Starting phenix.real_space_refine on Thu Mar 5 06:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ras_24385/03_2026/7ras_24385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ras_24385/03_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_24385/03_2026/7ras_24385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ras_24385/03_2026/7ras_24385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ras_24385/03_2026/7ras_24385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ras_24385/03_2026/7ras_24385.map" } 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-5986/lib/python3.9/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: 4.75, 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: 4.35 Conformation dependent library (CDL) restraints added in 925.5 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: 0.43 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: 3.11 Time building geometry restraints manager: 2.34 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: 225 45.43 - 60.57: 24 60.57 - 75.72: 24 Dihedral angle restraints: 12140 sinusoidal: 4964 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 12137 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: 0.05 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: 2.350 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.880 Find NCS groups from input model: 0.180 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 11.929 75.715 7476 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 covalent geometry : bond 0.01015 (20424) covalent geometry : angle 1.32722 (27620) hydrogen bonds : bond 0.31532 ( 989) hydrogen bonds : angle 9.67565 ( 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 : 0.820 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: 0.1349 time to fit residues: 103.7741 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 : 0.775 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4053 r_free = 0.4053 target = 0.134017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096348 restraints weight = 40498.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099802 restraints weight = 20414.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102043 restraints weight = 13543.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103424 restraints weight = 10577.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104167 restraints weight = 9122.444| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3031 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= 0.143 Angle : 0.715 12.927 27620 Z= 0.354 Chirality : 0.040 0.210 3152 Planarity : 0.005 0.048 3420 Dihedral : 6.584 46.314 2732 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.06 % Allowed : 12.69 % Favored : 84.26 % 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: -3.31 (0.14), residues: 2408 helix: -1.62 (0.11), residues: 1552 sheet: -0.73 (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 A 371 TYR 0.013 0.001 TYR D 321 PHE 0.013 0.001 PHE C 633 TRP 0.025 0.002 TRP A 493 HIS 0.005 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00307 (20424) covalent geometry : angle 0.71456 (27620) hydrogen bonds : bond 0.05001 ( 989) hydrogen bonds : angle 4.62989 ( 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: 66 poor density : 347 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7991 (tt0) cc_final: 0.7732 (tp30) REVERT: A 404 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7683 (mt) REVERT: A 411 THR cc_start: 0.8591 (p) cc_final: 0.8351 (t) REVERT: A 418 GLU cc_start: 0.8073 (tp30) cc_final: 0.7726 (tp30) REVERT: A 430 HIS cc_start: 0.7584 (t70) cc_final: 0.7092 (t70) REVERT: A 479 MET cc_start: 0.6198 (mpp) cc_final: 0.5707 (mpp) REVERT: A 493 TRP cc_start: 0.8065 (t-100) cc_final: 0.7711 (t-100) REVERT: A 521 TRP cc_start: 0.7468 (t60) cc_final: 0.6485 (t60) REVERT: A 532 LEU cc_start: 0.8953 (tp) cc_final: 0.8741 (tp) REVERT: A 550 CYS cc_start: 0.7784 (m) cc_final: 0.7436 (m) REVERT: A 574 MET cc_start: 0.8200 (tpp) cc_final: 0.7869 (tpp) REVERT: A 741 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7747 (pm20) REVERT: B 160 HIS cc_start: 0.8213 (m-70) cc_final: 0.7880 (m-70) REVERT: B 221 ILE cc_start: 0.8760 (mm) cc_final: 0.8441 (mt) REVERT: B 334 GLU cc_start: 0.8076 (tt0) cc_final: 0.7725 (tp30) REVERT: B 404 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7700 (mt) REVERT: B 411 THR cc_start: 0.8657 (p) cc_final: 0.8424 (t) REVERT: B 418 GLU cc_start: 0.8042 (tp30) cc_final: 0.7668 (tp30) REVERT: B 430 HIS cc_start: 0.7574 (t70) cc_final: 0.7107 (t70) REVERT: B 449 PHE cc_start: 0.8040 (t80) cc_final: 0.7824 (t80) REVERT: B 461 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7095 (t80) REVERT: B 479 MET cc_start: 0.6098 (mpp) cc_final: 0.5581 (mpp) REVERT: B 493 TRP cc_start: 0.8126 (t-100) cc_final: 0.7878 (t-100) REVERT: B 521 TRP cc_start: 0.7558 (t60) cc_final: 0.6621 (t60) REVERT: B 550 CYS cc_start: 0.7816 (m) cc_final: 0.7591 (m) REVERT: B 562 MET cc_start: 0.8639 (tpp) cc_final: 0.8373 (tpt) REVERT: B 574 MET cc_start: 0.8211 (tpp) cc_final: 0.7871 (tpp) REVERT: B 669 LEU cc_start: 0.9222 (tp) cc_final: 0.9022 (tt) REVERT: B 741 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: C 404 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7718 (mt) REVERT: C 411 THR cc_start: 0.8619 (p) cc_final: 0.8376 (t) REVERT: C 418 GLU cc_start: 0.8072 (tp30) cc_final: 0.7726 (tp30) REVERT: C 430 HIS cc_start: 0.7530 (t70) cc_final: 0.7049 (t70) REVERT: C 479 MET cc_start: 0.6298 (mpp) cc_final: 0.5808 (mpp) REVERT: C 521 TRP cc_start: 0.7484 (t60) cc_final: 0.6510 (t60) REVERT: C 532 LEU cc_start: 0.8971 (tp) cc_final: 0.8756 (tp) REVERT: C 550 CYS cc_start: 0.7715 (m) cc_final: 0.7367 (m) REVERT: C 574 MET cc_start: 0.8248 (tpp) cc_final: 0.7934 (tpp) REVERT: D 404 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7687 (mt) REVERT: D 411 THR cc_start: 0.8620 (p) cc_final: 0.8381 (t) REVERT: D 418 GLU cc_start: 0.8077 (tp30) cc_final: 0.7722 (tp30) REVERT: D 430 HIS cc_start: 0.7589 (t70) cc_final: 0.7100 (t70) REVERT: D 449 PHE cc_start: 0.8083 (t80) cc_final: 0.7874 (t80) REVERT: D 479 MET cc_start: 0.6204 (mpp) cc_final: 0.5717 (mpp) REVERT: D 493 TRP cc_start: 0.8114 (t-100) cc_final: 0.7913 (t-100) REVERT: D 521 TRP cc_start: 0.7489 (t60) cc_final: 0.6514 (t60) REVERT: D 532 LEU cc_start: 0.8962 (tp) cc_final: 0.8750 (tp) REVERT: D 550 CYS cc_start: 0.7796 (m) cc_final: 0.7451 (m) REVERT: D 555 MET cc_start: 0.8663 (ptp) cc_final: 0.8336 (ptp) REVERT: D 574 MET cc_start: 0.8193 (tpp) cc_final: 0.7862 (tpp) REVERT: D 741 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7736 (pm20) outliers start: 66 outliers final: 9 residues processed: 404 average time/residue: 0.1257 time to fit residues: 81.4526 Evaluate side-chains 259 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 230 optimal weight: 20.0000 chunk 38 optimal weight: 0.0870 chunk 160 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 197 ASN A 216 GLN A 410 ASN A 452 ASN A 735 ASN B 143 GLN B 197 ASN B 216 GLN B 410 ASN B 523 HIS B 735 ASN C 143 GLN C 197 ASN C 216 GLN C 410 ASN C 452 ASN C 735 ASN D 143 GLN D 197 ASN D 216 GLN D 410 ASN D 452 ASN D 529 GLN D 735 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.131611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.093892 restraints weight = 41061.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098196 restraints weight = 21128.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099525 restraints weight = 12540.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100381 restraints weight = 10702.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.100734 restraints weight = 9478.625| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20424 Z= 0.153 Angle : 0.675 12.662 27620 Z= 0.333 Chirality : 0.041 0.232 3152 Planarity : 0.004 0.043 3420 Dihedral : 6.251 44.771 2720 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.76 % Rotamer: Outliers : 3.38 % Allowed : 15.51 % Favored : 81.11 % 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: -0.23 (0.12), residues: 1560 sheet: -0.46 (0.45), residues: 92 loop : -3.32 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 371 TYR 0.016 0.001 TYR C 321 PHE 0.025 0.001 PHE A 489 TRP 0.022 0.002 TRP A 493 HIS 0.005 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00348 (20424) covalent geometry : angle 0.67465 (27620) hydrogen bonds : bond 0.04122 ( 989) hydrogen bonds : angle 4.15893 ( 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 324 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 251 time to evaluate : 0.868 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: 0.8205 (OUTLIER) cc_final: 0.7865 (mt) REVERT: A 418 GLU cc_start: 0.8168 (tp30) cc_final: 0.7914 (tp30) REVERT: A 430 HIS cc_start: 0.7665 (t70) cc_final: 0.7158 (t70) REVERT: A 479 MET cc_start: 0.6116 (mpp) cc_final: 0.5583 (mpp) REVERT: A 521 TRP cc_start: 0.7416 (t60) cc_final: 0.6693 (t60) REVERT: A 532 LEU cc_start: 0.8994 (tp) cc_final: 0.8772 (tp) REVERT: A 550 CYS cc_start: 0.7758 (m) cc_final: 0.7362 (m) REVERT: A 574 MET cc_start: 0.8243 (tpp) cc_final: 0.7924 (tpp) REVERT: A 581 LYS cc_start: 0.9141 (ttpm) cc_final: 0.8297 (tptt) REVERT: A 741 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: B 418 GLU cc_start: 0.8135 (tp30) cc_final: 0.7851 (tp30) REVERT: B 430 HIS cc_start: 0.7692 (t70) cc_final: 0.6962 (t70) REVERT: B 461 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7055 (t80) REVERT: B 488 MET cc_start: 0.7511 (tpt) cc_final: 0.7144 (tpp) REVERT: B 521 TRP cc_start: 0.7482 (t60) cc_final: 0.6795 (t60) REVERT: B 562 MET cc_start: 0.8720 (tpp) cc_final: 0.8312 (tpt) REVERT: B 574 MET cc_start: 0.8207 (tpp) cc_final: 0.7889 (tpp) REVERT: B 578 MET cc_start: 0.8611 (tpp) cc_final: 0.8321 (tpp) REVERT: B 741 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: C 404 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7961 (mt) REVERT: C 418 GLU cc_start: 0.8167 (tp30) cc_final: 0.7898 (tp30) REVERT: C 430 HIS cc_start: 0.7656 (t70) cc_final: 0.7442 (t-90) REVERT: C 479 MET cc_start: 0.6178 (mpp) cc_final: 0.5648 (mpp) REVERT: C 521 TRP cc_start: 0.7419 (t60) cc_final: 0.6703 (t60) REVERT: C 532 LEU cc_start: 0.9007 (tp) cc_final: 0.8783 (tp) REVERT: C 550 CYS cc_start: 0.7748 (m) cc_final: 0.7326 (m) REVERT: C 574 MET cc_start: 0.8223 (tpp) cc_final: 0.7887 (tpp) REVERT: C 581 LYS cc_start: 0.9126 (ttpm) cc_final: 0.8302 (tptt) REVERT: D 404 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7952 (mt) REVERT: D 418 GLU cc_start: 0.8173 (tp30) cc_final: 0.7910 (tp30) REVERT: D 430 HIS cc_start: 0.7684 (t70) cc_final: 0.7173 (t70) REVERT: D 479 MET cc_start: 0.6076 (mpp) cc_final: 0.5528 (mpp) REVERT: D 488 MET cc_start: 0.7432 (tpp) cc_final: 0.7171 (tpp) REVERT: D 521 TRP cc_start: 0.7441 (t60) cc_final: 0.6752 (t60) REVERT: D 550 CYS cc_start: 0.7787 (m) cc_final: 0.7423 (m) REVERT: D 574 MET cc_start: 0.8246 (tpp) cc_final: 0.7911 (tpp) REVERT: D 581 LYS cc_start: 0.9147 (ttpm) cc_final: 0.8313 (tptt) REVERT: D 741 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7707 (pm20) outliers start: 73 outliers final: 24 residues processed: 307 average time/residue: 0.1267 time to fit residues: 63.0094 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 : 0.637 ------------------------------------------------------------------------------- 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 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 160 HIS 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 452 ASN 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 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: 0.9980 chunk 207 optimal weight: 0.1980 chunk 47 optimal weight: 40.0000 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 0.0000 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 HIS B 529 GLN C 244 HIS C 580 GLN D 244 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.135407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098109 restraints weight = 40716.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.101600 restraints weight = 20702.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.103870 restraints weight = 13801.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.105153 restraints weight = 10767.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.106145 restraints weight = 9310.231| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20424 Z= 0.111 Angle : 0.597 10.251 27620 Z= 0.296 Chirality : 0.039 0.189 3152 Planarity : 0.004 0.040 3420 Dihedral : 5.605 43.762 2714 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.41 % Allowed : 16.25 % Favored : 81.34 % 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: -1.01 (0.16), residues: 2408 helix: 0.44 (0.13), residues: 1580 sheet: -0.10 (0.48), residues: 92 loop : -3.24 (0.18), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 371 TYR 0.018 0.001 TYR D 451 PHE 0.020 0.001 PHE D 590 TRP 0.018 0.001 TRP A 493 HIS 0.003 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00234 (20424) covalent geometry : angle 0.59666 (27620) hydrogen bonds : bond 0.03564 ( 989) hydrogen bonds : angle 3.87116 ( 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 332 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8105 (tp30) cc_final: 0.7810 (tp30) REVERT: A 430 HIS cc_start: 0.7592 (t70) cc_final: 0.6909 (t70) REVERT: A 521 TRP cc_start: 0.7307 (t60) cc_final: 0.6601 (t60) REVERT: A 532 LEU cc_start: 0.9036 (tp) cc_final: 0.8793 (tp) REVERT: A 550 CYS cc_start: 0.7786 (m) cc_final: 0.7358 (m) REVERT: A 574 MET cc_start: 0.8134 (tpp) cc_final: 0.7930 (tpp) REVERT: A 581 LYS cc_start: 0.9153 (ttpm) cc_final: 0.8254 (tptt) REVERT: B 272 THR cc_start: 0.6692 (p) cc_final: 0.6114 (t) REVERT: B 322 ASP cc_start: 0.8738 (t70) cc_final: 0.8535 (t0) REVERT: B 418 GLU cc_start: 0.8078 (tp30) cc_final: 0.7770 (tp30) REVERT: B 521 TRP cc_start: 0.7323 (t60) cc_final: 0.6614 (t60) REVERT: B 562 MET cc_start: 0.8536 (tpp) cc_final: 0.8021 (tpt) REVERT: B 574 MET cc_start: 0.8101 (tpp) cc_final: 0.7881 (tpp) REVERT: B 578 MET cc_start: 0.8675 (tpp) cc_final: 0.8365 (tpt) REVERT: C 418 GLU cc_start: 0.8113 (tp30) cc_final: 0.7789 (tp30) REVERT: C 430 HIS cc_start: 0.7566 (t70) cc_final: 0.6865 (t70) REVERT: C 521 TRP cc_start: 0.7287 (t60) cc_final: 0.6568 (t60) REVERT: C 532 LEU cc_start: 0.9073 (tp) cc_final: 0.8843 (tp) REVERT: C 550 CYS cc_start: 0.7759 (m) cc_final: 0.7323 (m) REVERT: C 574 MET cc_start: 0.8170 (tpp) cc_final: 0.7923 (tpp) REVERT: C 581 LYS cc_start: 0.9141 (ttpm) cc_final: 0.8232 (tptt) REVERT: D 418 GLU cc_start: 0.8104 (tp30) cc_final: 0.7801 (tp30) REVERT: D 430 HIS cc_start: 0.7609 (t70) cc_final: 0.6925 (t70) REVERT: D 521 TRP cc_start: 0.7283 (t60) cc_final: 0.6573 (t60) REVERT: D 574 MET cc_start: 0.8126 (tpp) cc_final: 0.7915 (tpp) REVERT: D 581 LYS cc_start: 0.9158 (ttpm) cc_final: 0.8259 (tptt) outliers start: 52 outliers final: 27 residues processed: 317 average time/residue: 0.1272 time to fit residues: 65.1812 Evaluate side-chains 244 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 HIS 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 508 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 160 HIS Chi-restraints excluded: chain C residue 230 ILE 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 508 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 597 PHE 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: 2.9990 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 216 GLN A 410 ASN A 452 ASN A 529 GLN B 182 ASN B 216 GLN B 410 ASN C 182 ASN C 216 GLN C 410 ASN C 452 ASN C 529 GLN C 580 GLN D 182 ASN D 216 GLN D 255 GLN D 410 ASN D 452 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.131823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089624 restraints weight = 42226.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092999 restraints weight = 21955.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095171 restraints weight = 14987.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.096574 restraints weight = 11924.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097317 restraints weight = 10368.980| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20424 Z= 0.201 Angle : 0.662 9.323 27620 Z= 0.335 Chirality : 0.042 0.183 3152 Planarity : 0.004 0.041 3420 Dihedral : 6.225 53.918 2708 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.48 % Favored : 94.48 % Rotamer: Outliers : 3.19 % Allowed : 16.39 % Favored : 80.42 % 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: -0.91 (0.17), residues: 2408 helix: 0.56 (0.13), residues: 1580 sheet: -0.27 (0.48), residues: 92 loop : -3.29 (0.18), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 147 TYR 0.020 0.002 TYR B 321 PHE 0.027 0.001 PHE D 590 TRP 0.013 0.001 TRP B 493 HIS 0.009 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00473 (20424) covalent geometry : angle 0.66242 (27620) hydrogen bonds : bond 0.03797 ( 989) hydrogen bonds : angle 4.07609 ( 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 296 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 227 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8333 (tp30) cc_final: 0.8091 (tp30) REVERT: A 479 MET cc_start: 0.6303 (mpp) cc_final: 0.5872 (mpp) REVERT: A 521 TRP cc_start: 0.7251 (t60) cc_final: 0.6514 (t60) REVERT: A 532 LEU cc_start: 0.9103 (tp) cc_final: 0.8882 (tp) REVERT: A 550 CYS cc_start: 0.7800 (m) cc_final: 0.7315 (m) REVERT: A 696 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8461 (tpp80) REVERT: B 521 TRP cc_start: 0.7295 (t60) cc_final: 0.6585 (t60) REVERT: B 562 MET cc_start: 0.8636 (tpp) cc_final: 0.8085 (tpt) REVERT: B 578 MET cc_start: 0.8739 (tpp) cc_final: 0.8538 (tpp) REVERT: B 696 ARG cc_start: 0.8715 (tpp80) cc_final: 0.8467 (tpp80) REVERT: B 717 MET cc_start: 0.7476 (tpt) cc_final: 0.7252 (tpt) REVERT: C 418 GLU cc_start: 0.8308 (tp30) cc_final: 0.8046 (tp30) REVERT: C 521 TRP cc_start: 0.7246 (t60) cc_final: 0.6514 (t60) REVERT: C 532 LEU cc_start: 0.9112 (tp) cc_final: 0.8878 (tp) REVERT: C 550 CYS cc_start: 0.7790 (m) cc_final: 0.7315 (m) REVERT: D 418 GLU cc_start: 0.8333 (tp30) cc_final: 0.8081 (tp30) REVERT: D 479 MET cc_start: 0.6146 (mpp) cc_final: 0.5713 (mpp) REVERT: D 521 TRP cc_start: 0.7296 (t60) cc_final: 0.6589 (t60) REVERT: D 696 ARG cc_start: 0.8732 (tpp80) cc_final: 0.8463 (tpp80) outliers start: 69 outliers final: 26 residues processed: 277 average time/residue: 0.1207 time to fit residues: 54.4100 Evaluate side-chains 228 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 496 CYS 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 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 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 461 TYR Chi-restraints excluded: chain C residue 496 CYS 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 496 CYS 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: 0.7980 chunk 27 optimal weight: 0.9980 chunk 156 optimal weight: 30.0000 chunk 228 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.131953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.093415 restraints weight = 40943.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096763 restraints weight = 21193.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098942 restraints weight = 14347.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.100274 restraints weight = 11298.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.101011 restraints weight = 9804.638| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20424 Z= 0.132 Angle : 0.631 15.066 27620 Z= 0.309 Chirality : 0.040 0.249 3152 Planarity : 0.003 0.041 3420 Dihedral : 5.935 55.016 2708 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.01 % Allowed : 16.76 % Favored : 80.23 % 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: -0.72 (0.17), residues: 2408 helix: 0.70 (0.13), residues: 1576 sheet: -0.19 (0.49), residues: 92 loop : -3.20 (0.18), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 147 TYR 0.018 0.001 TYR B 321 PHE 0.026 0.001 PHE B 715 TRP 0.011 0.001 TRP B 493 HIS 0.009 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00298 (20424) covalent geometry : angle 0.63057 (27620) hydrogen bonds : bond 0.03471 ( 989) hydrogen bonds : angle 3.89619 ( 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 284 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 219 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8200 (tp30) cc_final: 0.7922 (tp30) REVERT: A 479 MET cc_start: 0.6336 (mpp) cc_final: 0.6122 (mpp) REVERT: A 521 TRP cc_start: 0.7221 (t60) cc_final: 0.6503 (t60) REVERT: A 532 LEU cc_start: 0.9082 (tp) cc_final: 0.8832 (tp) REVERT: A 550 CYS cc_start: 0.7675 (m) cc_final: 0.7195 (m) REVERT: A 578 MET cc_start: 0.8588 (tpp) cc_final: 0.8363 (tpp) REVERT: A 696 ARG cc_start: 0.8684 (tpp80) cc_final: 0.8425 (tpp80) REVERT: A 715 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.6163 (m-80) REVERT: B 521 TRP cc_start: 0.7224 (t60) cc_final: 0.6485 (t60) REVERT: B 562 MET cc_start: 0.8559 (tpp) cc_final: 0.7946 (tpt) REVERT: B 578 MET cc_start: 0.8788 (tpp) cc_final: 0.8545 (tpp) REVERT: B 696 ARG cc_start: 0.8681 (tpp80) cc_final: 0.8454 (tpp80) REVERT: C 418 GLU cc_start: 0.8205 (tp30) cc_final: 0.7910 (tp30) REVERT: C 521 TRP cc_start: 0.7220 (t60) cc_final: 0.6497 (t60) REVERT: C 532 LEU cc_start: 0.9086 (tp) cc_final: 0.8843 (tp) REVERT: C 550 CYS cc_start: 0.7754 (m) cc_final: 0.7299 (m) REVERT: C 578 MET cc_start: 0.8625 (tpp) cc_final: 0.8379 (tpp) REVERT: D 418 GLU cc_start: 0.8243 (tp30) cc_final: 0.7957 (tp30) REVERT: D 479 MET cc_start: 0.6247 (mpp) cc_final: 0.5822 (mpp) REVERT: D 521 TRP cc_start: 0.7241 (t60) cc_final: 0.6514 (t60) REVERT: D 578 MET cc_start: 0.8604 (tpp) cc_final: 0.8381 (tpp) REVERT: D 696 ARG cc_start: 0.8688 (tpp80) cc_final: 0.8448 (tpp80) outliers start: 65 outliers final: 26 residues processed: 265 average time/residue: 0.1231 time to fit residues: 53.3992 Evaluate side-chains 233 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 452 ASN 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 496 CYS Chi-restraints excluded: chain B residue 669 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 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 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 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: 0.8980 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 452 ASN C 178 ASN C 410 ASN C 745 HIS D 178 ASN D 410 ASN D 452 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.130317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091158 restraints weight = 40983.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094411 restraints weight = 21536.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.096496 restraints weight = 14737.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097698 restraints weight = 11736.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.098627 restraints weight = 10246.062| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20424 Z= 0.172 Angle : 0.677 14.766 27620 Z= 0.329 Chirality : 0.041 0.205 3152 Planarity : 0.004 0.042 3420 Dihedral : 6.152 57.804 2708 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.41 % Allowed : 18.10 % Favored : 79.49 % 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: -0.75 (0.17), residues: 2408 helix: 0.71 (0.13), residues: 1560 sheet: -0.24 (0.50), residues: 92 loop : -3.21 (0.17), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 147 TYR 0.018 0.001 TYR B 321 PHE 0.018 0.001 PHE C 590 TRP 0.011 0.001 TRP D 710 HIS 0.008 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00405 (20424) covalent geometry : angle 0.67666 (27620) hydrogen bonds : bond 0.03547 ( 989) hydrogen bonds : angle 3.95420 ( 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 262 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 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 479 MET cc_start: 0.6215 (mpp) cc_final: 0.5997 (mpp) REVERT: A 521 TRP cc_start: 0.7214 (t60) cc_final: 0.6488 (t60) REVERT: A 550 CYS cc_start: 0.7858 (m) cc_final: 0.7441 (m) REVERT: A 715 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.6189 (m-80) REVERT: B 479 MET cc_start: 0.6010 (mpp) cc_final: 0.5713 (mpp) REVERT: B 521 TRP cc_start: 0.7211 (t60) cc_final: 0.6508 (t60) REVERT: B 545 LYS cc_start: 0.7387 (tptm) cc_final: 0.7135 (ptpt) REVERT: B 562 MET cc_start: 0.8638 (tpp) cc_final: 0.8085 (tpt) REVERT: B 696 ARG cc_start: 0.8728 (tpp80) cc_final: 0.8492 (tpp80) REVERT: C 521 TRP cc_start: 0.7198 (t60) cc_final: 0.6475 (t60) REVERT: C 550 CYS cc_start: 0.7865 (m) cc_final: 0.7454 (m) REVERT: D 479 MET cc_start: 0.6173 (mpp) cc_final: 0.5962 (mpp) REVERT: D 521 TRP cc_start: 0.7233 (t60) cc_final: 0.6528 (t60) REVERT: D 696 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8464 (tpp80) outliers start: 52 outliers final: 37 residues processed: 240 average time/residue: 0.1277 time to fit residues: 49.2847 Evaluate side-chains 233 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 587 VAL 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 177 LEU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 336 MET 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 669 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 291 SER Chi-restraints excluded: chain C residue 356 ILE 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 669 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 289 ILE Chi-restraints excluded: chain D residue 452 ASN 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 669 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: 3.9990 chunk 175 optimal weight: 0.0050 chunk 22 optimal weight: 0.4980 chunk 221 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN C 452 ASN C 580 GLN D 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.135242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097354 restraints weight = 40694.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.100782 restraints weight = 20999.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103054 restraints weight = 14160.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104472 restraints weight = 11085.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.105245 restraints weight = 9554.558| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20424 Z= 0.112 Angle : 0.656 14.956 27620 Z= 0.312 Chirality : 0.039 0.199 3152 Planarity : 0.003 0.043 3420 Dihedral : 5.797 58.242 2708 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.48 % Allowed : 19.49 % 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: -0.62 (0.17), residues: 2408 helix: 0.76 (0.13), residues: 1576 sheet: 0.05 (0.50), residues: 88 loop : -3.13 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 147 TYR 0.024 0.001 TYR A 451 PHE 0.017 0.001 PHE B 590 TRP 0.014 0.001 TRP D 710 HIS 0.008 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00236 (20424) covalent geometry : angle 0.65611 (27620) hydrogen bonds : bond 0.03349 ( 989) hydrogen bonds : angle 3.84289 ( 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 289 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.778 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 336 MET cc_start: 0.8700 (ttm) cc_final: 0.8402 (ttp) REVERT: A 418 GLU cc_start: 0.8101 (tp30) cc_final: 0.7656 (tt0) REVERT: A 479 MET cc_start: 0.6034 (mpp) cc_final: 0.5829 (mpp) REVERT: A 521 TRP cc_start: 0.7130 (t60) cc_final: 0.6381 (t60) REVERT: A 731 CYS cc_start: 0.8408 (m) cc_final: 0.7847 (m) REVERT: B 139 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9329 (pp) REVERT: B 172 LEU cc_start: 0.8669 (tp) cc_final: 0.8424 (tp) REVERT: B 336 MET cc_start: 0.8680 (ttm) cc_final: 0.8428 (ttp) REVERT: B 404 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7573 (mt) REVERT: B 479 MET cc_start: 0.5824 (mpp) cc_final: 0.5539 (mpp) REVERT: B 521 TRP cc_start: 0.7124 (t60) cc_final: 0.6419 (t60) REVERT: B 545 LYS cc_start: 0.7335 (tptm) cc_final: 0.7070 (ptpt) REVERT: B 562 MET cc_start: 0.8553 (tpp) cc_final: 0.7946 (tpt) REVERT: B 731 CYS cc_start: 0.8637 (m) cc_final: 0.8062 (m) REVERT: C 336 MET cc_start: 0.8670 (ttm) cc_final: 0.8374 (ttp) REVERT: C 461 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6684 (t80) REVERT: C 521 TRP cc_start: 0.7143 (t60) cc_final: 0.6417 (t60) REVERT: C 672 MET cc_start: 0.8953 (tpp) cc_final: 0.8572 (tpp) REVERT: C 731 CYS cc_start: 0.8566 (m) cc_final: 0.8036 (m) REVERT: D 336 MET cc_start: 0.8651 (ttm) cc_final: 0.8352 (ttp) REVERT: D 479 MET cc_start: 0.6046 (mpp) cc_final: 0.5837 (mpp) REVERT: D 521 TRP cc_start: 0.7172 (t60) cc_final: 0.6453 (t60) REVERT: D 731 CYS cc_start: 0.8429 (m) cc_final: 0.7857 (m) outliers start: 32 outliers final: 16 residues processed: 275 average time/residue: 0.1272 time to fit residues: 56.6422 Evaluate side-chains 240 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 404 LEU 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 C residue 289 ILE 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 289 ILE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 587 VAL 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: 1.9990 chunk 101 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 49 optimal weight: 50.0000 chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN C 452 ASN D 279 GLN D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.131063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091785 restraints weight = 40680.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095037 restraints weight = 21756.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097051 restraints weight = 15016.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.098227 restraints weight = 12018.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.099198 restraints weight = 10528.558| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20424 Z= 0.168 Angle : 0.709 14.069 27620 Z= 0.341 Chirality : 0.041 0.186 3152 Planarity : 0.004 0.046 3420 Dihedral : 6.278 74.476 2708 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.57 % Allowed : 20.09 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2408 helix: 0.72 (0.14), residues: 1548 sheet: 0.13 (0.51), residues: 88 loop : -3.09 (0.18), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 712 TYR 0.028 0.002 TYR D 321 PHE 0.020 0.001 PHE A 436 TRP 0.015 0.002 TRP D 710 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00392 (20424) covalent geometry : angle 0.70897 (27620) hydrogen bonds : bond 0.03563 ( 989) hydrogen bonds : angle 3.99195 ( 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 267 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 521 TRP cc_start: 0.7167 (t60) cc_final: 0.6432 (t60) REVERT: A 665 THR cc_start: 0.8987 (m) cc_final: 0.8666 (p) REVERT: A 731 CYS cc_start: 0.8492 (m) cc_final: 0.7925 (m) REVERT: B 479 MET cc_start: 0.5887 (mpp) cc_final: 0.5587 (mpp) REVERT: B 521 TRP cc_start: 0.7154 (t60) cc_final: 0.6458 (t60) REVERT: B 545 LYS cc_start: 0.7371 (tptm) cc_final: 0.7129 (ptpt) REVERT: B 555 MET cc_start: 0.8271 (mtm) cc_final: 0.7968 (mtm) REVERT: B 562 MET cc_start: 0.8599 (tpp) cc_final: 0.8035 (tpt) REVERT: B 731 CYS cc_start: 0.8631 (m) cc_final: 0.8069 (m) REVERT: C 461 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6754 (t80) REVERT: C 521 TRP cc_start: 0.7152 (t60) cc_final: 0.6411 (t60) REVERT: C 574 MET cc_start: 0.8303 (tpp) cc_final: 0.8039 (tpt) REVERT: C 672 MET cc_start: 0.8908 (tpp) cc_final: 0.8633 (tpp) REVERT: C 731 CYS cc_start: 0.8613 (m) cc_final: 0.8085 (m) REVERT: D 521 TRP cc_start: 0.7174 (t60) cc_final: 0.6434 (t60) REVERT: D 672 MET cc_start: 0.8920 (tpp) cc_final: 0.8634 (tpp) REVERT: D 731 CYS cc_start: 0.8532 (m) cc_final: 0.7951 (m) outliers start: 34 outliers final: 28 residues processed: 254 average time/residue: 0.1177 time to fit residues: 49.1515 Evaluate side-chains 246 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 452 ASN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 336 MET 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 711 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 289 ILE 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 D residue 177 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 694 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: 8.9990 chunk 84 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 191 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN B 410 ASN C 452 ASN D 452 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.132087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.092975 restraints weight = 40915.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.096277 restraints weight = 21801.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098291 restraints weight = 15007.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099705 restraints weight = 11996.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100389 restraints weight = 10435.994| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20424 Z= 0.143 Angle : 0.705 14.206 27620 Z= 0.336 Chirality : 0.041 0.186 3152 Planarity : 0.003 0.042 3420 Dihedral : 6.246 74.408 2708 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.53 % Allowed : 20.46 % 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: -0.68 (0.17), residues: 2408 helix: 0.66 (0.13), residues: 1568 sheet: 0.09 (0.51), residues: 88 loop : -2.97 (0.18), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 712 TYR 0.027 0.001 TYR C 321 PHE 0.029 0.001 PHE A 715 TRP 0.015 0.001 TRP D 710 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00329 (20424) covalent geometry : angle 0.70474 (27620) hydrogen bonds : bond 0.03513 ( 989) hydrogen bonds : angle 4.01171 ( 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 258 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.774 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 521 TRP cc_start: 0.7137 (t60) cc_final: 0.6416 (t60) REVERT: A 665 THR cc_start: 0.9001 (m) cc_final: 0.8689 (p) REVERT: A 731 CYS cc_start: 0.8462 (m) cc_final: 0.7907 (m) REVERT: B 479 MET cc_start: 0.5873 (mpp) cc_final: 0.5575 (mpp) REVERT: B 521 TRP cc_start: 0.7144 (t60) cc_final: 0.6440 (t60) REVERT: B 545 LYS cc_start: 0.7345 (tptm) cc_final: 0.7109 (ptpt) REVERT: B 555 MET cc_start: 0.8262 (mtm) cc_final: 0.7967 (mtm) REVERT: B 562 MET cc_start: 0.8600 (tpp) cc_final: 0.8069 (tpt) REVERT: B 731 CYS cc_start: 0.8637 (m) cc_final: 0.8112 (m) REVERT: C 461 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6818 (t80) REVERT: C 521 TRP cc_start: 0.7127 (t60) cc_final: 0.6379 (t60) REVERT: C 731 CYS cc_start: 0.8629 (m) cc_final: 0.8095 (m) REVERT: D 521 TRP cc_start: 0.7193 (t60) cc_final: 0.6454 (t60) REVERT: D 672 MET cc_start: 0.8871 (tpp) cc_final: 0.8546 (tpp) REVERT: D 731 CYS cc_start: 0.8498 (m) cc_final: 0.7921 (m) outliers start: 33 outliers final: 28 residues processed: 245 average time/residue: 0.1262 time to fit residues: 51.2520 Evaluate side-chains 248 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 452 ASN 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 711 LEU Chi-restraints excluded: chain B residue 177 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 711 LEU Chi-restraints excluded: chain C residue 289 ILE 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 D residue 172 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 711 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 40 optimal weight: 7.9990 chunk 125 optimal weight: 0.0670 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 0.0000 chunk 198 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.1726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN B 178 ASN D 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.133269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.094411 restraints weight = 40741.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097710 restraints weight = 21628.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.099718 restraints weight = 14866.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.101122 restraints weight = 11953.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.101999 restraints weight = 10362.744| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5378 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= 0.128 Angle : 0.701 13.984 27620 Z= 0.333 Chirality : 0.040 0.229 3152 Planarity : 0.003 0.043 3420 Dihedral : 6.137 74.625 2708 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.53 % Allowed : 20.51 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2408 helix: 0.69 (0.13), residues: 1572 sheet: 0.06 (0.51), residues: 88 loop : -2.92 (0.19), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 712 TYR 0.026 0.001 TYR D 321 PHE 0.025 0.001 PHE A 715 TRP 0.015 0.001 TRP D 710 HIS 0.007 0.001 HIS B 430 Details of bonding type rmsd covalent geometry : bond 0.00287 (20424) covalent geometry : angle 0.70070 (27620) hydrogen bonds : bond 0.03482 ( 989) hydrogen bonds : angle 4.03143 ( 2907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.69 seconds wall clock time: 59 minutes 50.56 seconds (3590.56 seconds total)