Starting phenix.real_space_refine on Sat Jun 21 03:13:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dij_46907/06_2025/9dij_46907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dij_46907/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dij_46907/06_2025/9dij_46907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dij_46907/06_2025/9dij_46907.map" model { file = "/net/cci-nas-00/data/ceres_data/9dij_46907/06_2025/9dij_46907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dij_46907/06_2025/9dij_46907.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D Time building chain proxies: 11.82, per 1000 atoms: 0.48 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: 5.59 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.19 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: 6.97 Time building geometry restraints manager: 6.67 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.940 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 48.870 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.110 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.530 ------------------------------------------------------------------------------- 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 : 7.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP C 559 HIS 0.003 0.001 HIS B 256 PHE 0.017 0.001 PHE E 656 TYR 0.021 0.001 TYR C 451 ARG 0.002 0.000 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.27519 ( 1100) hydrogen bonds : angle 7.32657 ( 3285) covalent geometry : bond 0.00215 (25075) covalent geometry : angle 0.49830 (33930) *********************** 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 : 2.603 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: 0.7707 (mmt) REVERT: A 323 MET cc_start: 0.8179 (ttp) cc_final: 0.7947 (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: 0.5358 (mt) REVERT: B 224 GLU cc_start: 0.6513 (tp30) cc_final: 0.5185 (tp30) REVERT: B 743 LYS cc_start: 0.9000 (ptpp) cc_final: 0.8547 (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: 0.8605 (pp) REVERT: C 382 TYR cc_start: 0.8104 (t80) cc_final: 0.7778 (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: 0.5572 (mt) REVERT: C 743 LYS cc_start: 0.9123 (ptpp) cc_final: 0.8499 (mmtt) REVERT: D 419 MET cc_start: 0.9147 (tpp) cc_final: 0.8946 (tpp) 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: 0.6379 (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: 0.8639 (mmmt) outliers start: 10 outliers final: 5 residues processed: 766 average time/residue: 0.3294 time to fit residues: 405.0125 Evaluate side-chains 541 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 536 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.9980 chunk 227 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.179764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142942 restraints weight = 47165.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147659 restraints weight = 29063.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150957 restraints weight = 20716.945| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25075 Z= 0.207 Angle : 0.680 9.627 33930 Z= 0.359 Chirality : 0.043 0.199 3880 Planarity : 0.004 0.039 4225 Dihedral : 3.941 14.354 3270 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.75 % Allowed : 7.64 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 2985 helix: 0.05 (0.12), residues: 1740 sheet: -0.95 (0.63), residues: 80 loop : -2.68 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 739 HIS 0.007 0.001 HIS C 301 PHE 0.040 0.002 PHE A 524 TYR 0.017 0.002 TYR C 382 ARG 0.005 0.000 ARG E 226 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 1100) hydrogen bonds : angle 4.77219 ( 3285) covalent geometry : bond 0.00448 (25075) covalent geometry : angle 0.67987 (33930) *********************** 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 687 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 667 time to evaluate : 2.899 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 123 ILE cc_start: 0.9154 (mt) cc_final: 0.8884 (tp) REVERT: A 131 CYS cc_start: 0.7746 (m) cc_final: 0.7256 (m) REVERT: A 346 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: A 435 LYS cc_start: 0.7892 (mmtm) cc_final: 0.6973 (mmtt) REVERT: A 527 PHE cc_start: 0.8510 (t80) cc_final: 0.8175 (t80) REVERT: A 578 MET cc_start: 0.8100 (tmm) cc_final: 0.7745 (tmm) REVERT: A 592 PHE cc_start: 0.6972 (p90) cc_final: 0.5978 (m-80) REVERT: B 224 GLU cc_start: 0.6807 (tp30) cc_final: 0.5545 (tp30) REVERT: B 346 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: B 351 MET cc_start: 0.7884 (ttm) cc_final: 0.7599 (ttm) REVERT: B 440 MET cc_start: 0.7331 (mmm) cc_final: 0.6853 (mmm) REVERT: B 527 PHE cc_start: 0.8509 (t80) cc_final: 0.8191 (t80) REVERT: B 592 PHE cc_start: 0.7180 (p90) cc_final: 0.6178 (m-80) REVERT: C 298 ASN cc_start: 0.7691 (t0) cc_final: 0.7405 (t0) REVERT: C 346 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: C 351 MET cc_start: 0.7836 (ttm) cc_final: 0.7445 (ttm) REVERT: C 382 TYR cc_start: 0.8445 (t80) cc_final: 0.8168 (t80) REVERT: C 435 LYS cc_start: 0.7561 (mmtm) cc_final: 0.6716 (mmtt) REVERT: C 578 MET cc_start: 0.8108 (tmm) cc_final: 0.7659 (tmm) REVERT: C 592 PHE cc_start: 0.7174 (p90) cc_final: 0.6136 (m-80) REVERT: C 743 LYS cc_start: 0.9198 (ptpt) cc_final: 0.8510 (mmmt) REVERT: D 298 ASN cc_start: 0.7872 (t0) cc_final: 0.7595 (t0) REVERT: D 435 LYS cc_start: 0.7769 (mmtm) cc_final: 0.6746 (mmtt) REVERT: D 527 PHE cc_start: 0.8496 (t80) cc_final: 0.8215 (t80) REVERT: D 578 MET cc_start: 0.8054 (tmm) cc_final: 0.7663 (tmm) REVERT: D 592 PHE cc_start: 0.7158 (p90) cc_final: 0.5972 (m-80) REVERT: D 743 LYS cc_start: 0.9262 (ptpt) cc_final: 0.8732 (mmmt) REVERT: E 131 CYS cc_start: 0.7567 (m) cc_final: 0.7293 (m) REVERT: E 134 GLU cc_start: 0.8599 (mp0) cc_final: 0.8272 (mp0) REVERT: E 346 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: E 527 PHE cc_start: 0.8369 (t80) cc_final: 0.8145 (t80) REVERT: E 578 MET cc_start: 0.8223 (tmm) cc_final: 0.7650 (tmm) REVERT: E 579 ILE cc_start: 0.5599 (mt) cc_final: 0.5210 (mt) REVERT: E 592 PHE cc_start: 0.7133 (p90) cc_final: 0.6086 (m-80) REVERT: E 717 MET cc_start: 0.6302 (ptm) cc_final: 0.6088 (ptp) REVERT: E 743 LYS cc_start: 0.9257 (ptpt) cc_final: 0.8736 (mmmt) outliers start: 20 outliers final: 1 residues processed: 677 average time/residue: 0.3286 time to fit residues: 357.0105 Evaluate side-chains 522 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 517 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 168 optimal weight: 4.9990 chunk 142 optimal weight: 0.0670 chunk 146 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 224 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 417 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.184642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.147820 restraints weight = 47369.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.152799 restraints weight = 28991.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.156268 restraints weight = 20550.895| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2653 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= 0.135 Angle : 0.567 6.957 33930 Z= 0.298 Chirality : 0.039 0.176 3880 Planarity : 0.004 0.045 4225 Dihedral : 3.811 14.980 3270 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 2985 helix: 0.37 (0.12), residues: 1720 sheet: -1.03 (0.63), residues: 80 loop : -2.51 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 739 HIS 0.003 0.001 HIS C 417 PHE 0.031 0.001 PHE A 524 TYR 0.014 0.001 TYR A 564 ARG 0.005 0.000 ARG D 327 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 1100) hydrogen bonds : angle 4.50587 ( 3285) covalent geometry : bond 0.00278 (25075) covalent geometry : angle 0.56726 (33930) *********************** 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 684 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 2.760 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: A 123 ILE cc_start: 0.9178 (mt) cc_final: 0.8908 (tp) REVERT: A 131 CYS cc_start: 0.7822 (m) cc_final: 0.7291 (m) REVERT: A 134 GLU cc_start: 0.8743 (mp0) cc_final: 0.8473 (mp0) REVERT: A 224 GLU cc_start: 0.6916 (tp30) cc_final: 0.5519 (tp30) REVERT: A 351 MET cc_start: 0.7961 (ttm) cc_final: 0.7593 (ttm) REVERT: A 523 HIS cc_start: 0.7305 (m170) cc_final: 0.6799 (m170) REVERT: A 578 MET cc_start: 0.8163 (tmm) cc_final: 0.7687 (tmm) REVERT: A 579 ILE cc_start: 0.5745 (mt) cc_final: 0.5231 (mt) REVERT: B 120 LYS cc_start: 0.8437 (pttm) cc_final: 0.8017 (mtpt) REVERT: B 131 CYS cc_start: 0.8325 (m) cc_final: 0.7936 (m) REVERT: B 134 GLU cc_start: 0.8611 (mp0) cc_final: 0.8295 (mp0) REVERT: B 224 GLU cc_start: 0.6594 (tp30) cc_final: 0.5175 (tp30) REVERT: B 309 ASP cc_start: 0.7706 (p0) cc_final: 0.7354 (p0) REVERT: B 351 MET cc_start: 0.7712 (ttm) cc_final: 0.7447 (ttm) REVERT: B 440 MET cc_start: 0.7124 (mmm) cc_final: 0.6613 (mmm) REVERT: B 578 MET cc_start: 0.7894 (ppp) cc_final: 0.7614 (tmm) REVERT: B 579 ILE cc_start: 0.5519 (mt) cc_final: 0.5268 (mt) REVERT: B 594 TYR cc_start: 0.7751 (t80) cc_final: 0.7425 (t80) REVERT: C 173 MET cc_start: 0.8853 (mpp) cc_final: 0.8490 (mtm) REVERT: C 224 GLU cc_start: 0.6981 (tp30) cc_final: 0.5606 (tp30) REVERT: C 489 PHE cc_start: 0.7341 (t80) cc_final: 0.6323 (t80) REVERT: C 574 MET cc_start: 0.7323 (ppp) cc_final: 0.7021 (ppp) REVERT: C 578 MET cc_start: 0.8154 (tmm) cc_final: 0.7670 (tmm) REVERT: C 704 GLU cc_start: 0.6683 (tm-30) cc_final: 0.6338 (mt-10) REVERT: C 743 LYS cc_start: 0.9185 (ptpt) cc_final: 0.8461 (mmtt) REVERT: D 120 LYS cc_start: 0.8254 (pttm) cc_final: 0.7840 (ptmt) REVERT: D 224 GLU cc_start: 0.6837 (tp30) cc_final: 0.5254 (tp30) REVERT: D 309 ASP cc_start: 0.7501 (p0) cc_final: 0.7216 (p0) REVERT: D 351 MET cc_start: 0.7933 (ttm) cc_final: 0.7445 (ttm) REVERT: D 489 PHE cc_start: 0.7033 (t80) cc_final: 0.6680 (t80) REVERT: D 578 MET cc_start: 0.8238 (tmm) cc_final: 0.7696 (tmm) REVERT: D 743 LYS cc_start: 0.9263 (ptpt) cc_final: 0.8714 (mmmt) REVERT: E 120 LYS cc_start: 0.8398 (pttm) cc_final: 0.7902 (mtpt) REVERT: E 131 CYS cc_start: 0.7754 (m) cc_final: 0.7474 (m) REVERT: E 134 GLU cc_start: 0.8609 (mp0) cc_final: 0.8314 (mp0) REVERT: E 523 HIS cc_start: 0.7599 (m170) cc_final: 0.7217 (m170) REVERT: E 578 MET cc_start: 0.8185 (tmm) cc_final: 0.7613 (tmm) REVERT: E 579 ILE cc_start: 0.5731 (mt) cc_final: 0.5314 (mt) REVERT: E 594 TYR cc_start: 0.7724 (t80) cc_final: 0.7419 (t80) REVERT: E 743 LYS cc_start: 0.9270 (ptpt) cc_final: 0.8669 (mmmt) outliers start: 0 outliers final: 0 residues processed: 684 average time/residue: 0.3384 time to fit residues: 370.9514 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 : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 274 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 0.0970 chunk 222 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 276 optimal weight: 0.6980 chunk 102 optimal weight: 0.0040 chunk 247 optimal weight: 5.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 561 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS E 561 ASN ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.185112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.148534 restraints weight = 48483.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.153513 restraints weight = 29700.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.156954 restraints weight = 21072.946| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25075 Z= 0.118 Angle : 0.551 6.684 33930 Z= 0.288 Chirality : 0.038 0.182 3880 Planarity : 0.003 0.046 4225 Dihedral : 3.773 15.094 3270 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2985 helix: 0.58 (0.12), residues: 1710 sheet: -1.11 (0.63), residues: 80 loop : -2.46 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 521 HIS 0.002 0.000 HIS E 301 PHE 0.021 0.001 PHE A 592 TYR 0.016 0.001 TYR A 564 ARG 0.004 0.000 ARG C 716 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 1100) hydrogen bonds : angle 4.35100 ( 3285) covalent geometry : bond 0.00250 (25075) covalent geometry : angle 0.55141 (33930) *********************** 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 655 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 3.186 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: A 123 ILE cc_start: 0.9166 (mt) cc_final: 0.8899 (tp) REVERT: A 124 PHE cc_start: 0.8555 (m-10) cc_final: 0.8348 (m-10) REVERT: A 131 CYS cc_start: 0.7851 (m) cc_final: 0.7334 (m) REVERT: A 134 GLU cc_start: 0.8684 (mp0) cc_final: 0.8468 (mp0) REVERT: A 224 GLU cc_start: 0.6862 (tp30) cc_final: 0.5457 (tp30) REVERT: A 309 ASP cc_start: 0.7607 (p0) cc_final: 0.7203 (p0) REVERT: A 489 PHE cc_start: 0.7059 (t80) cc_final: 0.6524 (t80) REVERT: A 523 HIS cc_start: 0.7209 (m170) cc_final: 0.6759 (m170) REVERT: A 578 MET cc_start: 0.8270 (tmm) cc_final: 0.7685 (tmm) REVERT: A 579 ILE cc_start: 0.5843 (mt) cc_final: 0.5256 (mt) REVERT: B 120 LYS cc_start: 0.8405 (pttm) cc_final: 0.7820 (mtpt) REVERT: B 131 CYS cc_start: 0.8299 (m) cc_final: 0.7979 (m) REVERT: B 134 GLU cc_start: 0.8584 (mp0) cc_final: 0.8294 (mp0) REVERT: B 174 LYS cc_start: 0.8678 (tttt) cc_final: 0.8267 (ttmt) REVERT: B 351 MET cc_start: 0.7680 (ttm) cc_final: 0.7434 (ttm) REVERT: B 440 MET cc_start: 0.7295 (mmm) cc_final: 0.6811 (mmm) REVERT: C 174 LYS cc_start: 0.8683 (tttt) cc_final: 0.8299 (tttt) REVERT: C 224 GLU cc_start: 0.6717 (tp30) cc_final: 0.5194 (tp30) REVERT: C 264 THR cc_start: 0.8929 (p) cc_final: 0.8687 (p) REVERT: C 308 GLU cc_start: 0.7955 (tp30) cc_final: 0.7652 (tp30) REVERT: C 309 ASP cc_start: 0.7521 (p0) cc_final: 0.7258 (p0) REVERT: C 489 PHE cc_start: 0.7375 (t80) cc_final: 0.6628 (t80) REVERT: C 574 MET cc_start: 0.7286 (ppp) cc_final: 0.6948 (ppp) REVERT: C 578 MET cc_start: 0.8280 (tmm) cc_final: 0.7648 (tmm) REVERT: C 579 ILE cc_start: 0.5535 (mt) cc_final: 0.4985 (mt) REVERT: C 743 LYS cc_start: 0.9183 (ptpt) cc_final: 0.8491 (mmtt) REVERT: D 120 LYS cc_start: 0.8316 (pttm) cc_final: 0.7871 (ptmt) REVERT: D 174 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7604 (tttt) REVERT: D 224 GLU cc_start: 0.6860 (tp30) cc_final: 0.5314 (tp30) REVERT: D 229 ASP cc_start: 0.7945 (p0) cc_final: 0.7712 (p0) REVERT: D 309 ASP cc_start: 0.7579 (p0) cc_final: 0.7327 (p0) REVERT: D 353 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8581 (mmtp) REVERT: D 419 MET cc_start: 0.8819 (tpp) cc_final: 0.8424 (tpp) REVERT: D 489 PHE cc_start: 0.6969 (t80) cc_final: 0.6396 (t80) REVERT: D 578 MET cc_start: 0.8269 (tmm) cc_final: 0.7955 (tmm) REVERT: D 732 LEU cc_start: 0.9196 (tt) cc_final: 0.8918 (tt) REVERT: D 743 LYS cc_start: 0.9281 (ptpt) cc_final: 0.8755 (mmmt) REVERT: E 120 LYS cc_start: 0.8385 (pttm) cc_final: 0.7802 (mtpt) REVERT: E 131 CYS cc_start: 0.7823 (m) cc_final: 0.7377 (m) REVERT: E 134 GLU cc_start: 0.8609 (mp0) cc_final: 0.8327 (mp0) REVERT: E 174 LYS cc_start: 0.8704 (tttt) cc_final: 0.8393 (tttt) REVERT: E 309 ASP cc_start: 0.7399 (p0) cc_final: 0.7151 (p0) REVERT: E 578 MET cc_start: 0.8098 (tmm) cc_final: 0.7476 (tmm) REVERT: E 579 ILE cc_start: 0.5855 (mt) cc_final: 0.5362 (mt) REVERT: E 732 LEU cc_start: 0.9235 (tt) cc_final: 0.8991 (tt) REVERT: E 743 LYS cc_start: 0.9289 (ptpt) cc_final: 0.8679 (mmmt) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.3830 time to fit residues: 405.2398 Evaluate side-chains 522 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 522 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 17 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 129 optimal weight: 0.0050 chunk 185 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 280 optimal weight: 0.8980 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN ** A 313 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 585 HIS ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 417 HIS C 452 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 561 ASN D 585 HIS E 297 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 = 0.4182 r_free = 0.4182 target = 0.184348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.147527 restraints weight = 48405.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152420 restraints weight = 30081.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155889 restraints weight = 21519.754| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25075 Z= 0.120 Angle : 0.546 6.835 33930 Z= 0.286 Chirality : 0.038 0.175 3880 Planarity : 0.003 0.045 4225 Dihedral : 3.782 15.252 3270 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.04 % Allowed : 3.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2985 helix: 0.68 (0.12), residues: 1720 sheet: -1.18 (0.63), residues: 80 loop : -2.49 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 559 HIS 0.003 0.001 HIS C 417 PHE 0.041 0.001 PHE C 524 TYR 0.013 0.001 TYR A 564 ARG 0.003 0.000 ARG A 716 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 1100) hydrogen bonds : angle 4.29076 ( 3285) covalent geometry : bond 0.00259 (25075) covalent geometry : angle 0.54614 (33930) *********************** 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 657 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 656 time to evaluate : 2.548 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 131 CYS cc_start: 0.7953 (m) cc_final: 0.7446 (m) REVERT: A 134 GLU cc_start: 0.8692 (mp0) cc_final: 0.8492 (mp0) REVERT: A 174 LYS cc_start: 0.8849 (tttt) cc_final: 0.8252 (tttt) REVERT: A 224 GLU cc_start: 0.6977 (tp30) cc_final: 0.5599 (tp30) REVERT: A 309 ASP cc_start: 0.7616 (p0) cc_final: 0.7265 (p0) REVERT: A 353 LYS cc_start: 0.8581 (mttm) cc_final: 0.8280 (mmtp) REVERT: A 578 MET cc_start: 0.8300 (tmm) cc_final: 0.7948 (tmm) REVERT: B 120 LYS cc_start: 0.8401 (pttm) cc_final: 0.7906 (mtpt) REVERT: B 131 CYS cc_start: 0.8325 (m) cc_final: 0.7995 (m) REVERT: B 134 GLU cc_start: 0.8502 (mp0) cc_final: 0.8216 (mp0) REVERT: B 174 LYS cc_start: 0.8605 (tttt) cc_final: 0.8170 (ttmt) REVERT: B 308 GLU cc_start: 0.8325 (tp30) cc_final: 0.7932 (tp30) REVERT: B 376 LYS cc_start: 0.5394 (tttt) cc_final: 0.4567 (tttt) REVERT: B 440 MET cc_start: 0.7238 (mmm) cc_final: 0.6785 (mmm) REVERT: B 578 MET cc_start: 0.7966 (ppp) cc_final: 0.7619 (tmm) REVERT: B 579 ILE cc_start: 0.5628 (mt) cc_final: 0.5373 (mt) REVERT: B 594 TYR cc_start: 0.7696 (t80) cc_final: 0.7376 (t80) REVERT: C 174 LYS cc_start: 0.8722 (tttt) cc_final: 0.8088 (tttt) REVERT: C 224 GLU cc_start: 0.6778 (tp30) cc_final: 0.5283 (tp30) REVERT: C 264 THR cc_start: 0.8974 (p) cc_final: 0.8729 (p) REVERT: C 489 PHE cc_start: 0.7239 (t80) cc_final: 0.6394 (t80) REVERT: C 523 HIS cc_start: 0.7468 (m170) cc_final: 0.7107 (m170) REVERT: C 574 MET cc_start: 0.7328 (ppp) cc_final: 0.6965 (ppp) REVERT: C 578 MET cc_start: 0.8344 (tmm) cc_final: 0.7791 (tmm) REVERT: C 579 ILE cc_start: 0.5920 (mt) cc_final: 0.5330 (mt) REVERT: C 704 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6286 (mt-10) REVERT: C 743 LYS cc_start: 0.9190 (ptpt) cc_final: 0.8480 (mmtt) REVERT: D 120 LYS cc_start: 0.8318 (pttm) cc_final: 0.7827 (ptmt) REVERT: D 174 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7583 (tttt) REVERT: D 224 GLU cc_start: 0.6970 (tp30) cc_final: 0.5323 (tp30) REVERT: D 351 MET cc_start: 0.7799 (ttm) cc_final: 0.7223 (ttm) REVERT: D 353 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8285 (mttm) REVERT: D 489 PHE cc_start: 0.6963 (t80) cc_final: 0.6444 (t80) REVERT: D 578 MET cc_start: 0.8282 (tmm) cc_final: 0.7930 (tmm) REVERT: D 732 LEU cc_start: 0.9224 (tt) cc_final: 0.8942 (tt) REVERT: D 743 LYS cc_start: 0.9287 (ptpt) cc_final: 0.8690 (mmmt) REVERT: E 120 LYS cc_start: 0.8457 (pttm) cc_final: 0.7981 (ptmt) REVERT: E 131 CYS cc_start: 0.8052 (m) cc_final: 0.7645 (m) REVERT: E 134 GLU cc_start: 0.8597 (mp0) cc_final: 0.8335 (mp0) REVERT: E 174 LYS cc_start: 0.8646 (tttt) cc_final: 0.8300 (tttt) REVERT: E 309 ASP cc_start: 0.7493 (p0) cc_final: 0.7217 (p0) REVERT: E 578 MET cc_start: 0.7948 (tmm) cc_final: 0.7668 (tmm) REVERT: E 579 ILE cc_start: 0.5847 (mt) cc_final: 0.5561 (mt) REVERT: E 594 TYR cc_start: 0.7798 (t80) cc_final: 0.7560 (t80) REVERT: E 743 LYS cc_start: 0.9301 (ptpt) cc_final: 0.8677 (mmmt) outliers start: 1 outliers final: 0 residues processed: 657 average time/residue: 0.3258 time to fit residues: 342.3633 Evaluate side-chains 514 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 183 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 265 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 257 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 313 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 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS C 439 HIS C 585 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 585 HIS ** 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 = 0.4067 r_free = 0.4067 target = 0.172692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135828 restraints weight = 48089.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140257 restraints weight = 29733.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143343 restraints weight = 21384.930| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 25075 Z= 0.261 Angle : 0.742 10.024 33930 Z= 0.387 Chirality : 0.044 0.207 3880 Planarity : 0.005 0.046 4225 Dihedral : 4.453 17.738 3270 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 2985 helix: 0.08 (0.12), residues: 1760 sheet: -1.06 (0.67), residues: 80 loop : -2.92 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 380 HIS 0.005 0.001 HIS E 523 PHE 0.045 0.002 PHE E 524 TYR 0.023 0.003 TYR E 565 ARG 0.018 0.001 ARG D 729 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 1100) hydrogen bonds : angle 4.83411 ( 3285) covalent geometry : bond 0.00577 (25075) covalent geometry : angle 0.74232 (33930) *********************** 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 632 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 631 time to evaluate : 2.673 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: A 131 CYS cc_start: 0.8337 (m) cc_final: 0.7999 (m) REVERT: A 134 GLU cc_start: 0.8621 (mp0) cc_final: 0.8371 (mp0) REVERT: A 174 LYS cc_start: 0.8957 (tttt) cc_final: 0.8695 (tttt) REVERT: A 370 LEU cc_start: 0.8966 (pp) cc_final: 0.8764 (pp) REVERT: A 578 MET cc_start: 0.8345 (tmm) cc_final: 0.7890 (tmm) REVERT: B 120 LYS cc_start: 0.8500 (pttm) cc_final: 0.7995 (mtpt) REVERT: B 134 GLU cc_start: 0.8445 (mp0) cc_final: 0.8201 (mp0) REVERT: B 174 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7495 (ttpt) REVERT: B 308 GLU cc_start: 0.8208 (tp30) cc_final: 0.7933 (tp30) REVERT: B 351 MET cc_start: 0.7745 (ttm) cc_final: 0.7407 (ttm) REVERT: B 559 TRP cc_start: 0.7208 (m-90) cc_final: 0.6982 (m-90) REVERT: B 695 GLN cc_start: 0.8169 (mt0) cc_final: 0.7967 (tt0) REVERT: B 732 LEU cc_start: 0.9330 (tt) cc_final: 0.9072 (tt) REVERT: B 742 TRP cc_start: 0.6781 (m-90) cc_final: 0.5675 (m-10) REVERT: C 172 LEU cc_start: 0.8680 (mp) cc_final: 0.8422 (mp) REVERT: C 174 LYS cc_start: 0.8820 (tttt) cc_final: 0.8074 (tttt) REVERT: C 224 GLU cc_start: 0.7379 (tp30) cc_final: 0.6162 (tp30) REVERT: C 244 HIS cc_start: 0.8432 (m-70) cc_final: 0.8165 (m-70) REVERT: C 264 THR cc_start: 0.9122 (p) cc_final: 0.8850 (p) REVERT: C 489 PHE cc_start: 0.7302 (t80) cc_final: 0.6742 (t80) REVERT: C 574 MET cc_start: 0.7574 (ppp) cc_final: 0.7136 (ppp) REVERT: C 578 MET cc_start: 0.8414 (tmm) cc_final: 0.7792 (tmm) REVERT: C 579 ILE cc_start: 0.6347 (mt) cc_final: 0.5750 (mt) REVERT: C 732 LEU cc_start: 0.9382 (tt) cc_final: 0.9111 (tt) REVERT: C 743 LYS cc_start: 0.9240 (ptpt) cc_final: 0.8536 (mmtt) REVERT: D 120 LYS cc_start: 0.8412 (pttm) cc_final: 0.7870 (ptmt) REVERT: D 224 GLU cc_start: 0.7269 (tp30) cc_final: 0.5892 (tp30) REVERT: D 308 GLU cc_start: 0.8121 (tp30) cc_final: 0.7770 (tp30) REVERT: D 309 ASP cc_start: 0.8017 (p0) cc_final: 0.7500 (p0) REVERT: D 351 MET cc_start: 0.7865 (ttm) cc_final: 0.7421 (ttm) REVERT: D 578 MET cc_start: 0.8387 (tmm) cc_final: 0.7981 (tmm) REVERT: D 732 LEU cc_start: 0.9325 (tt) cc_final: 0.9009 (tt) REVERT: D 743 LYS cc_start: 0.9328 (ptpt) cc_final: 0.8781 (mmmt) REVERT: E 120 LYS cc_start: 0.8473 (pttm) cc_final: 0.7892 (ptmt) REVERT: E 131 CYS cc_start: 0.8351 (m) cc_final: 0.8080 (m) REVERT: E 134 GLU cc_start: 0.8571 (mp0) cc_final: 0.8279 (mp0) REVERT: E 174 LYS cc_start: 0.8816 (tttt) cc_final: 0.8397 (tttt) REVERT: E 527 PHE cc_start: 0.8199 (t80) cc_final: 0.7965 (t80) REVERT: E 559 TRP cc_start: 0.7587 (m-90) cc_final: 0.7351 (m-90) REVERT: E 578 MET cc_start: 0.8133 (tmm) cc_final: 0.7680 (tmm) REVERT: E 579 ILE cc_start: 0.6141 (mt) cc_final: 0.5751 (mt) outliers start: 1 outliers final: 0 residues processed: 632 average time/residue: 0.3400 time to fit residues: 341.2413 Evaluate side-chains 495 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 298 optimal weight: 0.0670 chunk 212 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 254 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 234 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- 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 452 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.180366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.143979 restraints weight = 48004.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.148888 restraints weight = 29195.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152287 restraints weight = 20585.005| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25075 Z= 0.127 Angle : 0.613 8.479 33930 Z= 0.316 Chirality : 0.040 0.194 3880 Planarity : 0.004 0.045 4225 Dihedral : 4.136 16.397 3270 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.61 % Favored : 91.36 % Rotamer: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2985 helix: 0.50 (0.12), residues: 1720 sheet: -0.93 (0.66), residues: 80 loop : -2.66 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E 493 HIS 0.005 0.001 HIS B 301 PHE 0.041 0.001 PHE C 524 TYR 0.018 0.002 TYR E 260 ARG 0.006 0.000 ARG A 729 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 1100) hydrogen bonds : angle 4.42170 ( 3285) covalent geometry : bond 0.00274 (25075) covalent geometry : angle 0.61328 (33930) *********************** 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 633 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 632 time to evaluate : 2.696 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: A 131 CYS cc_start: 0.8284 (m) cc_final: 0.7977 (m) REVERT: A 134 GLU cc_start: 0.8675 (mp0) cc_final: 0.8464 (mp0) REVERT: A 174 LYS cc_start: 0.8833 (tttt) cc_final: 0.8188 (tttt) REVERT: A 260 TYR cc_start: 0.5595 (p90) cc_final: 0.4644 (p90) REVERT: A 523 HIS cc_start: 0.7114 (m170) cc_final: 0.6733 (m170) REVERT: A 578 MET cc_start: 0.7886 (tmm) cc_final: 0.7636 (tmm) REVERT: B 120 LYS cc_start: 0.8473 (pttm) cc_final: 0.7849 (ptmt) REVERT: B 131 CYS cc_start: 0.8628 (m) cc_final: 0.8281 (m) REVERT: B 134 GLU cc_start: 0.8473 (mp0) cc_final: 0.8155 (mp0) REVERT: B 174 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7365 (ttpt) REVERT: B 260 TYR cc_start: 0.6413 (p90) cc_final: 0.5468 (p90) REVERT: B 440 MET cc_start: 0.7006 (mmm) cc_final: 0.6569 (mmm) REVERT: B 523 HIS cc_start: 0.7117 (m170) cc_final: 0.6716 (m170) REVERT: B 594 TYR cc_start: 0.7659 (t80) cc_final: 0.7345 (t80) REVERT: B 731 CYS cc_start: 0.7871 (m) cc_final: 0.7362 (m) REVERT: B 732 LEU cc_start: 0.9296 (tt) cc_final: 0.8998 (tt) REVERT: C 174 LYS cc_start: 0.8607 (tttt) cc_final: 0.7850 (tttt) REVERT: C 224 GLU cc_start: 0.7037 (tp30) cc_final: 0.5652 (tp30) REVERT: C 244 HIS cc_start: 0.8320 (m-70) cc_final: 0.8075 (m-70) REVERT: C 264 THR cc_start: 0.8946 (p) cc_final: 0.8703 (p) REVERT: C 489 PHE cc_start: 0.7247 (t80) cc_final: 0.6621 (t80) REVERT: C 523 HIS cc_start: 0.7376 (m170) cc_final: 0.7020 (m170) REVERT: C 717 MET cc_start: 0.5409 (ptp) cc_final: 0.5122 (ptm) REVERT: C 732 LEU cc_start: 0.9301 (tt) cc_final: 0.9051 (tt) REVERT: C 743 LYS cc_start: 0.9202 (ptpt) cc_final: 0.8494 (mmmt) REVERT: D 120 LYS cc_start: 0.8405 (pttm) cc_final: 0.7848 (ptmt) REVERT: D 174 LYS cc_start: 0.8585 (tttt) cc_final: 0.8254 (tttt) REVERT: D 224 GLU cc_start: 0.6856 (tp30) cc_final: 0.5303 (tp30) REVERT: D 376 LYS cc_start: 0.5180 (tttt) cc_final: 0.4396 (tttt) REVERT: D 523 HIS cc_start: 0.7384 (m170) cc_final: 0.7042 (m170) REVERT: D 732 LEU cc_start: 0.9272 (tt) cc_final: 0.8979 (tt) REVERT: D 743 LYS cc_start: 0.9298 (ptpt) cc_final: 0.8722 (mmmt) REVERT: E 120 LYS cc_start: 0.8406 (pttm) cc_final: 0.7800 (ptmt) REVERT: E 131 CYS cc_start: 0.8285 (m) cc_final: 0.8020 (m) REVERT: E 134 GLU cc_start: 0.8552 (mp0) cc_final: 0.8311 (mp0) REVERT: E 174 LYS cc_start: 0.8629 (tttt) cc_final: 0.8198 (tttt) REVERT: E 578 MET cc_start: 0.7950 (tmm) cc_final: 0.7596 (tmm) REVERT: E 579 ILE cc_start: 0.5858 (mt) cc_final: 0.5505 (mt) outliers start: 1 outliers final: 0 residues processed: 633 average time/residue: 0.3483 time to fit residues: 352.2900 Evaluate side-chains 498 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 9 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 276 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS C 585 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS E 643 ASN E 671 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.143859 restraints weight = 48813.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.148638 restraints weight = 30135.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.151982 restraints weight = 21555.119| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25075 Z= 0.136 Angle : 0.614 8.864 33930 Z= 0.318 Chirality : 0.039 0.133 3880 Planarity : 0.004 0.045 4225 Dihedral : 4.084 16.428 3270 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.58 % Favored : 90.39 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2985 helix: 0.53 (0.12), residues: 1720 sheet: -1.02 (0.66), residues: 80 loop : -2.68 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 380 HIS 0.004 0.001 HIS C 301 PHE 0.037 0.002 PHE A 524 TYR 0.016 0.001 TYR C 260 ARG 0.002 0.000 ARG A 690 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 1100) hydrogen bonds : angle 4.43207 ( 3285) covalent geometry : bond 0.00300 (25075) covalent geometry : angle 0.61388 (33930) *********************** 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 628 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 628 time to evaluate : 2.931 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: A 129 GLU cc_start: 0.7525 (mp0) cc_final: 0.7160 (mp0) REVERT: A 131 CYS cc_start: 0.8325 (m) cc_final: 0.7921 (m) REVERT: A 134 GLU cc_start: 0.8691 (mp0) cc_final: 0.8478 (mp0) REVERT: A 174 LYS cc_start: 0.8776 (tttt) cc_final: 0.8207 (tttt) REVERT: A 260 TYR cc_start: 0.5940 (p90) cc_final: 0.4839 (p90) REVERT: A 323 MET cc_start: 0.8496 (ttt) cc_final: 0.8172 (ttm) REVERT: A 370 LEU cc_start: 0.8940 (pp) cc_final: 0.8739 (pp) REVERT: A 523 HIS cc_start: 0.7206 (m170) cc_final: 0.6742 (m170) REVERT: A 578 MET cc_start: 0.8007 (tmm) cc_final: 0.7666 (tmm) REVERT: B 120 LYS cc_start: 0.8473 (pttm) cc_final: 0.7937 (ptmt) REVERT: B 131 CYS cc_start: 0.8661 (m) cc_final: 0.8327 (m) REVERT: B 134 GLU cc_start: 0.8478 (mp0) cc_final: 0.8177 (mp0) REVERT: B 174 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7458 (tttt) REVERT: B 260 TYR cc_start: 0.6410 (p90) cc_final: 0.5486 (p90) REVERT: B 440 MET cc_start: 0.7028 (mmm) cc_final: 0.6606 (mmm) REVERT: B 523 HIS cc_start: 0.7130 (m170) cc_final: 0.6722 (m170) REVERT: B 594 TYR cc_start: 0.7622 (t80) cc_final: 0.7317 (t80) REVERT: B 732 LEU cc_start: 0.9299 (tt) cc_final: 0.9053 (tt) REVERT: C 174 LYS cc_start: 0.8620 (tttt) cc_final: 0.7871 (tttt) REVERT: C 224 GLU cc_start: 0.7087 (tp30) cc_final: 0.5702 (tp30) REVERT: C 244 HIS cc_start: 0.8298 (m-70) cc_final: 0.8048 (m-70) REVERT: C 264 THR cc_start: 0.8961 (p) cc_final: 0.8725 (p) REVERT: C 489 PHE cc_start: 0.7490 (t80) cc_final: 0.6804 (t80) REVERT: C 523 HIS cc_start: 0.7312 (m170) cc_final: 0.6921 (m170) REVERT: C 579 ILE cc_start: 0.5735 (mt) cc_final: 0.5430 (mt) REVERT: C 732 LEU cc_start: 0.9322 (tt) cc_final: 0.9068 (tt) REVERT: C 743 LYS cc_start: 0.9213 (ptpt) cc_final: 0.8502 (mmtt) REVERT: D 120 LYS cc_start: 0.8416 (pttm) cc_final: 0.7867 (ptmt) REVERT: D 174 LYS cc_start: 0.8587 (tttt) cc_final: 0.8184 (tttt) REVERT: D 224 GLU cc_start: 0.6942 (tp30) cc_final: 0.5356 (tp30) REVERT: D 351 MET cc_start: 0.7930 (ttm) cc_final: 0.7595 (ttm) REVERT: D 376 LYS cc_start: 0.5522 (tttt) cc_final: 0.4580 (tttt) REVERT: D 732 LEU cc_start: 0.9298 (tt) cc_final: 0.9014 (tt) REVERT: D 743 LYS cc_start: 0.9296 (ptpt) cc_final: 0.8741 (mmmt) REVERT: E 120 LYS cc_start: 0.8451 (pttm) cc_final: 0.7850 (ptmt) REVERT: E 131 CYS cc_start: 0.8259 (m) cc_final: 0.7947 (m) REVERT: E 134 GLU cc_start: 0.8592 (mp0) cc_final: 0.8348 (mp0) REVERT: E 174 LYS cc_start: 0.8613 (tttt) cc_final: 0.8154 (tttt) REVERT: E 309 ASP cc_start: 0.7660 (p0) cc_final: 0.7337 (p0) REVERT: E 578 MET cc_start: 0.7950 (tmm) cc_final: 0.7548 (tmm) REVERT: E 579 ILE cc_start: 0.5952 (mt) cc_final: 0.5579 (mt) outliers start: 0 outliers final: 0 residues processed: 628 average time/residue: 0.3522 time to fit residues: 352.2216 Evaluate side-chains 506 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 294 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS C 417 HIS C 585 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS D 643 ASN E 150 HIS E 671 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.180359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143399 restraints weight = 47976.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.148178 restraints weight = 29714.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151453 restraints weight = 21208.453| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25075 Z= 0.135 Angle : 0.618 7.864 33930 Z= 0.320 Chirality : 0.039 0.133 3880 Planarity : 0.004 0.045 4225 Dihedral : 4.083 16.885 3270 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.28 % Favored : 90.62 % Rotamer: Outliers : 0.04 % Allowed : 0.94 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.16), residues: 2985 helix: 0.55 (0.12), residues: 1720 sheet: -1.00 (0.66), residues: 80 loop : -2.68 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 380 HIS 0.004 0.001 HIS C 301 PHE 0.041 0.002 PHE C 524 TYR 0.017 0.002 TYR A 564 ARG 0.003 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 1100) hydrogen bonds : angle 4.40256 ( 3285) covalent geometry : bond 0.00297 (25075) covalent geometry : angle 0.61792 (33930) *********************** 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 626 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 625 time to evaluate : 3.232 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: A 131 CYS cc_start: 0.8564 (m) cc_final: 0.8201 (m) REVERT: A 134 GLU cc_start: 0.8687 (mp0) cc_final: 0.8479 (mp0) REVERT: A 174 LYS cc_start: 0.8790 (tttt) cc_final: 0.8198 (tttt) REVERT: A 323 MET cc_start: 0.8394 (ttt) cc_final: 0.8056 (ttm) REVERT: A 523 HIS cc_start: 0.7122 (m170) cc_final: 0.6659 (m170) REVERT: A 574 MET cc_start: 0.7319 (ppp) cc_final: 0.7076 (ppp) REVERT: A 578 MET cc_start: 0.8069 (tmm) cc_final: 0.7707 (tmm) REVERT: A 732 LEU cc_start: 0.9286 (tt) cc_final: 0.9073 (tt) REVERT: B 120 LYS cc_start: 0.8485 (pttm) cc_final: 0.7880 (ptmt) REVERT: B 131 CYS cc_start: 0.8703 (m) cc_final: 0.8357 (m) REVERT: B 134 GLU cc_start: 0.8449 (mp0) cc_final: 0.8158 (mp0) REVERT: B 174 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7443 (tttt) REVERT: B 440 MET cc_start: 0.7028 (mmm) cc_final: 0.6675 (mmm) REVERT: B 523 HIS cc_start: 0.7113 (m170) cc_final: 0.6730 (m170) REVERT: B 578 MET cc_start: 0.7829 (ppp) cc_final: 0.7613 (tmm) REVERT: B 732 LEU cc_start: 0.9336 (tt) cc_final: 0.9079 (tt) REVERT: B 743 LYS cc_start: 0.9232 (ptmt) cc_final: 0.8700 (mmmt) REVERT: C 174 LYS cc_start: 0.8630 (tttt) cc_final: 0.7829 (tttt) REVERT: C 224 GLU cc_start: 0.7030 (tp30) cc_final: 0.5632 (tp30) REVERT: C 244 HIS cc_start: 0.8295 (m-70) cc_final: 0.8026 (m-70) REVERT: C 264 THR cc_start: 0.8994 (p) cc_final: 0.8747 (p) REVERT: C 308 GLU cc_start: 0.7876 (tp30) cc_final: 0.7635 (tp30) REVERT: C 578 MET cc_start: 0.7850 (tmm) cc_final: 0.7621 (tmm) REVERT: C 717 MET cc_start: 0.5378 (ptp) cc_final: 0.5148 (ptm) REVERT: C 732 LEU cc_start: 0.9356 (tt) cc_final: 0.9083 (tt) REVERT: C 743 LYS cc_start: 0.9217 (ptpt) cc_final: 0.8505 (mmtt) REVERT: D 120 LYS cc_start: 0.8436 (pttm) cc_final: 0.7878 (ptmt) REVERT: D 174 LYS cc_start: 0.8625 (tttt) cc_final: 0.8144 (tttt) REVERT: D 224 GLU cc_start: 0.6898 (tp30) cc_final: 0.5297 (tp30) REVERT: D 282 MET cc_start: 0.8231 (mmt) cc_final: 0.7913 (mmm) REVERT: D 323 MET cc_start: 0.8555 (ttt) cc_final: 0.8324 (ttp) REVERT: D 369 ARG cc_start: 0.8594 (tmt170) cc_final: 0.8250 (tmm-80) REVERT: D 370 LEU cc_start: 0.8863 (pp) cc_final: 0.8661 (pp) REVERT: D 732 LEU cc_start: 0.9285 (tt) cc_final: 0.8929 (tt) REVERT: D 743 LYS cc_start: 0.9294 (ptpt) cc_final: 0.8741 (mmmt) REVERT: E 120 LYS cc_start: 0.8445 (pttm) cc_final: 0.7839 (ptmt) REVERT: E 131 CYS cc_start: 0.8284 (m) cc_final: 0.7817 (m) REVERT: E 134 GLU cc_start: 0.8583 (mp0) cc_final: 0.8336 (mp0) REVERT: E 174 LYS cc_start: 0.8633 (tttt) cc_final: 0.8097 (tttt) REVERT: E 557 LEU cc_start: 0.8616 (tp) cc_final: 0.8267 (tp) REVERT: E 578 MET cc_start: 0.7908 (tmm) cc_final: 0.7578 (tmm) REVERT: E 579 ILE cc_start: 0.6093 (mt) cc_final: 0.5637 (mt) REVERT: E 732 LEU cc_start: 0.9392 (tt) cc_final: 0.9162 (tt) outliers start: 1 outliers final: 0 residues processed: 626 average time/residue: 0.3526 time to fit residues: 353.4735 Evaluate side-chains 504 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 224 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 231 optimal weight: 0.8980 chunk 237 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 149 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS C 585 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.182348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145581 restraints weight = 48561.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.150360 restraints weight = 29818.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153785 restraints weight = 21232.826| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25075 Z= 0.127 Angle : 0.613 9.413 33930 Z= 0.316 Chirality : 0.039 0.134 3880 Planarity : 0.003 0.045 4225 Dihedral : 4.060 19.583 3270 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.11 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 2985 helix: 0.56 (0.12), residues: 1720 sheet: -0.97 (0.67), residues: 80 loop : -2.68 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 380 HIS 0.004 0.001 HIS C 301 PHE 0.037 0.001 PHE A 524 TYR 0.016 0.001 TYR E 565 ARG 0.003 0.000 ARG E 714 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 1100) hydrogen bonds : angle 4.38049 ( 3285) covalent geometry : bond 0.00280 (25075) covalent geometry : angle 0.61330 (33930) ********************** 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 626 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 3.916 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: A 131 CYS cc_start: 0.8551 (m) cc_final: 0.8223 (m) REVERT: A 134 GLU cc_start: 0.8659 (mp0) cc_final: 0.8458 (mp0) REVERT: A 174 LYS cc_start: 0.8759 (tttt) cc_final: 0.8188 (tttt) REVERT: A 323 MET cc_start: 0.8355 (ttt) cc_final: 0.8016 (ttm) REVERT: A 523 HIS cc_start: 0.7202 (m170) cc_final: 0.6689 (m170) REVERT: A 578 MET cc_start: 0.8018 (tmm) cc_final: 0.7654 (tmm) REVERT: A 732 LEU cc_start: 0.9272 (tt) cc_final: 0.9034 (tt) REVERT: B 120 LYS cc_start: 0.8495 (pttm) cc_final: 0.8000 (mtpt) REVERT: B 131 CYS cc_start: 0.8727 (m) cc_final: 0.8359 (m) REVERT: B 134 GLU cc_start: 0.8455 (mp0) cc_final: 0.8175 (mp0) REVERT: B 174 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7472 (tttt) REVERT: B 440 MET cc_start: 0.7095 (mmm) cc_final: 0.6668 (mmm) REVERT: B 523 HIS cc_start: 0.7056 (m170) cc_final: 0.6678 (m170) REVERT: B 557 LEU cc_start: 0.8287 (tp) cc_final: 0.8027 (tp) REVERT: B 732 LEU cc_start: 0.9322 (tt) cc_final: 0.9074 (tt) REVERT: B 743 LYS cc_start: 0.9221 (ptmt) cc_final: 0.8692 (mmmt) REVERT: C 224 GLU cc_start: 0.6820 (tp30) cc_final: 0.5326 (tp30) REVERT: C 244 HIS cc_start: 0.8299 (m-70) cc_final: 0.8045 (m-70) REVERT: C 264 THR cc_start: 0.8972 (p) cc_final: 0.8741 (p) REVERT: C 308 GLU cc_start: 0.7853 (tp30) cc_final: 0.7566 (tp30) REVERT: C 557 LEU cc_start: 0.8843 (tp) cc_final: 0.8601 (tp) REVERT: C 578 MET cc_start: 0.7803 (tmm) cc_final: 0.7566 (tmm) REVERT: C 717 MET cc_start: 0.5408 (ptp) cc_final: 0.5153 (ptm) REVERT: C 732 LEU cc_start: 0.9339 (tt) cc_final: 0.9088 (tt) REVERT: C 743 LYS cc_start: 0.9204 (ptpt) cc_final: 0.8489 (mmmt) REVERT: D 120 LYS cc_start: 0.8380 (pttm) cc_final: 0.7827 (ptmt) REVERT: D 174 LYS cc_start: 0.8588 (tttt) cc_final: 0.7971 (tttt) REVERT: D 224 GLU cc_start: 0.6840 (tp30) cc_final: 0.5209 (tp30) REVERT: D 323 MET cc_start: 0.8535 (ttt) cc_final: 0.8330 (ttp) REVERT: D 369 ARG cc_start: 0.8603 (tmt170) cc_final: 0.8264 (tmm-80) REVERT: D 370 LEU cc_start: 0.8815 (pp) cc_final: 0.8609 (pp) REVERT: D 732 LEU cc_start: 0.9276 (tt) cc_final: 0.8931 (tt) REVERT: D 742 TRP cc_start: 0.6617 (m-90) cc_final: 0.6261 (m-90) REVERT: D 743 LYS cc_start: 0.9298 (ptpt) cc_final: 0.8657 (mmmt) REVERT: E 120 LYS cc_start: 0.8470 (pttm) cc_final: 0.7898 (ptmt) REVERT: E 131 CYS cc_start: 0.8300 (m) cc_final: 0.7771 (m) REVERT: E 134 GLU cc_start: 0.8605 (mp0) cc_final: 0.8359 (mp0) REVERT: E 174 LYS cc_start: 0.8610 (tttt) cc_final: 0.8074 (tttt) REVERT: E 557 LEU cc_start: 0.8608 (tp) cc_final: 0.8262 (tp) REVERT: E 578 MET cc_start: 0.7898 (tmm) cc_final: 0.7572 (tmm) REVERT: E 579 ILE cc_start: 0.6136 (mt) cc_final: 0.5651 (mt) REVERT: E 732 LEU cc_start: 0.9362 (tt) cc_final: 0.9111 (tt) outliers start: 0 outliers final: 0 residues processed: 626 average time/residue: 0.3575 time to fit residues: 356.9216 Evaluate side-chains 510 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 212 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 177 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS C 585 HIS C 643 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.179965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142685 restraints weight = 48665.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.147489 restraints weight = 30070.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.150805 restraints weight = 21501.729| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25075 Z= 0.142 Angle : 0.628 8.517 33930 Z= 0.325 Chirality : 0.040 0.146 3880 Planarity : 0.004 0.045 4225 Dihedral : 4.121 17.200 3270 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.35 % Favored : 90.49 % Rotamer: Outliers : 0.04 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2985 helix: 0.55 (0.12), residues: 1720 sheet: -1.02 (0.67), residues: 80 loop : -2.72 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 380 HIS 0.004 0.001 HIS C 417 PHE 0.029 0.001 PHE E 524 TYR 0.016 0.002 TYR A 564 ARG 0.002 0.000 ARG C 690 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 1100) hydrogen bonds : angle 4.42557 ( 3285) covalent geometry : bond 0.00317 (25075) covalent geometry : angle 0.62783 (33930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9602.26 seconds wall clock time: 170 minutes 30.82 seconds (10230.82 seconds total)