 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 (0.17), residues: 2408 helix: 0.96 (0.13), residues: 1552 sheet: 0.39 (0.51), residues: 88 loop : -2.92 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 696 TYR 0.021 0.001 TYR D 321 PHE 0.023 0.001 PHE C 715 TRP 0.016 0.001 TRP B 710 HIS 0.004 0.001 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (20424) covalent geometry : angle 0.68832 / 0.33 (27620) hydrogen bonds : bond 0.03374 / 2.18 ( 989) hydrogen bonds : angle 3.86879 / 2.68 ( 2907) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6749 (t80) REVERT: A 479 MET cc_start: 0.5740 (mpp) cc_final: 0.5351 (mpp) REVERT: A 521 TRP cc_start: 0.7077 (t60) cc_final: 0.6343 (t60) REVERT: A 523 HIS cc_start: 0.6985 (m90) cc_final: 0.6743 (m170) REVERT: A 555 MET cc_start: 0.8349 (mtm) cc_final: 0.8081 (mtm) REVERT: A 574 MET cc_start: 0.8375 (tpp) cc_final: 0.8132 (tpt) REVERT: A 665 THR cc_start: 0.9006 (m) cc_final: 0.8692 (p) REVERT: A 731 CYS cc_start: 0.8542 (m) cc_final: 0.8022 (m) REVERT: B 479 MET cc_start: 0.5755 (mpp) cc_final: 0.5462 (mpp) REVERT: B 521 TRP cc_start: 0.7150 (t60) cc_final: 0.6471 (t60) REVERT: B 545 LYS cc_start: 0.7322 (tptm) cc_final: 0.7036 (ptpt) REVERT: B 562 MET cc_start: 0.8556 (tpp) cc_final: 0.8020 (tpt) REVERT: B 731 CYS cc_start: 0.8663 (m) cc_final: 0.8124 (m) REVERT: C 461 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6727 (t80) REVERT: C 521 TRP cc_start: 0.7082 (t60) cc_final: 0.6336 (t60) REVERT: C 523 HIS cc_start: 0.7106 (m90) cc_final: 0.6881 (m170) REVERT: C 550 CYS cc_start: 0.7777 (m) cc_final: 0.7356 (m) REVERT: C 731 CYS cc_start: 0.8591 (m) cc_final: 0.8078 (m) REVERT: C 738 LYS cc_start: 0.8634 (mttt) cc_final: 0.8422 (pttm) REVERT: D 479 MET cc_start: 0.5760 (mpp) cc_final: 0.5313 (mpp) REVERT: D 521 TRP cc_start: 0.7132 (t60) cc_final: 0.6376 (t60) REVERT: D 731 CYS cc_start: 0.8590 (m) cc_final: 0.8072 (m) outliers start: 31 outliers final: 27 residues processed: 245 average time/residue: 0.1244 time to fit residues: 49.1686 Evaluate side-chains 249 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 741 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 701 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 40 optimal weight: 20.0000 chunk 125 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN C 452 ASN D 523 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.132834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093853 restraints weight = 40675.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097166 restraints weight = 21677.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.099287 restraints weight = 14907.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100495 restraints weight = 11879.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101277 restraints weight = 10383.502| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20424 Z= 0.142 Angle : 0.699 13.755 27620 Z= 0.331 Chirality : 0.040 0.225 3152 Planarity : 0.004 0.051 3420 Dihedral : 5.056 48.651 2692 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.57 % Allowed : 20.42 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2408 helix: 0.93 (0.13), residues: 1552 sheet: 0.43 (0.51), residues: 88 loop : -2.93 (0.18), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 696 TYR 0.021 0.001 TYR D 321 PHE 0.022 0.001 PHE C 715 TRP 0.016 0.001 TRP B 710 HIS 0.004 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (20424) covalent geometry : angle 0.69939 / 0.33 (27620) hydrogen bonds : bond 0.03401 / 2.21 ( 989) hydrogen bonds : angle 3.88456 / 2.68 ( 2907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3255.24 seconds wall clock time: 57 minutes 4.97 seconds (3424.97 seconds total)