Starting phenix.real_space_refine on Fri Sep 19 08:09:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dij_46907/09_2025/9dij_46907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dij_46907/09_2025/9dij_46907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dij_46907/09_2025/9dij_46907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dij_46907/09_2025/9dij_46907.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dij_46907/09_2025/9dij_46907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dij_46907/09_2025/9dij_46907.map" } resolution = 4.07 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= 0.001 sd= 0.032 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 140 5.16 5 C 15990 2.51 5 N 4035 2.21 5 O 4375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24540 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4908 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 14, 'TRANS': 588} Chain breaks: 2 Restraints were copied for chains: B, C, D, E Time building chain proxies: 4.72, per 1000 atoms: 0.19 Number of scatterers: 24540 At special positions: 0 Unit cell: (173.236, 171.084, 118.36, 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 140 16.00 O 4375 8.00 N 4035 7.00 C 15990 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: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5770 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 5 sheets defined 61.5% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.866A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 178 removed outlier: 4.348A pdb=" N LYS A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 217 through 225 removed outlier: 4.011A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.562A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 298 through 307 Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.570A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.298A pdb=" N LEU A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.768A pdb=" N ALA A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.505A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.541A pdb=" N HIS A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 461 removed outlier: 3.932A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A 443 " --> pdb=" O HIS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 4.425A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 539 Processing helix chain 'A' and resid 546 through 565 removed outlier: 4.307A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 4.367A pdb=" N VAL A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 609 removed outlier: 3.756A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 removed outlier: 4.472A pdb=" N VAL A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 685 removed outlier: 3.661A pdb=" N PHE A 654 " --> pdb=" O TYR A 650 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.617A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.866A pdb=" N PHE B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 4.348A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 217 through 225 removed outlier: 4.011A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.563A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.570A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 4.298A pdb=" N LEU B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.768A pdb=" N ALA B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.505A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.541A pdb=" N HIS B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 461 removed outlier: 3.932A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 509 removed outlier: 4.425A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 497 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 539 Processing helix chain 'B' and resid 546 through 565 removed outlier: 4.307A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 4.367A pdb=" N VAL B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 609 removed outlier: 3.755A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 removed outlier: 4.472A pdb=" N VAL B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 685 removed outlier: 3.661A pdb=" N PHE B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 669 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 676 " --> pdb=" O MET B 672 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.617A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE B 700 " --> pdb=" O ARG B 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 133 through 146 Processing helix chain 'C' and resid 153 through 163 removed outlier: 3.866A pdb=" N PHE C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 178 removed outlier: 4.348A pdb=" N LYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 175 " --> pdb=" O CYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 217 through 225 removed outlier: 4.012A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.562A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.570A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 4.298A pdb=" N LEU C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.768A pdb=" N ALA C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.504A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.541A pdb=" N HIS C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 461 removed outlier: 3.931A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU C 443 " --> pdb=" O HIS C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 509 removed outlier: 4.424A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE C 497 " --> pdb=" O TRP C 493 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG C 509 " --> pdb=" O ILE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 539 Processing helix chain 'C' and resid 546 through 565 removed outlier: 4.306A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 586 removed outlier: 4.367A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 583 " --> pdb=" O ILE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 609 removed outlier: 3.755A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 removed outlier: 4.472A pdb=" N VAL C 629 " --> pdb=" O PHE C 625 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 685 removed outlier: 3.661A pdb=" N PHE C 654 " --> pdb=" O TYR C 650 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 669 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU C 670 " --> pdb=" O PHE C 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 676 " --> pdb=" O MET C 672 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.616A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN C 695 " --> pdb=" O ILE C 691 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 697 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG C 698 " --> pdb=" O LEU C 694 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE C 700 " --> pdb=" O ARG C 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 133 through 146 Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.866A pdb=" N PHE D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 178 removed outlier: 4.348A pdb=" N LYS D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA D 175 " --> pdb=" O CYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 Processing helix chain 'D' and resid 217 through 225 removed outlier: 4.012A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.563A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 283 Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.570A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 4.299A pdb=" N LEU D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 removed outlier: 3.768A pdb=" N ALA D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.505A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.541A pdb=" N HIS D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 461 removed outlier: 3.932A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU D 443 " --> pdb=" O HIS D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 509 removed outlier: 4.425A pdb=" N MET D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N CYS D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE D 497 " --> pdb=" O TRP D 493 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG D 509 " --> pdb=" O ILE D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 539 Processing helix chain 'D' and resid 546 through 565 removed outlier: 4.307A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 586 removed outlier: 4.367A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 609 removed outlier: 3.755A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 removed outlier: 4.472A pdb=" N VAL D 629 " --> pdb=" O PHE D 625 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 685 removed outlier: 3.661A pdb=" N PHE D 654 " --> pdb=" O TYR D 650 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 669 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU D 676 " --> pdb=" O MET D 672 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.617A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 695 " --> pdb=" O ILE D 691 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG D 698 " --> pdb=" O LEU D 694 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE D 700 " --> pdb=" O ARG D 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 133 through 146 Processing helix chain 'E' and resid 153 through 163 removed outlier: 3.866A pdb=" N PHE E 157 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E 158 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 178 removed outlier: 4.348A pdb=" N LYS E 174 " --> pdb=" O THR E 170 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA E 175 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 Processing helix chain 'E' and resid 217 through 225 removed outlier: 4.012A pdb=" N ILE E 221 " --> pdb=" O THR E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 264 through 272 removed outlier: 3.562A pdb=" N ALA E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 283 Processing helix chain 'E' and resid 298 through 307 Processing helix chain 'E' and resid 315 through 329 removed outlier: 3.570A pdb=" N ARG E 319 " --> pdb=" O ASP E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 removed outlier: 4.299A pdb=" N LEU E 333 " --> pdb=" O ASN E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 351 removed outlier: 3.768A pdb=" N ALA E 348 " --> pdb=" O PRO E 344 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA E 349 " --> pdb=" O LEU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 362 Processing helix chain 'E' and resid 402 through 409 Processing helix chain 'E' and resid 415 through 420 removed outlier: 3.504A pdb=" N LEU E 420 " --> pdb=" O ARG E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 436 removed outlier: 3.540A pdb=" N HIS E 426 " --> pdb=" O LEU E 422 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU E 428 " --> pdb=" O PRO E 424 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS E 434 " --> pdb=" O HIS E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 461 removed outlier: 3.932A pdb=" N PHE E 442 " --> pdb=" O LYS E 438 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU E 443 " --> pdb=" O HIS E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 509 removed outlier: 4.425A pdb=" N MET E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS E 496 " --> pdb=" O ILE E 492 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE E 497 " --> pdb=" O TRP E 493 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER E 498 " --> pdb=" O ALA E 494 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE E 503 " --> pdb=" O VAL E 499 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE E 506 " --> pdb=" O GLY E 502 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG E 509 " --> pdb=" O ILE E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 539 Processing helix chain 'E' and resid 546 through 565 removed outlier: 4.307A pdb=" N TRP E 559 " --> pdb=" O MET E 555 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 560 " --> pdb=" O ALA E 556 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 563 " --> pdb=" O TRP E 559 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR E 564 " --> pdb=" O ALA E 560 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR E 565 " --> pdb=" O ASN E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 586 removed outlier: 4.367A pdb=" N VAL E 577 " --> pdb=" O GLY E 573 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N MET E 578 " --> pdb=" O MET E 574 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 583 " --> pdb=" O ILE E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 609 removed outlier: 3.755A pdb=" N PHE E 597 " --> pdb=" O VAL E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 636 removed outlier: 4.472A pdb=" N VAL E 629 " --> pdb=" O PHE E 625 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 635 " --> pdb=" O GLU E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 685 removed outlier: 3.661A pdb=" N PHE E 654 " --> pdb=" O TYR E 650 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 669 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU E 670 " --> pdb=" O PHE E 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E 673 " --> pdb=" O LEU E 669 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU E 676 " --> pdb=" O MET E 672 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET E 677 " --> pdb=" O LEU E 673 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU E 679 " --> pdb=" O ALA E 675 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER E 685 " --> pdb=" O VAL E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 707 removed outlier: 3.617A pdb=" N ILE E 691 " --> pdb=" O GLU E 687 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 694 " --> pdb=" O ARG E 690 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN E 695 " --> pdb=" O ILE E 691 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA E 697 " --> pdb=" O ARG E 693 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG E 698 " --> pdb=" O LEU E 694 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR E 699 " --> pdb=" O GLN E 695 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE E 700 " --> pdb=" O ARG E 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 381 removed outlier: 6.874A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 381 removed outlier: 6.875A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 381 removed outlier: 6.875A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 381 removed outlier: 6.874A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 376 through 381 removed outlier: 6.875A pdb=" N SER E 387 " --> pdb=" O ASP E 379 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3285 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: 3.92 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7740 1.35 - 1.46: 6009 1.46 - 1.58: 11091 1.58 - 1.70: 0 1.70 - 1.82: 235 Bond restraints: 25075 Sorted by residual: bond pdb=" C GLN D 645 " pdb=" N GLN D 646 " ideal model delta sigma weight residual 1.335 1.284 0.051 1.35e-02 5.49e+03 1.43e+01 bond pdb=" C GLN E 645 " pdb=" N GLN E 646 " ideal model delta sigma weight residual 1.335 1.284 0.051 1.35e-02 5.49e+03 1.42e+01 bond pdb=" C GLN A 645 " pdb=" N GLN A 646 " ideal model delta sigma weight residual 1.335 1.284 0.051 1.35e-02 5.49e+03 1.42e+01 bond pdb=" C GLN B 645 " pdb=" N GLN B 646 " ideal model delta sigma weight residual 1.335 1.284 0.051 1.35e-02 5.49e+03 1.42e+01 bond pdb=" C GLN C 645 " pdb=" N GLN C 646 " ideal model delta sigma weight residual 1.335 1.285 0.050 1.35e-02 5.49e+03 1.35e+01 ... (remaining 25070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 32855 1.18 - 2.36: 724 2.36 - 3.53: 275 3.53 - 4.71: 51 4.71 - 5.89: 25 Bond angle restraints: 33930 Sorted by residual: angle pdb=" C SER C 518 " pdb=" CA SER C 518 " pdb=" CB SER C 518 " ideal model delta sigma weight residual 115.79 109.90 5.89 1.19e+00 7.06e-01 2.45e+01 angle pdb=" C SER E 518 " pdb=" CA SER E 518 " pdb=" CB SER E 518 " ideal model delta sigma weight residual 115.79 109.90 5.89 1.19e+00 7.06e-01 2.45e+01 angle pdb=" C SER B 518 " pdb=" CA SER B 518 " pdb=" CB SER B 518 " ideal model delta sigma weight residual 115.79 109.91 5.88 1.19e+00 7.06e-01 2.44e+01 angle pdb=" C SER A 518 " pdb=" CA SER A 518 " pdb=" CB SER A 518 " ideal model delta sigma weight residual 115.79 109.92 5.87 1.19e+00 7.06e-01 2.44e+01 angle pdb=" C SER D 518 " pdb=" CA SER D 518 " pdb=" CB SER D 518 " ideal model delta sigma weight residual 115.79 109.92 5.87 1.19e+00 7.06e-01 2.43e+01 ... (remaining 33925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 12785 15.05 - 30.11: 1631 30.11 - 45.16: 394 45.16 - 60.22: 75 60.22 - 75.27: 25 Dihedral angle restraints: 14910 sinusoidal: 6025 harmonic: 8885 Sorted by residual: dihedral pdb=" CA ASP E 752 " pdb=" CB ASP E 752 " pdb=" CG ASP E 752 " pdb=" OD1 ASP E 752 " ideal model delta sinusoidal sigma weight residual -30.00 -89.68 59.68 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP B 752 " pdb=" CB ASP B 752 " pdb=" CG ASP B 752 " pdb=" OD1 ASP B 752 " ideal model delta sinusoidal sigma weight residual -30.00 -89.65 59.65 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP D 752 " pdb=" CB ASP D 752 " pdb=" CG ASP D 752 " pdb=" OD1 ASP D 752 " ideal model delta sinusoidal sigma weight residual -30.00 -89.62 59.62 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 14907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 1977 0.023 - 0.046: 1176 0.046 - 0.069: 540 0.069 - 0.091: 111 0.091 - 0.114: 76 Chirality restraints: 3880 Sorted by residual: chirality pdb=" CA ILE B 413 " pdb=" N ILE B 413 " pdb=" C ILE B 413 " pdb=" CB ILE B 413 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.27e-01 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 2.40 0.11 2.00e-01 2.50e+01 3.24e-01 chirality pdb=" CA ILE C 413 " pdb=" N ILE C 413 " pdb=" C ILE C 413 " pdb=" CB ILE C 413 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.19e-01 ... (remaining 3877 not shown) Planarity restraints: 4225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 180 " -0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO B 181 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO A 181 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO C 181 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " -0.019 5.00e-02 4.00e+02 ... (remaining 4222 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5919 2.79 - 3.32: 24372 3.32 - 3.84: 38664 3.84 - 4.37: 44595 4.37 - 4.90: 73176 Nonbonded interactions: 186726 Sorted by model distance: nonbonded pdb=" O ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.261 3.040 nonbonded pdb=" O ASN E 180 " pdb=" OG1 THR E 183 " model vdw 2.261 3.040 nonbonded pdb=" O ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.261 3.040 nonbonded pdb=" O ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.261 3.040 nonbonded pdb=" O ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.261 3.040 ... (remaining 186721 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.600 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 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 : 0.002 0.051 25075 Z= 0.117 Angle : 0.498 5.889 33930 Z= 0.272 Chirality : 0.035 0.114 3880 Planarity : 0.002 0.035 4225 Dihedral : 14.419 75.271 9140 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.37 % Allowed : 0.97 % Favored : 98.65 % 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 aren not related in a simple way. whole: -1.65 (0.15), residues: 2985 helix: -0.12 (0.13), residues: 1660 sheet: -1.63 (0.49), residues: 105 loop : -2.42 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 225 TYR 0.021 0.001 TYR C 451 PHE 0.017 0.001 PHE E 656 TRP 0.007 0.001 TRP C 559 HIS 0.003 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00215 (25075) covalent geometry : angle 0.49830 (33930) hydrogen bonds : bond 0.27519 ( 1100) hydrogen bonds : angle 7.32657 ( 3285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 756 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ILE cc_start: 0.8738 (mt) cc_final: 0.8510 (tp) REVERT: A 282 MET cc_start: 0.7972 (mmt) cc_final: 0.7705 (mmt) REVERT: A 323 MET cc_start: 0.8179 (ttp) cc_final: 0.7946 (tpp) REVERT: A 370 LEU cc_start: 0.8874 (pp) cc_final: 0.8657 (pp) REVERT: A 382 TYR cc_start: 0.8102 (t80) cc_final: 0.7749 (t80) REVERT: A 579 ILE cc_start: 0.5634 (mt) cc_final: 0.5357 (mt) REVERT: B 224 GLU cc_start: 0.6513 (tp30) cc_final: 0.5177 (tp30) REVERT: B 743 LYS cc_start: 0.9000 (ptpp) cc_final: 0.8550 (mmtt) REVERT: C 244 HIS cc_start: 0.7763 (m90) cc_final: 0.7540 (m-70) REVERT: C 370 LEU cc_start: 0.8808 (pp) cc_final: 0.8604 (pp) REVERT: C 382 TYR cc_start: 0.8104 (t80) cc_final: 0.7776 (t80) REVERT: C 489 PHE cc_start: 0.6853 (t80) cc_final: 0.6593 (t80) REVERT: C 579 ILE cc_start: 0.5913 (mt) cc_final: 0.5571 (mt) REVERT: C 743 LYS cc_start: 0.9123 (ptpp) cc_final: 0.8494 (mmtt) REVERT: D 656 PHE cc_start: 0.7505 (t80) cc_final: 0.7305 (t80) REVERT: D 671 ASN cc_start: 0.7910 (t0) cc_final: 0.7682 (t0) REVERT: D 743 LYS cc_start: 0.9101 (ptpp) cc_final: 0.8660 (mmmt) REVERT: E 224 GLU cc_start: 0.6519 (tp30) cc_final: 0.4925 (tp30) REVERT: E 282 MET cc_start: 0.8043 (mmt) cc_final: 0.7677 (mmp) REVERT: E 415 ASN cc_start: 0.6712 (t0) cc_final: 0.6378 (t0) REVERT: E 578 MET cc_start: 0.7793 (tmm) cc_final: 0.7483 (tmm) REVERT: E 579 ILE cc_start: 0.5967 (mt) cc_final: 0.5621 (mt) REVERT: E 671 ASN cc_start: 0.8198 (t0) cc_final: 0.7989 (t0) REVERT: E 717 MET cc_start: 0.6266 (ptm) cc_final: 0.6037 (ptp) REVERT: E 743 LYS cc_start: 0.9174 (ptpp) cc_final: 0.8642 (mmmt) outliers start: 10 outliers final: 5 residues processed: 766 average time/residue: 0.1592 time to fit residues: 197.4674 Evaluate side-chains 542 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 537 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 643 ASN B 143 GLN B 251 ASN B 643 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 251 ASN C 643 ASN D 143 GLN D 251 ASN D 643 ASN D 671 ASN E 143 GLN E 251 ASN E 585 HIS E 643 ASN ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.185628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149421 restraints weight = 47299.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.154446 restraints weight = 28884.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.157947 restraints weight = 20287.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.160363 restraints weight = 15644.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.162165 restraints weight = 12935.544| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25075 Z= 0.150 Angle : 0.621 10.407 33930 Z= 0.324 Chirality : 0.040 0.173 3880 Planarity : 0.004 0.039 4225 Dihedral : 3.691 14.408 3270 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 0.45 % Allowed : 6.37 % Favored : 93.18 % 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 aren not related in a simple way. whole: -1.40 (0.15), residues: 2985 helix: 0.11 (0.12), residues: 1750 sheet: -0.91 (0.61), residues: 80 loop : -2.60 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 226 TYR 0.012 0.001 TYR D 359 PHE 0.037 0.001 PHE A 524 TRP 0.006 0.001 TRP E 433 HIS 0.007 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00316 (25075) covalent geometry : angle 0.62091 (33930) hydrogen bonds : bond 0.05294 ( 1100) hydrogen bonds : angle 4.63826 ( 3285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 673 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 123 ILE cc_start: 0.9105 (mt) cc_final: 0.8841 (tp) REVERT: A 131 CYS cc_start: 0.7440 (m) cc_final: 0.6911 (m) REVERT: A 346 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: A 435 LYS cc_start: 0.7643 (mmtm) cc_final: 0.6738 (mmtt) REVERT: A 578 MET cc_start: 0.8045 (tmm) cc_final: 0.7748 (tmm) REVERT: A 592 PHE cc_start: 0.6809 (p90) cc_final: 0.5921 (m-80) REVERT: B 123 ILE cc_start: 0.9130 (mt) cc_final: 0.8883 (tp) REVERT: B 224 GLU cc_start: 0.6542 (tp30) cc_final: 0.5182 (tp30) REVERT: B 346 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7339 (pm20) REVERT: B 351 MET cc_start: 0.7986 (ttm) cc_final: 0.7653 (ttm) REVERT: B 370 LEU cc_start: 0.8765 (pp) cc_final: 0.8554 (pp) REVERT: B 435 LYS cc_start: 0.7434 (mmtm) cc_final: 0.6490 (mmtt) REVERT: B 440 MET cc_start: 0.7135 (mmm) cc_final: 0.6707 (mmm) REVERT: B 592 PHE cc_start: 0.6999 (p90) cc_final: 0.6171 (m-80) REVERT: B 700 ILE cc_start: 0.8251 (pt) cc_final: 0.7693 (mp) REVERT: C 346 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: C 370 LEU cc_start: 0.8808 (pp) cc_final: 0.8594 (pp) REVERT: C 382 TYR cc_start: 0.8212 (t80) cc_final: 0.7764 (t80) REVERT: C 435 LYS cc_start: 0.7206 (mmtm) cc_final: 0.6441 (mmtt) REVERT: C 578 MET cc_start: 0.8040 (tmm) cc_final: 0.7645 (tmm) REVERT: C 743 LYS cc_start: 0.9162 (ptpt) cc_final: 0.8447 (mmtt) REVERT: D 120 LYS cc_start: 0.8649 (pttt) cc_final: 0.7738 (ptmt) REVERT: D 260 TYR cc_start: 0.5739 (p90) cc_final: 0.5004 (p90) REVERT: D 346 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: D 351 MET cc_start: 0.7562 (mtm) cc_final: 0.7326 (ttm) REVERT: D 370 LEU cc_start: 0.8817 (pp) cc_final: 0.8608 (pp) REVERT: D 419 MET cc_start: 0.8827 (tpp) cc_final: 0.8412 (tpp) REVERT: D 435 LYS cc_start: 0.7251 (mmtm) cc_final: 0.6348 (mmtt) REVERT: D 578 MET cc_start: 0.7927 (tmm) cc_final: 0.7568 (tmm) REVERT: D 592 PHE cc_start: 0.6928 (p90) cc_final: 0.5833 (m-80) REVERT: D 743 LYS cc_start: 0.9261 (ptpt) cc_final: 0.8627 (mmmt) REVERT: E 131 CYS cc_start: 0.7298 (m) cc_final: 0.7034 (m) REVERT: E 134 GLU cc_start: 0.8579 (mp0) cc_final: 0.8265 (mp0) REVERT: E 224 GLU cc_start: 0.6578 (tp30) cc_final: 0.5195 (tp30) REVERT: E 244 HIS cc_start: 0.8189 (m90) cc_final: 0.7767 (m-70) REVERT: E 264 THR cc_start: 0.8799 (p) cc_final: 0.8599 (p) REVERT: E 346 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: E 527 PHE cc_start: 0.8348 (t80) cc_final: 0.8096 (t80) REVERT: E 578 MET cc_start: 0.8173 (tmm) cc_final: 0.7744 (tmm) REVERT: E 579 ILE cc_start: 0.5739 (mt) cc_final: 0.5449 (mt) REVERT: E 592 PHE cc_start: 0.7022 (p90) cc_final: 0.6004 (m-80) REVERT: E 717 MET cc_start: 0.6480 (ptm) cc_final: 0.5969 (ptp) REVERT: E 743 LYS cc_start: 0.9275 (ptpt) cc_final: 0.8667 (mmmt) outliers start: 12 outliers final: 0 residues processed: 678 average time/residue: 0.1605 time to fit residues: 176.3378 Evaluate side-chains 547 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 542 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 130 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 73 optimal weight: 0.0980 chunk 251 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 561 ASN A 585 HIS ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.183663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146682 restraints weight = 48034.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.151558 restraints weight = 29485.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155000 restraints weight = 20989.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157487 restraints weight = 16357.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.159221 restraints weight = 13605.850| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25075 Z= 0.147 Angle : 0.574 6.710 33930 Z= 0.303 Chirality : 0.039 0.146 3880 Planarity : 0.004 0.045 4225 Dihedral : 3.759 15.947 3270 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 aren not related in a simple way. whole: -1.07 (0.16), residues: 2985 helix: 0.44 (0.12), residues: 1715 sheet: -0.93 (0.63), residues: 80 loop : -2.47 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 327 TYR 0.013 0.001 TYR D 650 PHE 0.033 0.001 PHE A 524 TRP 0.013 0.001 TRP A 380 HIS 0.003 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00321 (25075) covalent geometry : angle 0.57416 (33930) hydrogen bonds : bond 0.04536 ( 1100) hydrogen bonds : angle 4.46979 ( 3285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ILE cc_start: 0.9120 (mt) cc_final: 0.8858 (tp) REVERT: A 131 CYS cc_start: 0.7779 (m) cc_final: 0.7300 (m) REVERT: A 134 GLU cc_start: 0.8688 (mp0) cc_final: 0.8430 (mp0) REVERT: A 224 GLU cc_start: 0.7038 (tp30) cc_final: 0.5665 (tp30) REVERT: A 309 ASP cc_start: 0.7831 (p0) cc_final: 0.7095 (p0) REVERT: A 435 LYS cc_start: 0.7744 (mmtm) cc_final: 0.6868 (mmtt) REVERT: A 489 PHE cc_start: 0.7073 (t80) cc_final: 0.6268 (t80) REVERT: A 523 HIS cc_start: 0.7273 (m170) cc_final: 0.6748 (m170) REVERT: A 578 MET cc_start: 0.8163 (tmm) cc_final: 0.7696 (tmm) REVERT: A 579 ILE cc_start: 0.5895 (mt) cc_final: 0.5389 (mt) REVERT: B 120 LYS cc_start: 0.8422 (pttm) cc_final: 0.7989 (mtpt) REVERT: B 131 CYS cc_start: 0.8151 (m) cc_final: 0.7797 (m) REVERT: B 134 GLU cc_start: 0.8538 (mp0) cc_final: 0.8212 (mp0) REVERT: B 224 GLU cc_start: 0.6694 (tp30) cc_final: 0.5322 (tp30) REVERT: B 309 ASP cc_start: 0.7718 (p0) cc_final: 0.7388 (p0) REVERT: B 351 MET cc_start: 0.7712 (ttm) cc_final: 0.7427 (ttm) REVERT: B 435 LYS cc_start: 0.7566 (mmtm) cc_final: 0.6673 (mmtt) REVERT: B 440 MET cc_start: 0.7128 (mmm) cc_final: 0.6608 (mmm) REVERT: B 509 ARG cc_start: 0.7344 (ttt-90) cc_final: 0.7100 (mtm180) REVERT: B 519 ASP cc_start: 0.7651 (p0) cc_final: 0.7444 (p0) REVERT: B 578 MET cc_start: 0.7958 (ppp) cc_final: 0.7610 (tmm) REVERT: B 590 PHE cc_start: 0.7673 (t80) cc_final: 0.7347 (t80) REVERT: B 700 ILE cc_start: 0.8231 (pt) cc_final: 0.7655 (mp) REVERT: C 489 PHE cc_start: 0.7327 (t80) cc_final: 0.6279 (t80) REVERT: C 578 MET cc_start: 0.8189 (tmm) cc_final: 0.7740 (tmm) REVERT: C 579 ILE cc_start: 0.5540 (mt) cc_final: 0.5090 (mt) REVERT: C 743 LYS cc_start: 0.9187 (ptpt) cc_final: 0.8448 (mmtt) REVERT: D 120 LYS cc_start: 0.8251 (pttm) cc_final: 0.7820 (ptmt) REVERT: D 224 GLU cc_start: 0.6926 (tp30) cc_final: 0.5432 (tp30) REVERT: D 227 GLN cc_start: 0.8450 (mp10) cc_final: 0.8241 (mp10) REVERT: D 309 ASP cc_start: 0.7474 (p0) cc_final: 0.7268 (p0) REVERT: D 377 PHE cc_start: 0.7577 (m-80) cc_final: 0.7363 (m-80) REVERT: D 578 MET cc_start: 0.8263 (tmm) cc_final: 0.7832 (tmm) REVERT: D 732 LEU cc_start: 0.9089 (tt) cc_final: 0.8820 (tt) REVERT: D 743 LYS cc_start: 0.9290 (ptpt) cc_final: 0.8754 (mmmt) REVERT: E 120 LYS cc_start: 0.8382 (pttm) cc_final: 0.8056 (mtpt) REVERT: E 131 CYS cc_start: 0.7568 (m) cc_final: 0.7318 (m) REVERT: E 134 GLU cc_start: 0.8564 (mp0) cc_final: 0.8275 (mp0) REVERT: E 555 MET cc_start: 0.8462 (tpp) cc_final: 0.8237 (tpp) REVERT: E 578 MET cc_start: 0.8186 (tmm) cc_final: 0.7660 (tmm) REVERT: E 579 ILE cc_start: 0.5732 (mt) cc_final: 0.5302 (mt) REVERT: E 717 MET cc_start: 0.6293 (ptm) cc_final: 0.5830 (ptp) REVERT: E 732 LEU cc_start: 0.9124 (tt) cc_final: 0.8911 (tt) REVERT: E 743 LYS cc_start: 0.9275 (ptpt) cc_final: 0.8744 (mmmt) outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 0.1603 time to fit residues: 176.1520 Evaluate side-chains 528 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 128 optimal weight: 0.0970 chunk 183 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 585 HIS ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 561 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 452 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 452 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN E 561 ASN ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.183502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.146961 restraints weight = 47830.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.151910 restraints weight = 29269.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.155361 restraints weight = 20720.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157815 restraints weight = 16091.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159496 restraints weight = 13355.129| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25075 Z= 0.126 Angle : 0.556 7.530 33930 Z= 0.291 Chirality : 0.038 0.177 3880 Planarity : 0.004 0.045 4225 Dihedral : 3.779 16.049 3270 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.04 % Allowed : 3.97 % Favored : 95.99 % 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 aren not related in a simple way. whole: -0.88 (0.16), residues: 2985 helix: 0.63 (0.12), residues: 1710 sheet: -1.07 (0.64), residues: 80 loop : -2.42 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 716 TYR 0.015 0.001 TYR A 564 PHE 0.042 0.001 PHE E 524 TRP 0.018 0.002 TRP D 559 HIS 0.003 0.001 HIS E 417 Details of bonding type rmsd covalent geometry : bond 0.00270 (25075) covalent geometry : angle 0.55589 (33930) hydrogen bonds : bond 0.03879 ( 1100) hydrogen bonds : angle 4.34230 ( 3285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 667 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ILE cc_start: 0.9122 (mt) cc_final: 0.8863 (tp) REVERT: A 131 CYS cc_start: 0.7820 (m) cc_final: 0.7364 (m) REVERT: A 134 GLU cc_start: 0.8644 (mp0) cc_final: 0.8410 (mp0) REVERT: A 174 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8075 (tttm) REVERT: A 224 GLU cc_start: 0.6970 (tp30) cc_final: 0.5596 (tp30) REVERT: A 578 MET cc_start: 0.8263 (tmm) cc_final: 0.7695 (tmm) REVERT: A 579 ILE cc_start: 0.5875 (mt) cc_final: 0.5295 (mt) REVERT: B 120 LYS cc_start: 0.8414 (pttm) cc_final: 0.7942 (mtpt) REVERT: B 131 CYS cc_start: 0.8258 (m) cc_final: 0.7918 (m) REVERT: B 134 GLU cc_start: 0.8534 (mp0) cc_final: 0.8234 (mp0) REVERT: B 309 ASP cc_start: 0.7760 (p0) cc_final: 0.7385 (p0) REVERT: B 351 MET cc_start: 0.7615 (ttm) cc_final: 0.7414 (ttm) REVERT: B 440 MET cc_start: 0.7275 (mmm) cc_final: 0.6736 (mmm) REVERT: B 700 ILE cc_start: 0.8187 (pt) cc_final: 0.7601 (mp) REVERT: C 308 GLU cc_start: 0.7977 (tp30) cc_final: 0.7701 (tp30) REVERT: C 309 ASP cc_start: 0.7524 (p0) cc_final: 0.7271 (p0) REVERT: C 376 LYS cc_start: 0.5364 (tttt) cc_final: 0.4518 (tttt) REVERT: C 489 PHE cc_start: 0.7369 (t80) cc_final: 0.6460 (t80) REVERT: C 574 MET cc_start: 0.7554 (ppp) cc_final: 0.7310 (ppp) REVERT: C 578 MET cc_start: 0.8275 (tmm) cc_final: 0.7629 (tmm) REVERT: C 579 ILE cc_start: 0.5843 (mt) cc_final: 0.5304 (mt) REVERT: C 743 LYS cc_start: 0.9199 (ptpt) cc_final: 0.8454 (mmtt) REVERT: D 120 LYS cc_start: 0.8254 (pttm) cc_final: 0.7770 (ptmt) REVERT: D 174 LYS cc_start: 0.8628 (tttt) cc_final: 0.8136 (tttt) REVERT: D 351 MET cc_start: 0.7773 (ttm) cc_final: 0.7400 (ttm) REVERT: D 377 PHE cc_start: 0.7520 (m-80) cc_final: 0.7314 (m-80) REVERT: D 525 VAL cc_start: 0.8034 (t) cc_final: 0.7830 (t) REVERT: D 557 LEU cc_start: 0.8412 (tp) cc_final: 0.8005 (tp) REVERT: D 578 MET cc_start: 0.8298 (tmm) cc_final: 0.8016 (tmm) REVERT: D 732 LEU cc_start: 0.9125 (tt) cc_final: 0.8854 (tt) REVERT: D 743 LYS cc_start: 0.9297 (ptpt) cc_final: 0.8751 (mmmt) REVERT: E 120 LYS cc_start: 0.8440 (pttm) cc_final: 0.7975 (mtpt) REVERT: E 131 CYS cc_start: 0.7861 (m) cc_final: 0.7372 (m) REVERT: E 134 GLU cc_start: 0.8587 (mp0) cc_final: 0.8323 (mp0) REVERT: E 174 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7903 (tttt) REVERT: E 309 ASP cc_start: 0.7391 (p0) cc_final: 0.7187 (p0) REVERT: E 578 MET cc_start: 0.8178 (tmm) cc_final: 0.7536 (tmm) REVERT: E 579 ILE cc_start: 0.5869 (mt) cc_final: 0.5408 (mt) REVERT: E 594 TYR cc_start: 0.7729 (t80) cc_final: 0.7419 (t80) REVERT: E 717 MET cc_start: 0.6297 (ptm) cc_final: 0.5851 (ptp) outliers start: 1 outliers final: 0 residues processed: 668 average time/residue: 0.1594 time to fit residues: 171.8432 Evaluate side-chains 520 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 223 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 269 optimal weight: 0.0020 chunk 228 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 chunk 243 optimal weight: 20.0000 chunk 181 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 417 HIS D 452 ASN E 297 ASN ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.178859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141403 restraints weight = 48437.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146114 restraints weight = 30089.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.149388 restraints weight = 21622.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.151676 restraints weight = 17053.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.153148 restraints weight = 14361.073| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25075 Z= 0.181 Angle : 0.619 9.118 33930 Z= 0.323 Chirality : 0.041 0.191 3880 Planarity : 0.004 0.046 4225 Dihedral : 4.063 17.990 3270 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % 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 aren not related in a simple way. whole: -0.95 (0.16), residues: 2985 helix: 0.58 (0.12), residues: 1720 sheet: -1.01 (0.66), residues: 80 loop : -2.49 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 714 TYR 0.016 0.002 TYR A 564 PHE 0.045 0.002 PHE C 524 TRP 0.030 0.002 TRP A 493 HIS 0.002 0.001 HIS C 523 Details of bonding type rmsd covalent geometry : bond 0.00398 (25075) covalent geometry : angle 0.61939 (33930) hydrogen bonds : bond 0.03933 ( 1100) hydrogen bonds : angle 4.44965 ( 3285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 655 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8671 (m-10) cc_final: 0.8410 (m-10) REVERT: A 131 CYS cc_start: 0.8077 (m) cc_final: 0.7592 (m) REVERT: A 134 GLU cc_start: 0.8670 (mp0) cc_final: 0.8442 (mp0) REVERT: A 174 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8165 (tttt) REVERT: A 224 GLU cc_start: 0.7237 (tp30) cc_final: 0.5910 (tp30) REVERT: A 313 GLN cc_start: 0.7079 (pt0) cc_final: 0.6350 (pp30) REVERT: A 578 MET cc_start: 0.8297 (tmm) cc_final: 0.7954 (tmm) REVERT: B 120 LYS cc_start: 0.8451 (pttm) cc_final: 0.7920 (mtpt) REVERT: B 134 GLU cc_start: 0.8475 (mp0) cc_final: 0.8211 (mp0) REVERT: B 174 LYS cc_start: 0.8713 (tttt) cc_final: 0.8310 (ttmt) REVERT: B 309 ASP cc_start: 0.7861 (p0) cc_final: 0.7590 (p0) REVERT: B 351 MET cc_start: 0.7643 (ttm) cc_final: 0.7412 (ttm) REVERT: B 440 MET cc_start: 0.7360 (mmm) cc_final: 0.6879 (mmm) REVERT: B 555 MET cc_start: 0.8632 (tpp) cc_final: 0.8408 (tpp) REVERT: B 578 MET cc_start: 0.7941 (ppp) cc_final: 0.7468 (tmm) REVERT: B 672 MET cc_start: 0.7365 (ppp) cc_final: 0.7040 (tmm) REVERT: B 700 ILE cc_start: 0.8178 (pt) cc_final: 0.7652 (mp) REVERT: C 224 GLU cc_start: 0.7190 (tp30) cc_final: 0.5891 (tp30) REVERT: C 489 PHE cc_start: 0.7405 (t80) cc_final: 0.6618 (t80) REVERT: C 578 MET cc_start: 0.8353 (tmm) cc_final: 0.7729 (tmm) REVERT: C 579 ILE cc_start: 0.6175 (mt) cc_final: 0.5576 (mt) REVERT: C 717 MET cc_start: 0.4932 (ptp) cc_final: 0.4639 (ptm) REVERT: C 743 LYS cc_start: 0.9202 (ptpt) cc_final: 0.8485 (mmmt) REVERT: D 120 LYS cc_start: 0.8380 (pttm) cc_final: 0.7839 (ptmt) REVERT: D 224 GLU cc_start: 0.7137 (tp30) cc_final: 0.5702 (tp30) REVERT: D 309 ASP cc_start: 0.7767 (p0) cc_final: 0.7379 (p0) REVERT: D 313 GLN cc_start: 0.6782 (pt0) cc_final: 0.6032 (pp30) REVERT: D 351 MET cc_start: 0.7863 (ttm) cc_final: 0.7413 (ttm) REVERT: D 578 MET cc_start: 0.8335 (tmm) cc_final: 0.7973 (tmm) REVERT: D 732 LEU cc_start: 0.9261 (tt) cc_final: 0.8978 (tt) REVERT: D 743 LYS cc_start: 0.9317 (ptpt) cc_final: 0.8725 (mmmt) REVERT: E 120 LYS cc_start: 0.8471 (pttm) cc_final: 0.7965 (mtpt) REVERT: E 131 CYS cc_start: 0.8040 (m) cc_final: 0.7707 (m) REVERT: E 134 GLU cc_start: 0.8555 (mp0) cc_final: 0.8277 (mp0) REVERT: E 174 LYS cc_start: 0.8431 (ttmt) cc_final: 0.7948 (tttt) REVERT: E 578 MET cc_start: 0.8018 (tmm) cc_final: 0.7716 (tmm) REVERT: E 579 ILE cc_start: 0.5936 (mt) cc_final: 0.5698 (mt) REVERT: E 707 LEU cc_start: 0.7029 (tp) cc_final: 0.6753 (tt) REVERT: E 732 LEU cc_start: 0.9304 (tt) cc_final: 0.9063 (tt) outliers start: 1 outliers final: 0 residues processed: 655 average time/residue: 0.1591 time to fit residues: 168.1314 Evaluate side-chains 509 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 272 optimal weight: 1.9990 chunk 268 optimal weight: 0.0370 chunk 148 optimal weight: 0.0030 chunk 145 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 288 optimal weight: 0.4980 chunk 296 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 276 optimal weight: 0.0060 chunk 9 optimal weight: 6.9990 overall best weight: 0.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN C 417 HIS C 585 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS E 417 HIS E 671 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.183785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147461 restraints weight = 47722.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.152471 restraints weight = 28909.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.155938 restraints weight = 20351.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.158355 restraints weight = 15786.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.160048 restraints weight = 13092.040| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25075 Z= 0.116 Angle : 0.565 7.415 33930 Z= 0.293 Chirality : 0.038 0.176 3880 Planarity : 0.003 0.045 4225 Dihedral : 3.850 17.099 3270 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.67 % 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 aren not related in a simple way. whole: -0.81 (0.16), residues: 2985 helix: 0.74 (0.13), residues: 1710 sheet: -1.15 (0.63), residues: 80 loop : -2.47 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 716 TYR 0.011 0.001 TYR E 260 PHE 0.038 0.001 PHE D 524 TRP 0.028 0.001 TRP B 493 HIS 0.004 0.001 HIS E 301 Details of bonding type rmsd covalent geometry : bond 0.00242 (25075) covalent geometry : angle 0.56491 (33930) hydrogen bonds : bond 0.03566 ( 1100) hydrogen bonds : angle 4.20904 ( 3285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 656 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 131 CYS cc_start: 0.8012 (m) cc_final: 0.7476 (m) REVERT: A 134 GLU cc_start: 0.8636 (mp0) cc_final: 0.8432 (mp0) REVERT: A 174 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7904 (tttm) REVERT: A 260 TYR cc_start: 0.5478 (p90) cc_final: 0.4683 (p90) REVERT: A 523 HIS cc_start: 0.7078 (m170) cc_final: 0.6760 (m170) REVERT: A 578 MET cc_start: 0.8296 (tmm) cc_final: 0.7953 (tmm) REVERT: B 120 LYS cc_start: 0.8413 (pttm) cc_final: 0.7766 (mtpt) REVERT: B 131 CYS cc_start: 0.8371 (m) cc_final: 0.7990 (m) REVERT: B 134 GLU cc_start: 0.8410 (mp0) cc_final: 0.8103 (mp0) REVERT: B 174 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7459 (tttt) REVERT: B 260 TYR cc_start: 0.6099 (p90) cc_final: 0.5310 (p90) REVERT: B 309 ASP cc_start: 0.7848 (p0) cc_final: 0.7396 (p0) REVERT: B 440 MET cc_start: 0.7238 (mmm) cc_final: 0.6737 (mmm) REVERT: B 523 HIS cc_start: 0.7074 (m170) cc_final: 0.6742 (m170) REVERT: B 594 TYR cc_start: 0.7496 (t80) cc_final: 0.7167 (t80) REVERT: B 672 MET cc_start: 0.7262 (ppp) cc_final: 0.6735 (tmm) REVERT: B 700 ILE cc_start: 0.8073 (pt) cc_final: 0.7417 (mp) REVERT: C 224 GLU cc_start: 0.6752 (tp30) cc_final: 0.5208 (tp30) REVERT: C 489 PHE cc_start: 0.7167 (t80) cc_final: 0.6301 (t80) REVERT: C 574 MET cc_start: 0.7528 (ppp) cc_final: 0.7132 (ppp) REVERT: C 578 MET cc_start: 0.8371 (tmm) cc_final: 0.7826 (tmm) REVERT: C 579 ILE cc_start: 0.5899 (mt) cc_final: 0.5328 (mt) REVERT: C 717 MET cc_start: 0.5224 (ptp) cc_final: 0.4939 (ptm) REVERT: C 732 LEU cc_start: 0.9203 (tt) cc_final: 0.9000 (tt) REVERT: C 743 LYS cc_start: 0.9157 (ptpt) cc_final: 0.8376 (mmtt) REVERT: D 120 LYS cc_start: 0.8368 (pttm) cc_final: 0.7839 (ptmt) REVERT: D 174 LYS cc_start: 0.8599 (tttt) cc_final: 0.8067 (tttt) REVERT: D 224 GLU cc_start: 0.6867 (tp30) cc_final: 0.5199 (tp30) REVERT: D 229 ASP cc_start: 0.8010 (p0) cc_final: 0.7722 (p0) REVERT: D 282 MET cc_start: 0.8259 (mmt) cc_final: 0.7909 (mmm) REVERT: D 309 ASP cc_start: 0.7547 (p0) cc_final: 0.7338 (p0) REVERT: D 351 MET cc_start: 0.7787 (ttm) cc_final: 0.7367 (ttm) REVERT: D 523 HIS cc_start: 0.7355 (m170) cc_final: 0.7111 (m170) REVERT: D 557 LEU cc_start: 0.8535 (tp) cc_final: 0.8142 (tp) REVERT: D 578 MET cc_start: 0.8254 (tmm) cc_final: 0.7906 (tmm) REVERT: D 732 LEU cc_start: 0.9198 (tt) cc_final: 0.8838 (tt) REVERT: D 743 LYS cc_start: 0.9302 (ptpt) cc_final: 0.8726 (mmmt) REVERT: E 120 LYS cc_start: 0.8360 (pttm) cc_final: 0.7900 (mtpt) REVERT: E 131 CYS cc_start: 0.7945 (m) cc_final: 0.7496 (m) REVERT: E 134 GLU cc_start: 0.8532 (mp0) cc_final: 0.8309 (mp0) REVERT: E 174 LYS cc_start: 0.8414 (ttmt) cc_final: 0.7898 (tttt) REVERT: E 309 ASP cc_start: 0.7440 (p0) cc_final: 0.7175 (p0) REVERT: E 523 HIS cc_start: 0.7270 (m170) cc_final: 0.6874 (m170) REVERT: E 555 MET cc_start: 0.8682 (tpp) cc_final: 0.8474 (tpp) REVERT: E 578 MET cc_start: 0.8011 (tmm) cc_final: 0.7578 (tmm) REVERT: E 579 ILE cc_start: 0.5815 (mt) cc_final: 0.5496 (mt) REVERT: E 594 TYR cc_start: 0.7648 (t80) cc_final: 0.7329 (t80) REVERT: E 732 LEU cc_start: 0.9218 (tt) cc_final: 0.8945 (tt) outliers start: 3 outliers final: 0 residues processed: 659 average time/residue: 0.1577 time to fit residues: 167.9625 Evaluate side-chains 515 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 109 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.175934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138814 restraints weight = 48519.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143329 restraints weight = 30289.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146488 restraints weight = 21853.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.148681 restraints weight = 17313.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.150059 restraints weight = 14625.334| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25075 Z= 0.216 Angle : 0.698 10.434 33930 Z= 0.362 Chirality : 0.042 0.153 3880 Planarity : 0.004 0.046 4225 Dihedral : 4.305 19.086 3270 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % 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 aren not related in a simple way. whole: -1.11 (0.16), residues: 2985 helix: 0.48 (0.12), residues: 1695 sheet: -1.15 (0.66), residues: 80 loop : -2.54 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 567 TYR 0.027 0.002 TYR E 565 PHE 0.042 0.002 PHE B 524 TRP 0.029 0.003 TRP B 493 HIS 0.004 0.001 HIS B 523 Details of bonding type rmsd covalent geometry : bond 0.00481 (25075) covalent geometry : angle 0.69782 (33930) hydrogen bonds : bond 0.04004 ( 1100) hydrogen bonds : angle 4.62530 ( 3285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 628 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.8272 (m) cc_final: 0.7929 (m) REVERT: A 134 GLU cc_start: 0.8611 (mp0) cc_final: 0.8371 (mp0) REVERT: A 174 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8241 (tttm) REVERT: A 313 GLN cc_start: 0.7120 (pt0) cc_final: 0.6057 (pp30) REVERT: A 323 MET cc_start: 0.8475 (ttt) cc_final: 0.8033 (ttm) REVERT: A 523 HIS cc_start: 0.7195 (m170) cc_final: 0.6714 (m170) REVERT: A 578 MET cc_start: 0.7918 (tmm) cc_final: 0.7612 (tmm) REVERT: A 579 ILE cc_start: 0.5874 (mt) cc_final: 0.5494 (mt) REVERT: A 732 LEU cc_start: 0.9301 (tt) cc_final: 0.9067 (tt) REVERT: B 120 LYS cc_start: 0.8494 (pttm) cc_final: 0.7911 (ptmt) REVERT: B 131 CYS cc_start: 0.8607 (m) cc_final: 0.8297 (m) REVERT: B 134 GLU cc_start: 0.8419 (mp0) cc_final: 0.8093 (mp0) REVERT: B 174 LYS cc_start: 0.8377 (ttmt) cc_final: 0.7599 (tttt) REVERT: B 489 PHE cc_start: 0.6491 (t80) cc_final: 0.5770 (m-80) REVERT: B 503 ILE cc_start: 0.8658 (pt) cc_final: 0.8430 (tp) REVERT: B 578 MET cc_start: 0.7928 (ppp) cc_final: 0.7478 (tmm) REVERT: B 672 MET cc_start: 0.7409 (ppp) cc_final: 0.7160 (tmm) REVERT: B 700 ILE cc_start: 0.8197 (pt) cc_final: 0.7793 (mt) REVERT: B 732 LEU cc_start: 0.9361 (tt) cc_final: 0.9115 (tt) REVERT: C 224 GLU cc_start: 0.7259 (tp30) cc_final: 0.5974 (tp30) REVERT: C 489 PHE cc_start: 0.7236 (t80) cc_final: 0.6751 (t80) REVERT: C 574 MET cc_start: 0.7494 (ppp) cc_final: 0.7106 (ppp) REVERT: C 579 ILE cc_start: 0.5999 (mt) cc_final: 0.5737 (mt) REVERT: C 717 MET cc_start: 0.5163 (ptp) cc_final: 0.4857 (ptm) REVERT: C 732 LEU cc_start: 0.9377 (tt) cc_final: 0.9112 (tt) REVERT: C 743 LYS cc_start: 0.9214 (ptpt) cc_final: 0.8478 (mmtt) REVERT: D 120 LYS cc_start: 0.8387 (pttm) cc_final: 0.7831 (ptmt) REVERT: D 174 LYS cc_start: 0.8696 (tttt) cc_final: 0.7930 (tttt) REVERT: D 224 GLU cc_start: 0.7135 (tp30) cc_final: 0.5727 (tp30) REVERT: D 282 MET cc_start: 0.8388 (mmt) cc_final: 0.8056 (mmm) REVERT: D 308 GLU cc_start: 0.7985 (tp30) cc_final: 0.7643 (tp30) REVERT: D 309 ASP cc_start: 0.7963 (p0) cc_final: 0.7504 (p0) REVERT: D 557 LEU cc_start: 0.8633 (tp) cc_final: 0.8246 (tp) REVERT: D 732 LEU cc_start: 0.9329 (tt) cc_final: 0.9002 (tt) REVERT: D 743 LYS cc_start: 0.9331 (ptpt) cc_final: 0.8799 (mmmt) REVERT: E 120 LYS cc_start: 0.8405 (pttm) cc_final: 0.7788 (ptmt) REVERT: E 131 CYS cc_start: 0.8159 (m) cc_final: 0.7702 (m) REVERT: E 134 GLU cc_start: 0.8529 (mp0) cc_final: 0.8286 (mp0) REVERT: E 174 LYS cc_start: 0.8469 (ttmt) cc_final: 0.7969 (tttt) REVERT: E 353 LYS cc_start: 0.8674 (mppt) cc_final: 0.8382 (mppt) REVERT: E 523 HIS cc_start: 0.7471 (m170) cc_final: 0.7247 (m170) REVERT: E 578 MET cc_start: 0.8014 (tmm) cc_final: 0.7631 (tmm) REVERT: E 579 ILE cc_start: 0.6050 (mt) cc_final: 0.5692 (mt) REVERT: E 732 LEU cc_start: 0.9397 (tt) cc_final: 0.9095 (tt) outliers start: 2 outliers final: 0 residues processed: 630 average time/residue: 0.1610 time to fit residues: 162.9762 Evaluate side-chains 508 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 198 optimal weight: 0.7980 chunk 239 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 205 optimal weight: 0.0770 chunk 251 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 240 optimal weight: 20.0000 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 150 HIS ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 150 HIS C 417 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS D 417 HIS E 417 HIS E 671 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.178684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141976 restraints weight = 48409.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146706 restraints weight = 29748.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149967 restraints weight = 21214.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152274 restraints weight = 16663.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.153858 restraints weight = 13961.598| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25075 Z= 0.143 Angle : 0.618 9.361 33930 Z= 0.320 Chirality : 0.040 0.166 3880 Planarity : 0.004 0.044 4225 Dihedral : 4.202 19.458 3270 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.15 % Allowed : 1.61 % Favored : 98.24 % 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 aren not related in a simple way. whole: -0.96 (0.16), residues: 2985 helix: 0.62 (0.13), residues: 1695 sheet: -1.08 (0.65), residues: 80 loop : -2.51 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 716 TYR 0.016 0.001 TYR A 564 PHE 0.026 0.001 PHE A 527 TRP 0.025 0.002 TRP E 380 HIS 0.004 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00319 (25075) covalent geometry : angle 0.61804 (33930) hydrogen bonds : bond 0.03667 ( 1100) hydrogen bonds : angle 4.43667 ( 3285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 619 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 131 CYS cc_start: 0.8256 (m) cc_final: 0.7922 (m) REVERT: A 523 HIS cc_start: 0.7153 (m170) cc_final: 0.6720 (m170) REVERT: A 574 MET cc_start: 0.7507 (ppp) cc_final: 0.7262 (ppp) REVERT: A 578 MET cc_start: 0.7898 (tmm) cc_final: 0.7594 (tmm) REVERT: A 579 ILE cc_start: 0.5878 (mt) cc_final: 0.5467 (mt) REVERT: A 732 LEU cc_start: 0.9232 (tt) cc_final: 0.8957 (tt) REVERT: B 120 LYS cc_start: 0.8484 (pttm) cc_final: 0.7922 (ptmt) REVERT: B 131 CYS cc_start: 0.8617 (m) cc_final: 0.8280 (m) REVERT: B 134 GLU cc_start: 0.8379 (mp0) cc_final: 0.8075 (mp0) REVERT: B 174 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7515 (tttt) REVERT: B 440 MET cc_start: 0.7135 (mmm) cc_final: 0.6716 (mmm) REVERT: B 489 PHE cc_start: 0.6628 (t80) cc_final: 0.5844 (m-80) REVERT: B 594 TYR cc_start: 0.7702 (t80) cc_final: 0.7426 (t80) REVERT: B 672 MET cc_start: 0.7356 (ppp) cc_final: 0.7127 (tmm) REVERT: B 732 LEU cc_start: 0.9326 (tt) cc_final: 0.9079 (tt) REVERT: C 224 GLU cc_start: 0.7003 (tp30) cc_final: 0.5636 (tp30) REVERT: C 489 PHE cc_start: 0.7196 (t80) cc_final: 0.6471 (t80) REVERT: C 523 HIS cc_start: 0.7311 (m170) cc_final: 0.7030 (m170) REVERT: C 574 MET cc_start: 0.7395 (ppp) cc_final: 0.7011 (ppp) REVERT: C 717 MET cc_start: 0.5398 (ptp) cc_final: 0.5111 (ptm) REVERT: C 732 LEU cc_start: 0.9348 (tt) cc_final: 0.9083 (tt) REVERT: C 743 LYS cc_start: 0.9204 (ptpt) cc_final: 0.8420 (mmtt) REVERT: D 120 LYS cc_start: 0.8391 (pttm) cc_final: 0.7811 (ptmt) REVERT: D 174 LYS cc_start: 0.8699 (tttt) cc_final: 0.8187 (tttt) REVERT: D 224 GLU cc_start: 0.6877 (tp30) cc_final: 0.5314 (tp30) REVERT: D 282 MET cc_start: 0.8334 (mmt) cc_final: 0.7983 (mmm) REVERT: D 309 ASP cc_start: 0.7949 (p0) cc_final: 0.7552 (p0) REVERT: D 555 MET cc_start: 0.8593 (tpp) cc_final: 0.8345 (tpp) REVERT: D 557 LEU cc_start: 0.8597 (tp) cc_final: 0.8170 (tp) REVERT: D 732 LEU cc_start: 0.9313 (tt) cc_final: 0.8990 (tt) REVERT: D 743 LYS cc_start: 0.9338 (ptpt) cc_final: 0.8697 (mmmt) REVERT: E 120 LYS cc_start: 0.8427 (pttm) cc_final: 0.7805 (ptmt) REVERT: E 131 CYS cc_start: 0.8134 (m) cc_final: 0.7714 (m) REVERT: E 134 GLU cc_start: 0.8514 (mp0) cc_final: 0.8304 (mp0) REVERT: E 174 LYS cc_start: 0.8464 (ttmt) cc_final: 0.7911 (tttt) REVERT: E 523 HIS cc_start: 0.7441 (m170) cc_final: 0.7105 (m170) REVERT: E 578 MET cc_start: 0.7905 (tmm) cc_final: 0.7628 (tmm) REVERT: E 579 ILE cc_start: 0.5993 (mt) cc_final: 0.5614 (mt) REVERT: E 732 LEU cc_start: 0.9350 (tt) cc_final: 0.9045 (tt) outliers start: 4 outliers final: 0 residues processed: 622 average time/residue: 0.1611 time to fit residues: 161.0587 Evaluate side-chains 499 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 285 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 299 optimal weight: 0.0970 chunk 83 optimal weight: 7.9990 chunk 279 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 264 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN C 417 HIS C 585 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS E 150 HIS E 417 HIS E 671 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.178671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141997 restraints weight = 48327.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146670 restraints weight = 30033.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149864 restraints weight = 21509.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152043 restraints weight = 16961.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.153683 restraints weight = 14270.503| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25075 Z= 0.145 Angle : 0.630 7.991 33930 Z= 0.326 Chirality : 0.040 0.176 3880 Planarity : 0.004 0.044 4225 Dihedral : 4.210 19.559 3270 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.92 % Favored : 90.05 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % Favored : 99.25 % 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 aren not related in a simple way. whole: -1.01 (0.16), residues: 2985 helix: 0.61 (0.13), residues: 1685 sheet: -1.12 (0.66), residues: 80 loop : -2.56 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 690 TYR 0.016 0.002 TYR A 564 PHE 0.038 0.002 PHE A 524 TRP 0.030 0.002 TRP A 380 HIS 0.004 0.001 HIS E 417 Details of bonding type rmsd covalent geometry : bond 0.00323 (25075) covalent geometry : angle 0.62952 (33930) hydrogen bonds : bond 0.03656 ( 1100) hydrogen bonds : angle 4.42374 ( 3285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 616 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.7776 (mp0) cc_final: 0.7528 (mp0) REVERT: A 174 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8321 (ttmt) REVERT: A 431 MET cc_start: 0.8050 (ttt) cc_final: 0.7817 (ttp) REVERT: A 578 MET cc_start: 0.7900 (tmm) cc_final: 0.7529 (tmm) REVERT: A 579 ILE cc_start: 0.5862 (mt) cc_final: 0.5459 (mt) REVERT: A 732 LEU cc_start: 0.9228 (tt) cc_final: 0.8966 (tt) REVERT: B 131 CYS cc_start: 0.8655 (m) cc_final: 0.8325 (m) REVERT: B 134 GLU cc_start: 0.8370 (mp0) cc_final: 0.8068 (mp0) REVERT: B 174 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7511 (tttt) REVERT: B 308 GLU cc_start: 0.7907 (tp30) cc_final: 0.7695 (tp30) REVERT: B 440 MET cc_start: 0.7126 (mmm) cc_final: 0.6648 (mmm) REVERT: B 489 PHE cc_start: 0.6823 (t80) cc_final: 0.5782 (m-80) REVERT: B 503 ILE cc_start: 0.8618 (pt) cc_final: 0.8402 (tp) REVERT: B 594 TYR cc_start: 0.7581 (t80) cc_final: 0.7366 (t80) REVERT: B 672 MET cc_start: 0.7375 (ppp) cc_final: 0.6907 (tmm) REVERT: B 732 LEU cc_start: 0.9322 (tt) cc_final: 0.9084 (tt) REVERT: C 120 LYS cc_start: 0.8322 (ptpp) cc_final: 0.8015 (ptmt) REVERT: C 489 PHE cc_start: 0.7272 (t80) cc_final: 0.6494 (t80) REVERT: C 523 HIS cc_start: 0.7360 (m170) cc_final: 0.7068 (m170) REVERT: C 574 MET cc_start: 0.7354 (ppp) cc_final: 0.7035 (ppp) REVERT: C 717 MET cc_start: 0.5433 (ptp) cc_final: 0.5123 (ptm) REVERT: C 732 LEU cc_start: 0.9345 (tt) cc_final: 0.9078 (tt) REVERT: C 743 LYS cc_start: 0.9197 (ptpt) cc_final: 0.8422 (mmtt) REVERT: D 120 LYS cc_start: 0.8408 (pttm) cc_final: 0.7818 (ptmt) REVERT: D 174 LYS cc_start: 0.8677 (tttt) cc_final: 0.8202 (tttt) REVERT: D 224 GLU cc_start: 0.6941 (tp30) cc_final: 0.5385 (tp30) REVERT: D 282 MET cc_start: 0.8301 (mmt) cc_final: 0.7962 (mmm) REVERT: D 308 GLU cc_start: 0.7928 (tp30) cc_final: 0.7728 (tp30) REVERT: D 370 LEU cc_start: 0.8869 (pp) cc_final: 0.8663 (pp) REVERT: D 732 LEU cc_start: 0.9327 (tt) cc_final: 0.9004 (tt) REVERT: D 743 LYS cc_start: 0.9326 (ptpt) cc_final: 0.8695 (mmmt) REVERT: E 120 LYS cc_start: 0.8432 (pttm) cc_final: 0.7807 (ptmt) REVERT: E 131 CYS cc_start: 0.8110 (m) cc_final: 0.7715 (m) REVERT: E 134 GLU cc_start: 0.8550 (mp0) cc_final: 0.8335 (mp0) REVERT: E 174 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8024 (ttmt) REVERT: E 578 MET cc_start: 0.7931 (tmm) cc_final: 0.7623 (tmm) REVERT: E 579 ILE cc_start: 0.6107 (mt) cc_final: 0.5688 (mt) REVERT: E 732 LEU cc_start: 0.9384 (tt) cc_final: 0.9097 (tt) outliers start: 2 outliers final: 0 residues processed: 618 average time/residue: 0.1623 time to fit residues: 161.0764 Evaluate side-chains 493 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 493 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 115 optimal weight: 3.9990 chunk 229 optimal weight: 0.0070 chunk 247 optimal weight: 0.0470 chunk 196 optimal weight: 0.2980 chunk 188 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 163 optimal weight: 0.0270 chunk 112 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN C 417 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 HIS E 671 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.183778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147475 restraints weight = 48119.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.152395 restraints weight = 29447.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155787 restraints weight = 20909.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.158133 restraints weight = 16286.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.159815 restraints weight = 13567.650| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25075 Z= 0.119 Angle : 0.615 9.027 33930 Z= 0.313 Chirality : 0.039 0.154 3880 Planarity : 0.003 0.044 4225 Dihedral : 4.049 18.327 3270 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.11 % Favored : 90.82 % Rotamer: Outliers : 0.11 % Allowed : 0.60 % Favored : 99.29 % 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 aren not related in a simple way. whole: -0.91 (0.16), residues: 2985 helix: 0.70 (0.13), residues: 1685 sheet: -0.96 (0.67), residues: 80 loop : -2.55 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 363 TYR 0.011 0.001 TYR B 260 PHE 0.024 0.001 PHE A 527 TRP 0.023 0.001 TRP E 380 HIS 0.006 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00250 (25075) covalent geometry : angle 0.61489 (33930) hydrogen bonds : bond 0.03346 ( 1100) hydrogen bonds : angle 4.23663 ( 3285) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 624 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 129 GLU cc_start: 0.7774 (mp0) cc_final: 0.7482 (mp0) REVERT: A 174 LYS cc_start: 0.8772 (ttmt) cc_final: 0.8230 (tttm) REVERT: A 308 GLU cc_start: 0.8169 (tp30) cc_final: 0.7804 (tp30) REVERT: A 369 ARG cc_start: 0.8536 (tmt170) cc_final: 0.8174 (tmm-80) REVERT: A 431 MET cc_start: 0.7897 (ttt) cc_final: 0.7657 (ttp) REVERT: A 523 HIS cc_start: 0.7022 (m170) cc_final: 0.6499 (m170) REVERT: A 525 VAL cc_start: 0.8062 (t) cc_final: 0.7837 (t) REVERT: A 557 LEU cc_start: 0.8630 (tp) cc_final: 0.8323 (tp) REVERT: A 578 MET cc_start: 0.7852 (tmm) cc_final: 0.7532 (tmm) REVERT: A 579 ILE cc_start: 0.6111 (mt) cc_final: 0.5681 (mt) REVERT: A 717 MET cc_start: 0.5290 (ptp) cc_final: 0.4982 (ptm) REVERT: A 732 LEU cc_start: 0.9126 (tt) cc_final: 0.8861 (tt) REVERT: B 131 CYS cc_start: 0.8594 (m) cc_final: 0.8253 (m) REVERT: B 134 GLU cc_start: 0.8387 (mp0) cc_final: 0.8137 (mp0) REVERT: B 174 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7238 (tttt) REVERT: B 308 GLU cc_start: 0.7921 (tp30) cc_final: 0.7641 (tp30) REVERT: B 489 PHE cc_start: 0.6849 (t80) cc_final: 0.5741 (m-80) REVERT: B 503 ILE cc_start: 0.8609 (pt) cc_final: 0.8395 (tp) REVERT: B 672 MET cc_start: 0.7286 (ppp) cc_final: 0.6988 (tmm) REVERT: B 732 LEU cc_start: 0.9268 (tt) cc_final: 0.9042 (tt) REVERT: C 120 LYS cc_start: 0.8396 (ptpp) cc_final: 0.8087 (ptmt) REVERT: C 489 PHE cc_start: 0.7129 (t80) cc_final: 0.6489 (t80) REVERT: C 523 HIS cc_start: 0.7248 (m170) cc_final: 0.6980 (m170) REVERT: C 550 CYS cc_start: 0.8296 (m) cc_final: 0.7963 (p) REVERT: C 574 MET cc_start: 0.7314 (ppp) cc_final: 0.7018 (ppp) REVERT: C 717 MET cc_start: 0.5281 (ptp) cc_final: 0.4971 (ptm) REVERT: C 732 LEU cc_start: 0.9252 (tt) cc_final: 0.8979 (tt) REVERT: C 743 LYS cc_start: 0.9165 (ptpt) cc_final: 0.8410 (mmtt) REVERT: D 120 LYS cc_start: 0.8377 (pttm) cc_final: 0.7804 (ptmt) REVERT: D 174 LYS cc_start: 0.8683 (tttt) cc_final: 0.8166 (tttt) REVERT: D 224 GLU cc_start: 0.6744 (tp30) cc_final: 0.5202 (tp30) REVERT: D 282 MET cc_start: 0.8174 (mmt) cc_final: 0.7842 (mmm) REVERT: D 308 GLU cc_start: 0.7828 (tp30) cc_final: 0.7620 (tp30) REVERT: D 369 ARG cc_start: 0.8562 (tmt170) cc_final: 0.8274 (tmm-80) REVERT: D 732 LEU cc_start: 0.9264 (tt) cc_final: 0.8958 (tt) REVERT: D 743 LYS cc_start: 0.9323 (ptpt) cc_final: 0.8691 (mmmt) REVERT: E 120 LYS cc_start: 0.8445 (pttm) cc_final: 0.7822 (ptmt) REVERT: E 523 HIS cc_start: 0.7343 (m170) cc_final: 0.7033 (m170) REVERT: E 550 CYS cc_start: 0.7853 (m) cc_final: 0.7568 (p) REVERT: E 578 MET cc_start: 0.7844 (tmm) cc_final: 0.7553 (tmm) REVERT: E 579 ILE cc_start: 0.6202 (mt) cc_final: 0.5766 (mt) REVERT: E 732 LEU cc_start: 0.9325 (tt) cc_final: 0.9056 (tt) outliers start: 3 outliers final: 0 residues processed: 626 average time/residue: 0.1618 time to fit residues: 162.1387 Evaluate side-chains 497 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 60 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 278 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 274 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 HIS E 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.174331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137662 restraints weight = 48571.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142164 restraints weight = 29966.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.145297 restraints weight = 21477.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.147439 restraints weight = 16936.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148993 restraints weight = 14292.034| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25075 Z= 0.215 Angle : 0.726 9.857 33930 Z= 0.377 Chirality : 0.043 0.190 3880 Planarity : 0.005 0.045 4225 Dihedral : 4.483 19.761 3270 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.85 % Favored : 90.12 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % 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 aren not related in a simple way. whole: -1.26 (0.16), residues: 2985 helix: 0.40 (0.13), residues: 1685 sheet: -1.43 (0.64), residues: 80 loop : -2.65 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 729 TYR 0.023 0.002 TYR D 565 PHE 0.028 0.002 PHE C 436 TRP 0.034 0.003 TRP E 380 HIS 0.004 0.001 HIS D 745 Details of bonding type rmsd covalent geometry : bond 0.00479 (25075) covalent geometry : angle 0.72641 (33930) hydrogen bonds : bond 0.03932 ( 1100) hydrogen bonds : angle 4.65230 ( 3285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4882.87 seconds wall clock time: 85 minutes 2.27 seconds (5102.27 seconds total)