Starting phenix.real_space_refine on Thu Feb 5 22:28:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pvl_20492/02_2026/6pvl_20492.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvl_20492/02_2026/6pvl_20492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pvl_20492/02_2026/6pvl_20492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvl_20492/02_2026/6pvl_20492.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pvl_20492/02_2026/6pvl_20492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvl_20492/02_2026/6pvl_20492.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 124 5.16 5 Na 2 4.78 5 C 13648 2.51 5 N 3480 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21006 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "B" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "C" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "D" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.73, per 1000 atoms: 0.23 Number of scatterers: 21006 At special positions: 0 Unit cell: (136.74, 136.74, 128.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 Na 2 11.00 O 3752 8.00 N 3480 7.00 C 13648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 989.6 milliseconds 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4936 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 62.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.563A pdb=" N LYS A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 147 removed outlier: 3.598A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 162 removed outlier: 4.037A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.866A pdb=" N LYS A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.548A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.523A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 removed outlier: 4.090A pdb=" N GLU A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.672A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.765A pdb=" N PHE A 250 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.725A pdb=" N GLU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.714A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.574A pdb=" N ASP A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.557A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 422 through 436 removed outlier: 5.062A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.504A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 455 " --> pdb=" O TYR A 451 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 508 removed outlier: 3.514A pdb=" N ARG A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.595A pdb=" N GLN A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 4.074A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 569 through 586 removed outlier: 3.762A pdb=" N MET A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 611 removed outlier: 3.582A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 651 through 677 removed outlier: 3.680A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 705 removed outlier: 4.307A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.561A pdb=" N LYS B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 147 removed outlier: 3.598A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 162 removed outlier: 4.037A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.866A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.547A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.523A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 214 removed outlier: 4.089A pdb=" N GLU B 214 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.673A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.765A pdb=" N PHE B 250 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.725A pdb=" N GLU B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.715A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 326 removed outlier: 3.575A pdb=" N ASP B 322 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.556A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 422 through 436 removed outlier: 5.062A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.503A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 443 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 455 " --> pdb=" O TYR B 451 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 508 removed outlier: 3.515A pdb=" N ARG B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 541 removed outlier: 3.595A pdb=" N GLN B 529 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 4.075A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 569 through 586 removed outlier: 3.762A pdb=" N MET B 574 " --> pdb=" O GLN B 570 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 611 removed outlier: 3.582A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 651 through 677 removed outlier: 3.680A pdb=" N LEU B 655 " --> pdb=" O PRO B 651 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 705 removed outlier: 4.306A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.562A pdb=" N LYS C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.597A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 162 removed outlier: 4.038A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.867A pdb=" N LYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.546A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.522A pdb=" N ASN C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 removed outlier: 4.090A pdb=" N GLU C 214 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.672A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.764A pdb=" N PHE C 250 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.724A pdb=" N GLU C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.714A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 326 removed outlier: 3.575A pdb=" N ASP C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 354 through 363 removed outlier: 3.556A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 422 through 436 removed outlier: 5.061A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.503A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 443 " --> pdb=" O TYR C 439 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 455 " --> pdb=" O TYR C 451 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 508 removed outlier: 3.515A pdb=" N ARG C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 498 " --> pdb=" O ALA C 494 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 541 removed outlier: 3.595A pdb=" N GLN C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 4.074A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 551 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 566 Processing helix chain 'C' and resid 569 through 586 removed outlier: 3.762A pdb=" N MET C 574 " --> pdb=" O GLN C 570 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 583 " --> pdb=" O ILE C 579 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 611 removed outlier: 3.582A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 634 Processing helix chain 'C' and resid 635 through 637 No H-bonds generated for 'chain 'C' and resid 635 through 637' Processing helix chain 'C' and resid 651 through 677 removed outlier: 3.680A pdb=" N LEU C 655 " --> pdb=" O PRO C 651 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 660 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 664 " --> pdb=" O THR C 660 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 705 removed outlier: 4.307A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 130 removed outlier: 3.562A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 147 removed outlier: 3.597A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 162 removed outlier: 4.038A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 161 " --> pdb=" O PHE D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.866A pdb=" N LYS D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 removed outlier: 3.546A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.523A pdb=" N ASN D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 removed outlier: 4.089A pdb=" N GLU D 214 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.673A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 removed outlier: 3.764A pdb=" N PHE D 250 " --> pdb=" O GLY D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.725A pdb=" N GLU D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN D 284 " --> pdb=" O LEU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 303 removed outlier: 3.714A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 326 removed outlier: 3.574A pdb=" N ASP D 322 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 354 through 363 removed outlier: 3.556A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 5.062A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.503A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU D 443 " --> pdb=" O TYR D 439 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 455 " --> pdb=" O TYR D 451 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR D 456 " --> pdb=" O ASN D 452 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 508 removed outlier: 3.514A pdb=" N ARG D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 541 removed outlier: 3.595A pdb=" N GLN D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 4.074A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 551 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 569 through 586 removed outlier: 3.763A pdb=" N MET D 574 " --> pdb=" O GLN D 570 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 611 removed outlier: 3.581A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 611 " --> pdb=" O SER D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 634 Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 651 through 677 removed outlier: 3.680A pdb=" N LEU D 655 " --> pdb=" O PRO D 651 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR D 660 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 664 " --> pdb=" O THR D 660 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 705 removed outlier: 4.307A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 378 removed outlier: 3.746A pdb=" N SER A 386 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 378 removed outlier: 3.745A pdb=" N SER B 386 " --> pdb=" O VAL B 737 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 378 removed outlier: 3.746A pdb=" N SER C 386 " --> pdb=" O VAL C 737 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 378 removed outlier: 3.747A pdb=" N SER D 386 " --> pdb=" O VAL D 737 " (cutoff:3.500A) 888 hydrogen bonds defined for protein. 2580 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.22 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6536 1.34 - 1.46: 4668 1.46 - 1.58: 10048 1.58 - 1.70: 4 1.70 - 1.82: 204 Bond restraints: 21460 Sorted by residual: bond pdb=" C VAL A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.76e+00 bond pdb=" CB TRP B 380 " pdb=" CG TRP B 380 " ideal model delta sigma weight residual 1.498 1.430 0.068 3.10e-02 1.04e+03 4.74e+00 bond pdb=" C VAL D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.71e+00 bond pdb=" CB TRP C 380 " pdb=" CG TRP C 380 " ideal model delta sigma weight residual 1.498 1.431 0.067 3.10e-02 1.04e+03 4.64e+00 bond pdb=" C VAL B 154 " pdb=" N PRO B 155 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.63e+00 ... (remaining 21455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 27547 2.25 - 4.50: 1180 4.50 - 6.75: 217 6.75 - 9.00: 72 9.00 - 11.25: 16 Bond angle restraints: 29032 Sorted by residual: angle pdb=" C THR C 740 " pdb=" N GLU C 741 " pdb=" CA GLU C 741 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C THR B 740 " pdb=" N GLU B 741 " pdb=" CA GLU B 741 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" C THR A 740 " pdb=" N GLU A 741 " pdb=" CA GLU A 741 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" C THR D 740 " pdb=" N GLU D 741 " pdb=" CA GLU D 741 " ideal model delta sigma weight residual 121.54 132.71 -11.17 1.91e+00 2.74e-01 3.42e+01 angle pdb=" C GLN A 313 " pdb=" N ASN A 314 " pdb=" CA ASN A 314 " ideal model delta sigma weight residual 121.54 130.72 -9.18 1.91e+00 2.74e-01 2.31e+01 ... (remaining 29027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.76: 11509 13.76 - 27.52: 979 27.52 - 41.27: 324 41.27 - 55.03: 32 55.03 - 68.79: 12 Dihedral angle restraints: 12856 sinusoidal: 5252 harmonic: 7604 Sorted by residual: dihedral pdb=" CA SER A 613 " pdb=" C SER A 613 " pdb=" N LYS A 614 " pdb=" CA LYS A 614 " ideal model delta harmonic sigma weight residual 180.00 -142.00 -38.00 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA SER C 613 " pdb=" C SER C 613 " pdb=" N LYS C 614 " pdb=" CA LYS C 614 " ideal model delta harmonic sigma weight residual -180.00 -142.00 -38.00 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA SER B 613 " pdb=" C SER B 613 " pdb=" N LYS B 614 " pdb=" CA LYS B 614 " ideal model delta harmonic sigma weight residual 180.00 -142.00 -38.00 0 5.00e+00 4.00e-02 5.77e+01 ... (remaining 12853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2012 0.048 - 0.096: 965 0.096 - 0.144: 246 0.144 - 0.192: 66 0.192 - 0.239: 19 Chirality restraints: 3308 Sorted by residual: chirality pdb=" CA ASN D 314 " pdb=" N ASN D 314 " pdb=" C ASN D 314 " pdb=" CB ASN D 314 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ASN B 314 " pdb=" N ASN B 314 " pdb=" C ASN B 314 " pdb=" CB ASN B 314 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ASN C 314 " pdb=" N ASN C 314 " pdb=" C ASN C 314 " pdb=" CB ASN C 314 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 3305 not shown) Planarity restraints: 3624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 248 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C VAL B 248 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL B 248 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE B 249 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 248 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C VAL A 248 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL A 248 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE A 249 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 248 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C VAL D 248 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL D 248 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE D 249 " 0.015 2.00e-02 2.50e+03 ... (remaining 3621 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2354 2.74 - 3.28: 21239 3.28 - 3.82: 33328 3.82 - 4.36: 38443 4.36 - 4.90: 62494 Nonbonded interactions: 157858 Sorted by model distance: nonbonded pdb=" OH TYR C 260 " pdb=" OD1 ASN C 297 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR B 260 " pdb=" OD1 ASN B 297 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR D 260 " pdb=" OD1 ASN D 297 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 260 " pdb=" OD1 ASN A 297 " model vdw 2.202 3.040 nonbonded pdb=" OG SER A 620 " pdb=" O GLY A 623 " model vdw 2.242 3.040 ... (remaining 157853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 115 through 758) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.020 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.008 0.068 21460 Z= 0.352 Angle : 1.131 11.246 29032 Z= 0.592 Chirality : 0.060 0.239 3308 Planarity : 0.006 0.054 3624 Dihedral : 11.673 68.789 7920 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.47 % Allowed : 15.38 % Favored : 84.15 % Rotamer: Outliers : 1.39 % Allowed : 7.65 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.53 (0.12), residues: 2568 helix: -3.55 (0.08), residues: 1380 sheet: -2.82 (0.60), residues: 68 loop : -3.81 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 226 TYR 0.013 0.002 TYR D 382 PHE 0.018 0.002 PHE A 715 TRP 0.021 0.003 TRP A 380 HIS 0.005 0.002 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00757 (21460) covalent geometry : angle 1.13053 (29032) hydrogen bonds : bond 0.28589 ( 888) hydrogen bonds : angle 9.34867 ( 2580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 825 time to evaluate : 0.854 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 144 ASP cc_start: 0.9203 (t70) cc_final: 0.8725 (t0) REVERT: A 198 ASP cc_start: 0.7749 (m-30) cc_final: 0.7544 (t0) REVERT: A 248 VAL cc_start: 0.9188 (t) cc_final: 0.8981 (m) REVERT: A 282 MET cc_start: 0.8867 (tpp) cc_final: 0.8528 (tpp) REVERT: A 322 ASP cc_start: 0.8908 (t0) cc_final: 0.8588 (t0) REVERT: A 326 LEU cc_start: 0.9262 (mp) cc_final: 0.9020 (mp) REVERT: A 335 THR cc_start: 0.9298 (p) cc_final: 0.9047 (m) REVERT: A 351 MET cc_start: 0.8940 (mmt) cc_final: 0.8665 (mmm) REVERT: A 414 ASP cc_start: 0.7711 (m-30) cc_final: 0.6848 (t0) REVERT: A 506 PHE cc_start: 0.9026 (t80) cc_final: 0.8516 (m-80) REVERT: A 565 TYR cc_start: 0.9059 (m-80) cc_final: 0.8854 (m-80) REVERT: A 630 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8790 (tm) REVERT: A 634 LYS cc_start: 0.9074 (mttt) cc_final: 0.8814 (mmmt) REVERT: A 677 MET cc_start: 0.8461 (mmm) cc_final: 0.8034 (mmt) REVERT: A 704 GLU cc_start: 0.8643 (mm-30) cc_final: 0.7997 (tp30) REVERT: A 728 PHE cc_start: 0.7572 (m-80) cc_final: 0.7253 (m-80) REVERT: A 735 ASN cc_start: 0.8835 (m-40) cc_final: 0.8327 (m110) REVERT: B 144 ASP cc_start: 0.9212 (t70) cc_final: 0.8718 (t0) REVERT: B 198 ASP cc_start: 0.7797 (m-30) cc_final: 0.7586 (t0) REVERT: B 282 MET cc_start: 0.8880 (tpp) cc_final: 0.8518 (tpp) REVERT: B 322 ASP cc_start: 0.8901 (t0) cc_final: 0.8612 (t0) REVERT: B 326 LEU cc_start: 0.9288 (mp) cc_final: 0.9078 (mp) REVERT: B 351 MET cc_start: 0.8927 (mmt) cc_final: 0.8655 (mmm) REVERT: B 414 ASP cc_start: 0.7691 (m-30) cc_final: 0.6885 (t0) REVERT: B 506 PHE cc_start: 0.9032 (t80) cc_final: 0.8514 (m-80) REVERT: B 627 ASP cc_start: 0.9220 (t0) cc_final: 0.8987 (m-30) REVERT: B 677 MET cc_start: 0.8469 (mmm) cc_final: 0.8105 (mmt) REVERT: B 688 SER cc_start: 0.8727 (t) cc_final: 0.8521 (t) REVERT: B 704 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8007 (tp30) REVERT: B 728 PHE cc_start: 0.7566 (m-80) cc_final: 0.7242 (m-80) REVERT: B 735 ASN cc_start: 0.8837 (m-40) cc_final: 0.8329 (m110) REVERT: B 752 ASP cc_start: 0.7853 (m-30) cc_final: 0.7622 (m-30) REVERT: C 144 ASP cc_start: 0.9200 (t70) cc_final: 0.8726 (t0) REVERT: C 198 ASP cc_start: 0.7782 (m-30) cc_final: 0.7573 (t0) REVERT: C 256 HIS cc_start: 0.6785 (p90) cc_final: 0.6087 (p90) REVERT: C 282 MET cc_start: 0.8876 (tpp) cc_final: 0.8509 (tpp) REVERT: C 322 ASP cc_start: 0.8893 (t0) cc_final: 0.8598 (t0) REVERT: C 326 LEU cc_start: 0.9282 (mp) cc_final: 0.9074 (mp) REVERT: C 351 MET cc_start: 0.8906 (mmt) cc_final: 0.8632 (mmm) REVERT: C 414 ASP cc_start: 0.7638 (m-30) cc_final: 0.6837 (t0) REVERT: C 506 PHE cc_start: 0.9045 (t80) cc_final: 0.8516 (m-80) REVERT: C 627 ASP cc_start: 0.9215 (t0) cc_final: 0.8986 (m-30) REVERT: C 663 ILE cc_start: 0.9510 (mt) cc_final: 0.9274 (tp) REVERT: C 677 MET cc_start: 0.8493 (mmm) cc_final: 0.8082 (mmt) REVERT: C 704 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7962 (tp30) REVERT: C 728 PHE cc_start: 0.7581 (m-80) cc_final: 0.7239 (m-80) REVERT: C 735 ASN cc_start: 0.8840 (m-40) cc_final: 0.8354 (m110) REVERT: C 752 ASP cc_start: 0.7756 (m-30) cc_final: 0.7553 (m-30) REVERT: D 144 ASP cc_start: 0.9181 (t70) cc_final: 0.8713 (t0) REVERT: D 198 ASP cc_start: 0.7789 (m-30) cc_final: 0.7580 (t0) REVERT: D 256 HIS cc_start: 0.6755 (p90) cc_final: 0.6066 (p90) REVERT: D 282 MET cc_start: 0.8900 (tpp) cc_final: 0.8524 (tpp) REVERT: D 322 ASP cc_start: 0.8897 (t0) cc_final: 0.8554 (t0) REVERT: D 326 LEU cc_start: 0.9287 (mp) cc_final: 0.9079 (mp) REVERT: D 351 MET cc_start: 0.8921 (mmt) cc_final: 0.8644 (mmm) REVERT: D 414 ASP cc_start: 0.7621 (m-30) cc_final: 0.6811 (t0) REVERT: D 506 PHE cc_start: 0.9039 (t80) cc_final: 0.8541 (m-80) REVERT: D 565 TYR cc_start: 0.9022 (m-80) cc_final: 0.8803 (m-80) REVERT: D 627 ASP cc_start: 0.9236 (t0) cc_final: 0.8938 (m-30) REVERT: D 663 ILE cc_start: 0.9526 (mt) cc_final: 0.9296 (tp) REVERT: D 677 MET cc_start: 0.8475 (mmm) cc_final: 0.8085 (mmt) REVERT: D 704 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7937 (tp30) REVERT: D 728 PHE cc_start: 0.7580 (m-80) cc_final: 0.7248 (m-80) REVERT: D 735 ASN cc_start: 0.8838 (m-40) cc_final: 0.8388 (m110) REVERT: D 752 ASP cc_start: 0.7811 (m-30) cc_final: 0.7557 (m-30) outliers start: 32 outliers final: 12 residues processed: 841 average time/residue: 0.1523 time to fit residues: 198.4279 Evaluate side-chains 560 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 547 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 297 ASN A 417 HIS A 452 ASN A 585 HIS A 643 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 GLN B 256 HIS B 297 ASN B 452 ASN B 585 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 417 HIS C 452 ASN C 585 HIS C 695 GLN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 417 HIS D 452 ASN D 585 HIS ** D 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.079726 restraints weight = 59410.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.082224 restraints weight = 36102.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.084141 restraints weight = 24826.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085516 restraints weight = 18967.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.086454 restraints weight = 15145.965| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21460 Z= 0.153 Angle : 0.749 11.100 29032 Z= 0.379 Chirality : 0.043 0.183 3308 Planarity : 0.005 0.088 3624 Dihedral : 6.251 33.091 2808 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.25 % Favored : 88.59 % Rotamer: Outliers : 0.17 % Allowed : 5.00 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.14), residues: 2568 helix: -1.66 (0.11), residues: 1492 sheet: -3.38 (0.46), residues: 68 loop : -3.63 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 567 TYR 0.013 0.001 TYR A 622 PHE 0.044 0.002 PHE D 633 TRP 0.010 0.002 TRP D 742 HIS 0.003 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00327 (21460) covalent geometry : angle 0.74863 (29032) hydrogen bonds : bond 0.04210 ( 888) hydrogen bonds : angle 4.74807 ( 2580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 760 time to evaluate : 0.816 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: A 139 LEU cc_start: 0.9282 (mm) cc_final: 0.9020 (tp) REVERT: A 173 MET cc_start: 0.8358 (mmt) cc_final: 0.8114 (mmt) REVERT: A 185 GLU cc_start: 0.9014 (mp0) cc_final: 0.8361 (pm20) REVERT: A 220 ASN cc_start: 0.9132 (m-40) cc_final: 0.8741 (m-40) REVERT: A 282 MET cc_start: 0.8723 (tpp) cc_final: 0.8523 (tpp) REVERT: A 290 THR cc_start: 0.9378 (m) cc_final: 0.9127 (p) REVERT: A 322 ASP cc_start: 0.8811 (t0) cc_final: 0.8204 (t0) REVERT: A 323 MET cc_start: 0.8927 (ttm) cc_final: 0.8561 (tmm) REVERT: A 326 LEU cc_start: 0.9144 (mp) cc_final: 0.8940 (mp) REVERT: A 351 MET cc_start: 0.9063 (mmt) cc_final: 0.8815 (mmm) REVERT: A 414 ASP cc_start: 0.7716 (m-30) cc_final: 0.6918 (t0) REVERT: A 439 TYR cc_start: 0.8905 (m-80) cc_final: 0.8608 (m-10) REVERT: A 452 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8311 (t0) REVERT: A 461 TYR cc_start: 0.6988 (t80) cc_final: 0.6740 (t80) REVERT: A 501 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7929 (tp30) REVERT: A 506 PHE cc_start: 0.8991 (t80) cc_final: 0.8557 (m-80) REVERT: A 565 TYR cc_start: 0.9188 (m-80) cc_final: 0.8970 (m-80) REVERT: A 567 ARG cc_start: 0.8363 (mtt180) cc_final: 0.7802 (mtm-85) REVERT: A 591 LEU cc_start: 0.8906 (tp) cc_final: 0.8479 (tt) REVERT: A 595 ILE cc_start: 0.9317 (mt) cc_final: 0.9083 (mt) REVERT: A 677 MET cc_start: 0.8346 (mmm) cc_final: 0.7939 (tpp) REVERT: A 688 SER cc_start: 0.8919 (t) cc_final: 0.8576 (t) REVERT: A 699 THR cc_start: 0.9678 (p) cc_final: 0.9376 (t) REVERT: A 704 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8205 (tp30) REVERT: A 717 MET cc_start: 0.7986 (tpp) cc_final: 0.7427 (tmm) REVERT: A 728 PHE cc_start: 0.7688 (m-80) cc_final: 0.7280 (m-80) REVERT: A 742 TRP cc_start: 0.7215 (m-90) cc_final: 0.6906 (m-90) REVERT: A 752 ASP cc_start: 0.8051 (t0) cc_final: 0.7628 (t0) REVERT: B 139 LEU cc_start: 0.9293 (mm) cc_final: 0.9033 (tp) REVERT: B 185 GLU cc_start: 0.8991 (mp0) cc_final: 0.8284 (pm20) REVERT: B 220 ASN cc_start: 0.9149 (m-40) cc_final: 0.8761 (m-40) REVERT: B 290 THR cc_start: 0.9371 (m) cc_final: 0.9125 (p) REVERT: B 322 ASP cc_start: 0.8856 (t0) cc_final: 0.8221 (t0) REVERT: B 323 MET cc_start: 0.8958 (ttm) cc_final: 0.8627 (tmm) REVERT: B 326 LEU cc_start: 0.9142 (mp) cc_final: 0.8926 (mp) REVERT: B 351 MET cc_start: 0.9039 (mmt) cc_final: 0.8800 (mmm) REVERT: B 414 ASP cc_start: 0.7949 (m-30) cc_final: 0.7033 (t0) REVERT: B 439 TYR cc_start: 0.8914 (m-80) cc_final: 0.8627 (m-10) REVERT: B 452 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8397 (t0) REVERT: B 461 TYR cc_start: 0.6961 (t80) cc_final: 0.6729 (t80) REVERT: B 501 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7948 (tp30) REVERT: B 506 PHE cc_start: 0.8993 (t80) cc_final: 0.8539 (m-80) REVERT: B 519 ASP cc_start: 0.8442 (m-30) cc_final: 0.8098 (m-30) REVERT: B 567 ARG cc_start: 0.8329 (mtt180) cc_final: 0.7931 (mtt90) REVERT: B 591 LEU cc_start: 0.8884 (tp) cc_final: 0.8512 (tt) REVERT: B 677 MET cc_start: 0.8370 (mmm) cc_final: 0.8039 (tpp) REVERT: B 682 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 688 SER cc_start: 0.8977 (t) cc_final: 0.8513 (t) REVERT: B 699 THR cc_start: 0.9675 (p) cc_final: 0.9438 (t) REVERT: B 704 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8206 (tp30) REVERT: B 717 MET cc_start: 0.7950 (tpp) cc_final: 0.7404 (tmm) REVERT: B 728 PHE cc_start: 0.7639 (m-80) cc_final: 0.7233 (m-80) REVERT: B 742 TRP cc_start: 0.7167 (m-90) cc_final: 0.6950 (m-90) REVERT: C 139 LEU cc_start: 0.9298 (mm) cc_final: 0.9050 (tp) REVERT: C 185 GLU cc_start: 0.9001 (mp0) cc_final: 0.8288 (pm20) REVERT: C 220 ASN cc_start: 0.9133 (m-40) cc_final: 0.8737 (m-40) REVERT: C 256 HIS cc_start: 0.6948 (p90) cc_final: 0.6206 (p90) REVERT: C 290 THR cc_start: 0.9380 (m) cc_final: 0.9138 (p) REVERT: C 322 ASP cc_start: 0.8846 (t0) cc_final: 0.8211 (t0) REVERT: C 323 MET cc_start: 0.8956 (ttm) cc_final: 0.8644 (tmm) REVERT: C 326 LEU cc_start: 0.9138 (mp) cc_final: 0.8930 (mp) REVERT: C 351 MET cc_start: 0.9054 (mmt) cc_final: 0.8794 (mmm) REVERT: C 414 ASP cc_start: 0.7912 (m-30) cc_final: 0.7028 (t0) REVERT: C 439 TYR cc_start: 0.8911 (m-80) cc_final: 0.8633 (m-10) REVERT: C 452 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8368 (t0) REVERT: C 461 TYR cc_start: 0.6998 (t80) cc_final: 0.6757 (t80) REVERT: C 501 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7940 (tp30) REVERT: C 506 PHE cc_start: 0.8982 (t80) cc_final: 0.8544 (m-80) REVERT: C 567 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7738 (mtm-85) REVERT: C 591 LEU cc_start: 0.8868 (tp) cc_final: 0.8515 (tt) REVERT: C 677 MET cc_start: 0.8381 (mmm) cc_final: 0.8075 (tpp) REVERT: C 688 SER cc_start: 0.9004 (t) cc_final: 0.8535 (t) REVERT: C 699 THR cc_start: 0.9667 (p) cc_final: 0.9372 (t) REVERT: C 704 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8223 (tp30) REVERT: C 717 MET cc_start: 0.7949 (tpp) cc_final: 0.7401 (tmm) REVERT: C 728 PHE cc_start: 0.7682 (m-80) cc_final: 0.7246 (m-80) REVERT: C 742 TRP cc_start: 0.7163 (m-90) cc_final: 0.6913 (m-90) REVERT: D 139 LEU cc_start: 0.9306 (mm) cc_final: 0.9053 (tp) REVERT: D 185 GLU cc_start: 0.9017 (mp0) cc_final: 0.8285 (pm20) REVERT: D 220 ASN cc_start: 0.9153 (m-40) cc_final: 0.8742 (m-40) REVERT: D 256 HIS cc_start: 0.6972 (p90) cc_final: 0.6196 (p90) REVERT: D 282 MET cc_start: 0.8745 (tpp) cc_final: 0.8540 (tpp) REVERT: D 290 THR cc_start: 0.9387 (m) cc_final: 0.9162 (p) REVERT: D 322 ASP cc_start: 0.8832 (t0) cc_final: 0.8201 (t0) REVERT: D 323 MET cc_start: 0.8963 (ttm) cc_final: 0.8636 (tmm) REVERT: D 326 LEU cc_start: 0.9143 (mp) cc_final: 0.8900 (mp) REVERT: D 351 MET cc_start: 0.9074 (mmt) cc_final: 0.8813 (mmm) REVERT: D 414 ASP cc_start: 0.7929 (m-30) cc_final: 0.7024 (t0) REVERT: D 439 TYR cc_start: 0.8898 (m-80) cc_final: 0.8601 (m-10) REVERT: D 440 MET cc_start: 0.8287 (tpp) cc_final: 0.7676 (tpp) REVERT: D 452 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8368 (t0) REVERT: D 501 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7920 (tp30) REVERT: D 506 PHE cc_start: 0.8982 (t80) cc_final: 0.8573 (m-80) REVERT: D 519 ASP cc_start: 0.8469 (m-30) cc_final: 0.8082 (m-30) REVERT: D 532 LEU cc_start: 0.9626 (mt) cc_final: 0.9353 (mm) REVERT: D 550 CYS cc_start: 0.8860 (p) cc_final: 0.8069 (t) REVERT: D 567 ARG cc_start: 0.8336 (mtt180) cc_final: 0.7943 (mtt90) REVERT: D 591 LEU cc_start: 0.8875 (tp) cc_final: 0.8517 (tt) REVERT: D 595 ILE cc_start: 0.9309 (mt) cc_final: 0.9103 (mt) REVERT: D 677 MET cc_start: 0.8346 (mmm) cc_final: 0.8033 (tpp) REVERT: D 688 SER cc_start: 0.9012 (t) cc_final: 0.8523 (t) REVERT: D 699 THR cc_start: 0.9675 (p) cc_final: 0.9445 (t) REVERT: D 704 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8134 (tp30) REVERT: D 717 MET cc_start: 0.7911 (tpp) cc_final: 0.7324 (tmm) REVERT: D 728 PHE cc_start: 0.7660 (m-80) cc_final: 0.7203 (m-80) REVERT: D 742 TRP cc_start: 0.7171 (m-90) cc_final: 0.6943 (m-90) outliers start: 4 outliers final: 0 residues processed: 764 average time/residue: 0.1321 time to fit residues: 161.7483 Evaluate side-chains 544 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 540 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 140 optimal weight: 0.0070 chunk 249 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 212 optimal weight: 0.2980 chunk 148 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN A 683 ASN A 735 ASN B 452 ASN B 735 ASN C 256 HIS C 452 ASN C 735 ASN D 256 HIS D 452 ASN D 671 ASN D 735 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.101619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.083843 restraints weight = 58923.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.086020 restraints weight = 35443.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087942 restraints weight = 24906.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.089187 restraints weight = 18938.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.090239 restraints weight = 15420.915| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21460 Z= 0.127 Angle : 0.686 8.801 29032 Z= 0.341 Chirality : 0.041 0.179 3308 Planarity : 0.004 0.055 3624 Dihedral : 5.645 32.881 2808 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.07 % Favored : 87.77 % Rotamer: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.15), residues: 2568 helix: -0.68 (0.12), residues: 1472 sheet: -3.36 (0.46), residues: 68 loop : -3.47 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 464 TYR 0.014 0.001 TYR D 382 PHE 0.011 0.001 PHE B 715 TRP 0.009 0.001 TRP B 493 HIS 0.003 0.001 HIS C 745 Details of bonding type rmsd covalent geometry : bond 0.00262 (21460) covalent geometry : angle 0.68625 (29032) hydrogen bonds : bond 0.03661 ( 888) hydrogen bonds : angle 4.32635 ( 2580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 744 time to evaluate : 0.809 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: A 139 LEU cc_start: 0.9328 (mm) cc_final: 0.8997 (tp) REVERT: A 160 HIS cc_start: 0.8058 (t70) cc_final: 0.7841 (t-90) REVERT: A 176 LEU cc_start: 0.9660 (mm) cc_final: 0.9455 (mm) REVERT: A 185 GLU cc_start: 0.8995 (mp0) cc_final: 0.8362 (pm20) REVERT: A 220 ASN cc_start: 0.9048 (m-40) cc_final: 0.8645 (m-40) REVERT: A 322 ASP cc_start: 0.8960 (t0) cc_final: 0.8701 (t70) REVERT: A 351 MET cc_start: 0.9099 (mmt) cc_final: 0.8855 (mmm) REVERT: A 414 ASP cc_start: 0.7913 (m-30) cc_final: 0.7095 (t0) REVERT: A 440 MET cc_start: 0.8176 (tpp) cc_final: 0.7746 (tpp) REVERT: A 461 TYR cc_start: 0.7171 (t80) cc_final: 0.6789 (t80) REVERT: A 471 HIS cc_start: 0.7313 (p90) cc_final: 0.6977 (p90) REVERT: A 501 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8111 (tp30) REVERT: A 506 PHE cc_start: 0.8873 (t80) cc_final: 0.8504 (m-80) REVERT: A 555 MET cc_start: 0.9125 (mtm) cc_final: 0.8547 (mpp) REVERT: A 561 ASN cc_start: 0.8640 (m110) cc_final: 0.8223 (m110) REVERT: A 572 MET cc_start: 0.8499 (tmm) cc_final: 0.8186 (tmm) REVERT: A 585 HIS cc_start: 0.8084 (t-90) cc_final: 0.7729 (t-90) REVERT: A 595 ILE cc_start: 0.9211 (mt) cc_final: 0.8991 (mt) REVERT: A 677 MET cc_start: 0.8241 (mmm) cc_final: 0.7875 (tpp) REVERT: A 699 THR cc_start: 0.9624 (p) cc_final: 0.9397 (t) REVERT: A 717 MET cc_start: 0.7752 (tpp) cc_final: 0.7552 (tmm) REVERT: B 139 LEU cc_start: 0.9381 (mm) cc_final: 0.9076 (tp) REVERT: B 176 LEU cc_start: 0.9649 (mm) cc_final: 0.9439 (mm) REVERT: B 185 GLU cc_start: 0.9005 (mp0) cc_final: 0.8338 (pm20) REVERT: B 220 ASN cc_start: 0.9005 (m-40) cc_final: 0.8597 (m-40) REVERT: B 256 HIS cc_start: 0.6709 (p-80) cc_final: 0.6162 (p-80) REVERT: B 290 THR cc_start: 0.9307 (m) cc_final: 0.9092 (p) REVERT: B 308 GLU cc_start: 0.6286 (pm20) cc_final: 0.6061 (pm20) REVERT: B 322 ASP cc_start: 0.8959 (t0) cc_final: 0.8269 (t70) REVERT: B 351 MET cc_start: 0.9123 (mmt) cc_final: 0.8847 (mmm) REVERT: B 414 ASP cc_start: 0.7883 (m-30) cc_final: 0.7074 (t0) REVERT: B 440 MET cc_start: 0.8203 (tpp) cc_final: 0.7747 (tpp) REVERT: B 461 TYR cc_start: 0.7117 (t80) cc_final: 0.6766 (t80) REVERT: B 471 HIS cc_start: 0.7367 (p90) cc_final: 0.7045 (p90) REVERT: B 501 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8057 (tp30) REVERT: B 505 ILE cc_start: 0.9483 (pt) cc_final: 0.9111 (tt) REVERT: B 506 PHE cc_start: 0.8880 (t80) cc_final: 0.8470 (m-80) REVERT: B 517 LEU cc_start: 0.9286 (pt) cc_final: 0.9069 (pt) REVERT: B 555 MET cc_start: 0.9094 (mtm) cc_final: 0.8545 (mpp) REVERT: B 561 ASN cc_start: 0.8594 (m110) cc_final: 0.8164 (m110) REVERT: B 572 MET cc_start: 0.8430 (tmm) cc_final: 0.8115 (tmm) REVERT: B 585 HIS cc_start: 0.8229 (t-90) cc_final: 0.7926 (t-90) REVERT: B 677 MET cc_start: 0.8260 (mmm) cc_final: 0.7888 (tpp) REVERT: B 699 THR cc_start: 0.9631 (p) cc_final: 0.9420 (t) REVERT: B 722 LYS cc_start: 0.7180 (mttt) cc_final: 0.6958 (tttt) REVERT: C 139 LEU cc_start: 0.9378 (mm) cc_final: 0.9059 (tp) REVERT: C 160 HIS cc_start: 0.8031 (t70) cc_final: 0.7808 (t-90) REVERT: C 176 LEU cc_start: 0.9648 (mm) cc_final: 0.9436 (mm) REVERT: C 185 GLU cc_start: 0.8980 (mp0) cc_final: 0.8266 (pm20) REVERT: C 220 ASN cc_start: 0.9021 (m-40) cc_final: 0.8617 (m-40) REVERT: C 322 ASP cc_start: 0.8962 (t0) cc_final: 0.8270 (t70) REVERT: C 351 MET cc_start: 0.9113 (mmt) cc_final: 0.8855 (mmm) REVERT: C 414 ASP cc_start: 0.7872 (m-30) cc_final: 0.7030 (t0) REVERT: C 440 MET cc_start: 0.8196 (tpp) cc_final: 0.7793 (tpp) REVERT: C 461 TYR cc_start: 0.7138 (t80) cc_final: 0.6777 (t80) REVERT: C 471 HIS cc_start: 0.7350 (p90) cc_final: 0.7020 (p90) REVERT: C 501 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8058 (tp30) REVERT: C 505 ILE cc_start: 0.9464 (pt) cc_final: 0.9109 (tt) REVERT: C 506 PHE cc_start: 0.8854 (t80) cc_final: 0.8481 (m-80) REVERT: C 555 MET cc_start: 0.8820 (mtp) cc_final: 0.8323 (mtt) REVERT: C 561 ASN cc_start: 0.8641 (m110) cc_final: 0.8275 (m110) REVERT: C 567 ARG cc_start: 0.8831 (mtt180) cc_final: 0.8366 (mtt180) REVERT: C 572 MET cc_start: 0.8460 (tmm) cc_final: 0.8109 (tmm) REVERT: C 585 HIS cc_start: 0.8208 (t-90) cc_final: 0.7920 (t-90) REVERT: C 677 MET cc_start: 0.8230 (mmm) cc_final: 0.7924 (tpp) REVERT: C 699 THR cc_start: 0.9620 (p) cc_final: 0.9375 (t) REVERT: D 139 LEU cc_start: 0.9371 (mm) cc_final: 0.9064 (tp) REVERT: D 160 HIS cc_start: 0.8033 (t70) cc_final: 0.7801 (t-90) REVERT: D 185 GLU cc_start: 0.8966 (mp0) cc_final: 0.8259 (pm20) REVERT: D 220 ASN cc_start: 0.9038 (m-40) cc_final: 0.8622 (m-40) REVERT: D 308 GLU cc_start: 0.6245 (pm20) cc_final: 0.6042 (pm20) REVERT: D 322 ASP cc_start: 0.8937 (t0) cc_final: 0.8235 (t70) REVERT: D 351 MET cc_start: 0.9141 (mmt) cc_final: 0.8859 (mmm) REVERT: D 414 ASP cc_start: 0.7895 (m-30) cc_final: 0.7019 (t0) REVERT: D 440 MET cc_start: 0.8164 (tpp) cc_final: 0.7694 (tpp) REVERT: D 471 HIS cc_start: 0.7369 (p90) cc_final: 0.7012 (p90) REVERT: D 501 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8092 (tp30) REVERT: D 506 PHE cc_start: 0.8851 (t80) cc_final: 0.8536 (m-80) REVERT: D 517 LEU cc_start: 0.9265 (pt) cc_final: 0.9040 (pt) REVERT: D 532 LEU cc_start: 0.9590 (mt) cc_final: 0.9303 (mm) REVERT: D 550 CYS cc_start: 0.8810 (p) cc_final: 0.8167 (t) REVERT: D 561 ASN cc_start: 0.8661 (m110) cc_final: 0.8251 (m110) REVERT: D 585 HIS cc_start: 0.8229 (t-90) cc_final: 0.7894 (t-90) REVERT: D 595 ILE cc_start: 0.9213 (mt) cc_final: 0.9003 (mt) REVERT: D 677 MET cc_start: 0.8300 (mmm) cc_final: 0.8074 (tpp) REVERT: D 699 THR cc_start: 0.9627 (p) cc_final: 0.9417 (t) REVERT: D 717 MET cc_start: 0.7728 (tpp) cc_final: 0.7514 (tmm) outliers start: 1 outliers final: 0 residues processed: 745 average time/residue: 0.1227 time to fit residues: 150.2360 Evaluate side-chains 562 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 16 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 190 optimal weight: 0.0270 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 overall best weight: 0.5652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 273 ASN A 452 ASN A 695 GLN A 735 ASN B 273 ASN B 452 ASN B 643 ASN B 735 ASN C 273 ASN C 452 ASN C 643 ASN C 735 ASN D 273 ASN D 452 ASN D 643 ASN D 735 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.083760 restraints weight = 59484.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.086521 restraints weight = 35539.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088317 restraints weight = 24531.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089752 restraints weight = 18662.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.090648 restraints weight = 15082.509| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21460 Z= 0.126 Angle : 0.688 7.720 29032 Z= 0.342 Chirality : 0.041 0.187 3308 Planarity : 0.004 0.047 3624 Dihedral : 5.313 28.958 2808 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.80 % Favored : 88.05 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.16), residues: 2568 helix: -0.18 (0.13), residues: 1492 sheet: -2.99 (0.48), residues: 68 loop : -3.48 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 567 TYR 0.013 0.001 TYR A 359 PHE 0.012 0.001 PHE D 666 TRP 0.011 0.001 TRP C 692 HIS 0.010 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00255 (21460) covalent geometry : angle 0.68838 (29032) hydrogen bonds : bond 0.03320 ( 888) hydrogen bonds : angle 4.15435 ( 2580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9412 (mm) cc_final: 0.8944 (pp) REVERT: A 191 LEU cc_start: 0.9619 (mt) cc_final: 0.9401 (mt) REVERT: A 322 ASP cc_start: 0.8724 (t0) cc_final: 0.8193 (t70) REVERT: A 351 MET cc_start: 0.9114 (mmt) cc_final: 0.8904 (mmm) REVERT: A 440 MET cc_start: 0.8360 (tpp) cc_final: 0.7903 (tpp) REVERT: A 461 TYR cc_start: 0.7236 (t80) cc_final: 0.7008 (t80) REVERT: A 506 PHE cc_start: 0.8922 (t80) cc_final: 0.8540 (m-80) REVERT: A 519 ASP cc_start: 0.8541 (m-30) cc_final: 0.5617 (m-30) REVERT: A 555 MET cc_start: 0.9090 (mtm) cc_final: 0.8399 (mtt) REVERT: A 585 HIS cc_start: 0.8223 (t-90) cc_final: 0.7840 (t-90) REVERT: A 591 LEU cc_start: 0.8838 (tp) cc_final: 0.8428 (tt) REVERT: A 595 ILE cc_start: 0.9128 (mt) cc_final: 0.8857 (mt) REVERT: A 677 MET cc_start: 0.8331 (mmm) cc_final: 0.7755 (tpp) REVERT: A 689 GLU cc_start: 0.9228 (tt0) cc_final: 0.9015 (tt0) REVERT: A 699 THR cc_start: 0.9684 (p) cc_final: 0.9443 (t) REVERT: B 139 LEU cc_start: 0.9406 (mm) cc_final: 0.9081 (tp) REVERT: B 185 GLU cc_start: 0.9010 (mp0) cc_final: 0.8362 (pm20) REVERT: B 191 LEU cc_start: 0.9624 (mt) cc_final: 0.9420 (mt) REVERT: B 220 ASN cc_start: 0.9017 (m-40) cc_final: 0.8646 (m-40) REVERT: B 256 HIS cc_start: 0.6743 (p-80) cc_final: 0.6299 (p-80) REVERT: B 320 MET cc_start: 0.8797 (ttm) cc_final: 0.8478 (ttp) REVERT: B 322 ASP cc_start: 0.8807 (t0) cc_final: 0.7988 (t70) REVERT: B 351 MET cc_start: 0.9125 (mmt) cc_final: 0.8907 (mmm) REVERT: B 440 MET cc_start: 0.8413 (tpp) cc_final: 0.7959 (tpp) REVERT: B 461 TYR cc_start: 0.7210 (t80) cc_final: 0.6989 (t80) REVERT: B 506 PHE cc_start: 0.8913 (t80) cc_final: 0.8530 (m-80) REVERT: B 522 PHE cc_start: 0.8183 (m-10) cc_final: 0.7949 (m-10) REVERT: B 555 MET cc_start: 0.9079 (mtm) cc_final: 0.8383 (mtt) REVERT: B 585 HIS cc_start: 0.8315 (t-90) cc_final: 0.8076 (t-90) REVERT: B 677 MET cc_start: 0.8237 (mmm) cc_final: 0.7996 (tpp) REVERT: B 682 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7833 (mm-30) REVERT: B 699 THR cc_start: 0.9704 (p) cc_final: 0.9495 (t) REVERT: B 732 LEU cc_start: 0.8726 (mt) cc_final: 0.7929 (mt) REVERT: C 139 LEU cc_start: 0.9382 (mm) cc_final: 0.9024 (tp) REVERT: C 220 ASN cc_start: 0.9067 (m-40) cc_final: 0.8714 (m-40) REVERT: C 255 GLN cc_start: 0.8581 (pm20) cc_final: 0.8059 (pp30) REVERT: C 256 HIS cc_start: 0.7023 (p-80) cc_final: 0.5521 (p-80) REVERT: C 320 MET cc_start: 0.8827 (ttm) cc_final: 0.8470 (ttp) REVERT: C 322 ASP cc_start: 0.8792 (t0) cc_final: 0.7948 (t70) REVERT: C 440 MET cc_start: 0.8365 (tpp) cc_final: 0.7951 (tpp) REVERT: C 461 TYR cc_start: 0.7262 (t80) cc_final: 0.7057 (t80) REVERT: C 506 PHE cc_start: 0.8873 (t80) cc_final: 0.8525 (m-80) REVERT: C 551 LEU cc_start: 0.9528 (tp) cc_final: 0.9316 (tp) REVERT: C 555 MET cc_start: 0.8828 (mtp) cc_final: 0.8309 (mtt) REVERT: C 567 ARG cc_start: 0.8807 (mtt180) cc_final: 0.8256 (mtt180) REVERT: C 585 HIS cc_start: 0.8328 (t-90) cc_final: 0.8119 (t-90) REVERT: C 677 MET cc_start: 0.8307 (mmm) cc_final: 0.8093 (tpp) REVERT: C 682 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7778 (mm-30) REVERT: C 699 THR cc_start: 0.9669 (p) cc_final: 0.9351 (t) REVERT: D 139 LEU cc_start: 0.9377 (mm) cc_final: 0.9022 (tp) REVERT: D 185 GLU cc_start: 0.9000 (mp0) cc_final: 0.8305 (pm20) REVERT: D 191 LEU cc_start: 0.9632 (mt) cc_final: 0.9424 (mt) REVERT: D 220 ASN cc_start: 0.9034 (m-40) cc_final: 0.8665 (m-40) REVERT: D 255 GLN cc_start: 0.8565 (pm20) cc_final: 0.8014 (pp30) REVERT: D 256 HIS cc_start: 0.7100 (p-80) cc_final: 0.5648 (p-80) REVERT: D 320 MET cc_start: 0.8844 (ttm) cc_final: 0.8543 (ttp) REVERT: D 322 ASP cc_start: 0.8785 (t0) cc_final: 0.8174 (t0) REVERT: D 351 MET cc_start: 0.9093 (mmt) cc_final: 0.8887 (mmm) REVERT: D 440 MET cc_start: 0.8387 (tpp) cc_final: 0.7827 (tpp) REVERT: D 506 PHE cc_start: 0.8856 (t80) cc_final: 0.8490 (m-80) REVERT: D 522 PHE cc_start: 0.8224 (m-10) cc_final: 0.7955 (m-10) REVERT: D 585 HIS cc_start: 0.8340 (t-90) cc_final: 0.8103 (t-90) REVERT: D 591 LEU cc_start: 0.8850 (tp) cc_final: 0.8434 (tt) REVERT: D 595 ILE cc_start: 0.9111 (mt) cc_final: 0.8839 (mt) REVERT: D 682 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7556 (mm-30) REVERT: D 699 THR cc_start: 0.9698 (p) cc_final: 0.9495 (t) outliers start: 0 outliers final: 0 residues processed: 679 average time/residue: 0.1173 time to fit residues: 131.4360 Evaluate side-chains 515 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 47 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN A 523 HIS A 735 ASN B 452 ASN B 523 HIS B 580 GLN B 735 ASN C 452 ASN C 523 HIS C 735 ASN D 273 ASN D 452 ASN D 523 HIS D 735 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.102632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.084036 restraints weight = 58799.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.086582 restraints weight = 35978.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088463 restraints weight = 25460.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.089631 restraints weight = 19325.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.090667 restraints weight = 16070.669| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21460 Z= 0.123 Angle : 0.682 8.737 29032 Z= 0.339 Chirality : 0.041 0.181 3308 Planarity : 0.004 0.048 3624 Dihedral : 5.144 25.258 2808 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.37 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2568 helix: 0.11 (0.13), residues: 1492 sheet: -2.91 (0.49), residues: 68 loop : -3.42 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 464 TYR 0.015 0.001 TYR B 565 PHE 0.021 0.001 PHE D 489 TRP 0.013 0.001 TRP A 742 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00259 (21460) covalent geometry : angle 0.68245 (29032) hydrogen bonds : bond 0.03237 ( 888) hydrogen bonds : angle 4.11882 ( 2580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9408 (mm) cc_final: 0.8895 (pp) REVERT: A 159 MET cc_start: 0.8491 (mmm) cc_final: 0.8274 (mmm) REVERT: A 220 ASN cc_start: 0.9149 (m-40) cc_final: 0.8883 (m-40) REVERT: A 244 HIS cc_start: 0.8659 (m-70) cc_final: 0.8365 (m-70) REVERT: A 256 HIS cc_start: 0.6696 (p-80) cc_final: 0.6399 (p-80) REVERT: A 320 MET cc_start: 0.8159 (ttm) cc_final: 0.7754 (ttt) REVERT: A 322 ASP cc_start: 0.8517 (t0) cc_final: 0.7950 (t0) REVERT: A 351 MET cc_start: 0.9061 (mmt) cc_final: 0.8799 (mmm) REVERT: A 440 MET cc_start: 0.8401 (tpp) cc_final: 0.7963 (tpp) REVERT: A 461 TYR cc_start: 0.7219 (t80) cc_final: 0.6933 (t80) REVERT: A 506 PHE cc_start: 0.8900 (t80) cc_final: 0.8493 (m-80) REVERT: A 532 LEU cc_start: 0.9481 (mm) cc_final: 0.9089 (mm) REVERT: A 550 CYS cc_start: 0.8934 (p) cc_final: 0.8240 (t) REVERT: A 555 MET cc_start: 0.9042 (mtm) cc_final: 0.8305 (mtt) REVERT: A 585 HIS cc_start: 0.8310 (t-90) cc_final: 0.7993 (t-90) REVERT: A 591 LEU cc_start: 0.8879 (tp) cc_final: 0.8463 (tt) REVERT: A 595 ILE cc_start: 0.9103 (mt) cc_final: 0.8808 (mt) REVERT: A 677 MET cc_start: 0.8126 (mmm) cc_final: 0.7905 (tpp) REVERT: B 139 LEU cc_start: 0.9380 (mm) cc_final: 0.9078 (tp) REVERT: B 159 MET cc_start: 0.8491 (mmm) cc_final: 0.8269 (mmm) REVERT: B 185 GLU cc_start: 0.9010 (mp0) cc_final: 0.8355 (pm20) REVERT: B 220 ASN cc_start: 0.9076 (m-40) cc_final: 0.8677 (m-40) REVERT: B 244 HIS cc_start: 0.8684 (m-70) cc_final: 0.8430 (m-70) REVERT: B 256 HIS cc_start: 0.6672 (p-80) cc_final: 0.6149 (p-80) REVERT: B 308 GLU cc_start: 0.6567 (pm20) cc_final: 0.6347 (pm20) REVERT: B 320 MET cc_start: 0.8587 (ttm) cc_final: 0.8322 (ttp) REVERT: B 322 ASP cc_start: 0.8747 (t0) cc_final: 0.8402 (t0) REVERT: B 351 MET cc_start: 0.9086 (mmt) cc_final: 0.8832 (mmm) REVERT: B 440 MET cc_start: 0.8384 (tpp) cc_final: 0.7946 (tpp) REVERT: B 461 TYR cc_start: 0.7217 (t80) cc_final: 0.6941 (t80) REVERT: B 506 PHE cc_start: 0.8888 (t80) cc_final: 0.8477 (m-80) REVERT: B 532 LEU cc_start: 0.9435 (mm) cc_final: 0.9025 (mm) REVERT: B 550 CYS cc_start: 0.8897 (p) cc_final: 0.8195 (t) REVERT: B 555 MET cc_start: 0.9019 (mtm) cc_final: 0.8287 (mtt) REVERT: B 585 HIS cc_start: 0.8351 (t-90) cc_final: 0.8112 (t-90) REVERT: B 677 MET cc_start: 0.8178 (mmm) cc_final: 0.7967 (tpp) REVERT: B 682 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7545 (mm-30) REVERT: C 139 LEU cc_start: 0.9371 (mm) cc_final: 0.9050 (tp) REVERT: C 159 MET cc_start: 0.8481 (mmm) cc_final: 0.8262 (mmm) REVERT: C 185 GLU cc_start: 0.8993 (mp0) cc_final: 0.8353 (pm20) REVERT: C 220 ASN cc_start: 0.9120 (m-40) cc_final: 0.8720 (m-40) REVERT: C 244 HIS cc_start: 0.8693 (m-70) cc_final: 0.8436 (m-70) REVERT: C 256 HIS cc_start: 0.7003 (p-80) cc_final: 0.6195 (p-80) REVERT: C 271 CYS cc_start: 0.9420 (m) cc_final: 0.9214 (m) REVERT: C 320 MET cc_start: 0.8625 (ttm) cc_final: 0.8252 (ttp) REVERT: C 322 ASP cc_start: 0.8741 (t0) cc_final: 0.8394 (t0) REVERT: C 440 MET cc_start: 0.8389 (tpp) cc_final: 0.7898 (tpp) REVERT: C 461 TYR cc_start: 0.7237 (t80) cc_final: 0.6994 (t80) REVERT: C 506 PHE cc_start: 0.8920 (t80) cc_final: 0.8496 (m-80) REVERT: C 551 LEU cc_start: 0.9549 (tp) cc_final: 0.9337 (tp) REVERT: C 555 MET cc_start: 0.8809 (mtp) cc_final: 0.8257 (mtt) REVERT: C 585 HIS cc_start: 0.8360 (t-90) cc_final: 0.8137 (t-90) REVERT: C 677 MET cc_start: 0.8208 (mmm) cc_final: 0.7985 (tpp) REVERT: C 682 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7782 (mm-30) REVERT: D 139 LEU cc_start: 0.9349 (mm) cc_final: 0.9029 (tp) REVERT: D 159 MET cc_start: 0.8468 (mmm) cc_final: 0.8250 (mmm) REVERT: D 185 GLU cc_start: 0.8988 (mp0) cc_final: 0.8354 (pm20) REVERT: D 244 HIS cc_start: 0.8690 (m-70) cc_final: 0.8404 (m-70) REVERT: D 256 HIS cc_start: 0.7009 (p-80) cc_final: 0.6183 (p-80) REVERT: D 271 CYS cc_start: 0.9413 (m) cc_final: 0.9206 (m) REVERT: D 322 ASP cc_start: 0.8688 (t0) cc_final: 0.8095 (t70) REVERT: D 351 MET cc_start: 0.9115 (mmt) cc_final: 0.8841 (mmm) REVERT: D 506 PHE cc_start: 0.8912 (t80) cc_final: 0.8486 (m-80) REVERT: D 555 MET cc_start: 0.9072 (mtt) cc_final: 0.8769 (mtm) REVERT: D 585 HIS cc_start: 0.8354 (t-90) cc_final: 0.8105 (t-90) REVERT: D 595 ILE cc_start: 0.9090 (mt) cc_final: 0.8850 (mt) REVERT: D 616 LYS cc_start: 0.9098 (mptt) cc_final: 0.8732 (mptt) REVERT: D 682 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7541 (mm-30) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.1143 time to fit residues: 124.2209 Evaluate side-chains 497 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.7980 chunk 136 optimal weight: 0.0570 chunk 108 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 0.0170 chunk 126 optimal weight: 7.9990 chunk 223 optimal weight: 0.8980 chunk 199 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 292 GLN A 452 ASN A 735 ASN A 745 HIS B 273 ASN B 735 ASN C 273 ASN C 452 ASN C 695 GLN C 735 ASN D 452 ASN D 735 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.084887 restraints weight = 59080.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.087354 restraints weight = 36616.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.089239 restraints weight = 25803.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.090337 restraints weight = 19781.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.091371 restraints weight = 16687.586| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21460 Z= 0.123 Angle : 0.672 8.830 29032 Z= 0.331 Chirality : 0.041 0.182 3308 Planarity : 0.004 0.046 3624 Dihedral : 4.998 24.000 2808 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.19 % Favored : 87.66 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.16), residues: 2568 helix: 0.23 (0.13), residues: 1500 sheet: -2.94 (0.47), residues: 68 loop : -3.33 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 122 TYR 0.016 0.001 TYR C 565 PHE 0.009 0.001 PHE A 633 TRP 0.012 0.001 TRP D 742 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00258 (21460) covalent geometry : angle 0.67198 (29032) hydrogen bonds : bond 0.03128 ( 888) hydrogen bonds : angle 4.10012 ( 2580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 0.809 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: A 139 LEU cc_start: 0.9403 (mm) cc_final: 0.9059 (tp) REVERT: A 220 ASN cc_start: 0.9174 (m-40) cc_final: 0.8920 (m-40) REVERT: A 244 HIS cc_start: 0.8718 (m-70) cc_final: 0.8413 (m170) REVERT: A 256 HIS cc_start: 0.6667 (p-80) cc_final: 0.6285 (p-80) REVERT: A 320 MET cc_start: 0.8142 (ttm) cc_final: 0.7769 (ttp) REVERT: A 351 MET cc_start: 0.9111 (mmt) cc_final: 0.8794 (mmm) REVERT: A 440 MET cc_start: 0.8427 (tpp) cc_final: 0.7937 (tpp) REVERT: A 461 TYR cc_start: 0.7262 (t80) cc_final: 0.6955 (t80) REVERT: A 488 MET cc_start: 0.8738 (ttp) cc_final: 0.8455 (ttm) REVERT: A 506 PHE cc_start: 0.8804 (t80) cc_final: 0.8475 (m-80) REVERT: A 555 MET cc_start: 0.9034 (mtm) cc_final: 0.8303 (mtt) REVERT: A 585 HIS cc_start: 0.8321 (t-90) cc_final: 0.8054 (t-90) REVERT: A 591 LEU cc_start: 0.8887 (tp) cc_final: 0.8426 (tt) REVERT: A 595 ILE cc_start: 0.9079 (mt) cc_final: 0.8806 (mt) REVERT: A 677 MET cc_start: 0.8069 (mmm) cc_final: 0.7844 (tpp) REVERT: A 686 LYS cc_start: 0.9423 (mmtt) cc_final: 0.9115 (mtpt) REVERT: B 139 LEU cc_start: 0.9402 (mm) cc_final: 0.9078 (tp) REVERT: B 185 GLU cc_start: 0.8977 (mp0) cc_final: 0.8359 (pm20) REVERT: B 220 ASN cc_start: 0.9091 (m-40) cc_final: 0.8766 (m-40) REVERT: B 256 HIS cc_start: 0.6664 (p-80) cc_final: 0.6021 (p-80) REVERT: B 320 MET cc_start: 0.8524 (ttm) cc_final: 0.8277 (ttp) REVERT: B 322 ASP cc_start: 0.8679 (t0) cc_final: 0.8009 (t0) REVERT: B 351 MET cc_start: 0.9106 (mmt) cc_final: 0.8816 (mmm) REVERT: B 440 MET cc_start: 0.8377 (tpp) cc_final: 0.7911 (tpp) REVERT: B 461 TYR cc_start: 0.7246 (t80) cc_final: 0.6942 (t80) REVERT: B 506 PHE cc_start: 0.8817 (t80) cc_final: 0.8460 (m-80) REVERT: B 555 MET cc_start: 0.9021 (mtm) cc_final: 0.8266 (mtt) REVERT: B 572 MET cc_start: 0.8761 (tmm) cc_final: 0.8332 (tmm) REVERT: B 574 MET cc_start: 0.8755 (tpp) cc_final: 0.8506 (tpp) REVERT: B 585 HIS cc_start: 0.8370 (t-90) cc_final: 0.8128 (t-90) REVERT: B 616 LYS cc_start: 0.8974 (mptt) cc_final: 0.8470 (mptt) REVERT: B 677 MET cc_start: 0.8213 (mmm) cc_final: 0.7754 (tpp) REVERT: B 682 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 715 PHE cc_start: 0.7073 (t80) cc_final: 0.6198 (t80) REVERT: B 735 ASN cc_start: 0.8051 (m-40) cc_final: 0.7817 (m110) REVERT: C 139 LEU cc_start: 0.9395 (mm) cc_final: 0.9073 (tp) REVERT: C 185 GLU cc_start: 0.8977 (mp0) cc_final: 0.8365 (pm20) REVERT: C 244 HIS cc_start: 0.8739 (m-70) cc_final: 0.8416 (m170) REVERT: C 256 HIS cc_start: 0.7032 (p-80) cc_final: 0.6121 (p-80) REVERT: C 271 CYS cc_start: 0.9447 (m) cc_final: 0.9191 (m) REVERT: C 322 ASP cc_start: 0.8665 (t0) cc_final: 0.7990 (t0) REVERT: C 364 GLU cc_start: 0.8407 (tp30) cc_final: 0.8187 (tp30) REVERT: C 440 MET cc_start: 0.8421 (tpp) cc_final: 0.7901 (tpp) REVERT: C 461 TYR cc_start: 0.7290 (t80) cc_final: 0.7018 (t80) REVERT: C 506 PHE cc_start: 0.8820 (t80) cc_final: 0.8486 (m-80) REVERT: C 532 LEU cc_start: 0.9419 (mm) cc_final: 0.8979 (mm) REVERT: C 550 CYS cc_start: 0.8821 (p) cc_final: 0.8183 (t) REVERT: C 551 LEU cc_start: 0.9520 (tp) cc_final: 0.9284 (tp) REVERT: C 555 MET cc_start: 0.8768 (mtp) cc_final: 0.8240 (mtt) REVERT: C 567 ARG cc_start: 0.8521 (mtt180) cc_final: 0.8165 (mtt180) REVERT: C 572 MET cc_start: 0.8845 (tmm) cc_final: 0.8415 (tmm) REVERT: C 574 MET cc_start: 0.8804 (tpp) cc_final: 0.8510 (tpp) REVERT: C 585 HIS cc_start: 0.8353 (t-90) cc_final: 0.8116 (t-90) REVERT: C 616 LYS cc_start: 0.8965 (mptt) cc_final: 0.8499 (mptt) REVERT: C 682 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7617 (mm-30) REVERT: C 695 GLN cc_start: 0.8588 (tt0) cc_final: 0.8159 (tt0) REVERT: D 139 LEU cc_start: 0.9383 (mm) cc_final: 0.9054 (tp) REVERT: D 185 GLU cc_start: 0.8980 (mp0) cc_final: 0.8360 (pm20) REVERT: D 220 ASN cc_start: 0.9166 (m-40) cc_final: 0.8902 (m-40) REVERT: D 244 HIS cc_start: 0.8716 (m-70) cc_final: 0.8414 (m170) REVERT: D 256 HIS cc_start: 0.7013 (p-80) cc_final: 0.6099 (p-80) REVERT: D 271 CYS cc_start: 0.9361 (m) cc_final: 0.9115 (m) REVERT: D 320 MET cc_start: 0.8243 (ttm) cc_final: 0.7851 (ttp) REVERT: D 322 ASP cc_start: 0.8487 (t0) cc_final: 0.7898 (t0) REVERT: D 351 MET cc_start: 0.9114 (mmt) cc_final: 0.8815 (mmm) REVERT: D 440 MET cc_start: 0.8298 (tpp) cc_final: 0.7849 (tpp) REVERT: D 488 MET cc_start: 0.8789 (ttp) cc_final: 0.8509 (ttm) REVERT: D 506 PHE cc_start: 0.8816 (t80) cc_final: 0.8482 (m-80) REVERT: D 585 HIS cc_start: 0.8345 (t-90) cc_final: 0.8141 (t-90) REVERT: D 595 ILE cc_start: 0.9056 (mt) cc_final: 0.8787 (mt) REVERT: D 616 LYS cc_start: 0.9057 (mptt) cc_final: 0.8727 (mptt) REVERT: D 682 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7600 (mm-30) REVERT: D 735 ASN cc_start: 0.8093 (m-40) cc_final: 0.7877 (m110) outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 0.1160 time to fit residues: 122.1573 Evaluate side-chains 508 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 57 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 ASN B 292 GLN B 683 ASN B 745 HIS ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 735 ASN C 745 HIS ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN D 745 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.101382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.082451 restraints weight = 59790.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.084914 restraints weight = 37335.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.086765 restraints weight = 26140.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087954 restraints weight = 20275.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088700 restraints weight = 16915.164| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21460 Z= 0.139 Angle : 0.689 8.152 29032 Z= 0.342 Chirality : 0.042 0.187 3308 Planarity : 0.004 0.048 3624 Dihedral : 5.008 23.904 2808 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.76 % Favored : 88.20 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.16), residues: 2568 helix: 0.34 (0.13), residues: 1504 sheet: -2.82 (0.45), residues: 68 loop : -3.25 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 464 TYR 0.015 0.001 TYR B 359 PHE 0.023 0.001 PHE D 489 TRP 0.012 0.001 TRP D 742 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00307 (21460) covalent geometry : angle 0.68897 (29032) hydrogen bonds : bond 0.03134 ( 888) hydrogen bonds : angle 4.13704 ( 2580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 636 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9425 (mm) cc_final: 0.9122 (tp) REVERT: A 185 GLU cc_start: 0.9005 (mp0) cc_final: 0.8347 (pm20) REVERT: A 220 ASN cc_start: 0.9175 (m-40) cc_final: 0.8957 (m-40) REVERT: A 320 MET cc_start: 0.8133 (ttm) cc_final: 0.7754 (ttp) REVERT: A 326 LEU cc_start: 0.9057 (mp) cc_final: 0.8819 (mp) REVERT: A 351 MET cc_start: 0.9104 (mmt) cc_final: 0.8869 (mmm) REVERT: A 440 MET cc_start: 0.8478 (tpp) cc_final: 0.8075 (tpp) REVERT: A 461 TYR cc_start: 0.7200 (t80) cc_final: 0.6907 (t80) REVERT: A 462 ARG cc_start: 0.6309 (mmt90) cc_final: 0.5420 (mtm110) REVERT: A 488 MET cc_start: 0.8790 (ttp) cc_final: 0.8501 (ttm) REVERT: A 506 PHE cc_start: 0.8898 (t80) cc_final: 0.8502 (m-80) REVERT: A 532 LEU cc_start: 0.9496 (mm) cc_final: 0.9065 (mm) REVERT: A 550 CYS cc_start: 0.8874 (p) cc_final: 0.8250 (t) REVERT: A 555 MET cc_start: 0.9018 (mtm) cc_final: 0.8264 (mtt) REVERT: A 567 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8340 (mtt180) REVERT: A 572 MET cc_start: 0.8847 (tmm) cc_final: 0.8479 (tmm) REVERT: A 585 HIS cc_start: 0.8381 (t-90) cc_final: 0.8162 (t-90) REVERT: A 591 LEU cc_start: 0.8934 (tp) cc_final: 0.8433 (tt) REVERT: A 595 ILE cc_start: 0.9176 (mt) cc_final: 0.8765 (mt) REVERT: A 616 LYS cc_start: 0.9014 (mptt) cc_final: 0.8525 (mptt) REVERT: A 686 LYS cc_start: 0.9489 (mmtt) cc_final: 0.9268 (mmmm) REVERT: A 695 GLN cc_start: 0.8321 (tp-100) cc_final: 0.7239 (tp40) REVERT: B 139 LEU cc_start: 0.9420 (mm) cc_final: 0.9152 (tp) REVERT: B 159 MET cc_start: 0.8496 (mmm) cc_final: 0.8260 (mmm) REVERT: B 185 GLU cc_start: 0.9001 (mp0) cc_final: 0.8372 (pm20) REVERT: B 320 MET cc_start: 0.8372 (ttm) cc_final: 0.8009 (ttp) REVERT: B 322 ASP cc_start: 0.8618 (t0) cc_final: 0.7992 (t0) REVERT: B 351 MET cc_start: 0.9112 (mmt) cc_final: 0.8876 (mmm) REVERT: B 440 MET cc_start: 0.8447 (tpp) cc_final: 0.8067 (tpp) REVERT: B 461 TYR cc_start: 0.7213 (t80) cc_final: 0.6935 (t80) REVERT: B 462 ARG cc_start: 0.6281 (mmt90) cc_final: 0.5397 (mtm110) REVERT: B 506 PHE cc_start: 0.8906 (t80) cc_final: 0.8518 (m-80) REVERT: B 532 LEU cc_start: 0.9452 (mm) cc_final: 0.9012 (mm) REVERT: B 550 CYS cc_start: 0.8905 (p) cc_final: 0.8243 (t) REVERT: B 555 MET cc_start: 0.9010 (mtm) cc_final: 0.8239 (mtt) REVERT: B 616 LYS cc_start: 0.8980 (mptt) cc_final: 0.8503 (mptt) REVERT: B 677 MET cc_start: 0.7978 (mmm) cc_final: 0.7553 (tpp) REVERT: B 682 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 715 PHE cc_start: 0.7187 (t80) cc_final: 0.5805 (t80) REVERT: C 139 LEU cc_start: 0.9408 (mm) cc_final: 0.9102 (tp) REVERT: C 159 MET cc_start: 0.8487 (mmm) cc_final: 0.8265 (mmm) REVERT: C 185 GLU cc_start: 0.8980 (mp0) cc_final: 0.8372 (pm20) REVERT: C 220 ASN cc_start: 0.9196 (m-40) cc_final: 0.8954 (m-40) REVERT: C 256 HIS cc_start: 0.7001 (p-80) cc_final: 0.6651 (p-80) REVERT: C 271 CYS cc_start: 0.9405 (m) cc_final: 0.9160 (m) REVERT: C 320 MET cc_start: 0.8111 (ttm) cc_final: 0.7833 (ttp) REVERT: C 322 ASP cc_start: 0.8602 (t0) cc_final: 0.7982 (t0) REVERT: C 364 GLU cc_start: 0.8507 (tp30) cc_final: 0.8218 (tp30) REVERT: C 440 MET cc_start: 0.8477 (tpp) cc_final: 0.8084 (tpp) REVERT: C 461 TYR cc_start: 0.7226 (t80) cc_final: 0.6960 (t80) REVERT: C 462 ARG cc_start: 0.6321 (mmt90) cc_final: 0.5412 (mtm110) REVERT: C 506 PHE cc_start: 0.8849 (t80) cc_final: 0.8491 (m-80) REVERT: C 532 LEU cc_start: 0.9460 (mm) cc_final: 0.9043 (mm) REVERT: C 550 CYS cc_start: 0.8817 (p) cc_final: 0.8262 (t) REVERT: C 551 LEU cc_start: 0.9542 (tp) cc_final: 0.9319 (tp) REVERT: C 555 MET cc_start: 0.8759 (mtp) cc_final: 0.8247 (mtt) REVERT: C 561 ASN cc_start: 0.8643 (m110) cc_final: 0.8172 (m110) REVERT: C 616 LYS cc_start: 0.8947 (mptt) cc_final: 0.8481 (mptt) REVERT: C 652 ILE cc_start: 0.8430 (pt) cc_final: 0.8069 (mm) REVERT: C 682 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7651 (mm-30) REVERT: C 715 PHE cc_start: 0.7167 (t80) cc_final: 0.6375 (t80) REVERT: C 735 ASN cc_start: 0.8077 (m-40) cc_final: 0.7753 (m110) REVERT: D 139 LEU cc_start: 0.9387 (mm) cc_final: 0.9116 (tp) REVERT: D 159 MET cc_start: 0.8478 (mmm) cc_final: 0.8251 (mmm) REVERT: D 185 GLU cc_start: 0.8973 (mp0) cc_final: 0.8361 (pm20) REVERT: D 220 ASN cc_start: 0.9188 (m-40) cc_final: 0.8937 (m-40) REVERT: D 256 HIS cc_start: 0.7052 (p-80) cc_final: 0.6713 (p-80) REVERT: D 271 CYS cc_start: 0.9407 (m) cc_final: 0.9163 (m) REVERT: D 320 MET cc_start: 0.8050 (ttm) cc_final: 0.7811 (ttp) REVERT: D 326 LEU cc_start: 0.8967 (mp) cc_final: 0.8698 (mp) REVERT: D 351 MET cc_start: 0.9132 (mmt) cc_final: 0.8820 (mmm) REVERT: D 440 MET cc_start: 0.8319 (tpp) cc_final: 0.7953 (tpp) REVERT: D 462 ARG cc_start: 0.6094 (mmt90) cc_final: 0.5068 (ptm160) REVERT: D 488 MET cc_start: 0.8768 (ttp) cc_final: 0.8479 (ttm) REVERT: D 506 PHE cc_start: 0.8932 (t80) cc_final: 0.8542 (m-80) REVERT: D 532 LEU cc_start: 0.9497 (mm) cc_final: 0.9060 (mm) REVERT: D 550 CYS cc_start: 0.8927 (p) cc_final: 0.8261 (t) REVERT: D 551 LEU cc_start: 0.9581 (tp) cc_final: 0.9305 (tp) REVERT: D 555 MET cc_start: 0.9035 (mtt) cc_final: 0.8657 (mtt) REVERT: D 591 LEU cc_start: 0.8946 (tp) cc_final: 0.8427 (tt) REVERT: D 595 ILE cc_start: 0.9145 (mt) cc_final: 0.8850 (mt) REVERT: D 616 LYS cc_start: 0.8977 (mptt) cc_final: 0.8669 (mptt) REVERT: D 682 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7846 (mm-30) outliers start: 0 outliers final: 0 residues processed: 636 average time/residue: 0.1134 time to fit residues: 117.2273 Evaluate side-chains 488 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 102 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 256 HIS A 452 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 HIS ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.078304 restraints weight = 59784.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.080700 restraints weight = 36686.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.082353 restraints weight = 25956.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.083537 restraints weight = 20139.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.084483 restraints weight = 16717.319| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21460 Z= 0.179 Angle : 0.734 8.034 29032 Z= 0.366 Chirality : 0.044 0.189 3308 Planarity : 0.004 0.052 3624 Dihedral : 5.171 22.644 2808 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.54 % Favored : 87.31 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.17), residues: 2568 helix: 0.34 (0.13), residues: 1500 sheet: -3.04 (0.43), residues: 68 loop : -3.14 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 464 TYR 0.017 0.001 TYR A 359 PHE 0.018 0.001 PHE A 203 TRP 0.010 0.002 TRP D 742 HIS 0.007 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00399 (21460) covalent geometry : angle 0.73385 (29032) hydrogen bonds : bond 0.03352 ( 888) hydrogen bonds : angle 4.27396 ( 2580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 0.846 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 139 LEU cc_start: 0.9409 (mm) cc_final: 0.9122 (tp) REVERT: A 185 GLU cc_start: 0.9051 (mp0) cc_final: 0.8401 (pm20) REVERT: A 220 ASN cc_start: 0.9219 (m-40) cc_final: 0.8997 (m-40) REVERT: A 244 HIS cc_start: 0.8626 (m-70) cc_final: 0.8368 (m-70) REVERT: A 323 MET cc_start: 0.9179 (tmm) cc_final: 0.8969 (tmm) REVERT: A 326 LEU cc_start: 0.9044 (mp) cc_final: 0.8832 (mp) REVERT: A 351 MET cc_start: 0.9049 (mmt) cc_final: 0.8724 (mmm) REVERT: A 440 MET cc_start: 0.8615 (tpp) cc_final: 0.8195 (tpp) REVERT: A 461 TYR cc_start: 0.7271 (t80) cc_final: 0.6953 (t80) REVERT: A 488 MET cc_start: 0.8820 (ttp) cc_final: 0.8532 (ttm) REVERT: A 506 PHE cc_start: 0.8905 (t80) cc_final: 0.8512 (m-80) REVERT: A 555 MET cc_start: 0.9109 (mtm) cc_final: 0.8358 (mtt) REVERT: A 585 HIS cc_start: 0.8508 (t-90) cc_final: 0.8256 (t-90) REVERT: A 591 LEU cc_start: 0.8987 (tp) cc_final: 0.8481 (tt) REVERT: A 595 ILE cc_start: 0.9260 (mt) cc_final: 0.8861 (mt) REVERT: A 722 LYS cc_start: 0.7040 (tttt) cc_final: 0.6767 (mttt) REVERT: A 735 ASN cc_start: 0.8090 (m-40) cc_final: 0.7861 (m110) REVERT: B 139 LEU cc_start: 0.9414 (mm) cc_final: 0.9143 (tp) REVERT: B 159 MET cc_start: 0.8526 (mmm) cc_final: 0.8263 (mmm) REVERT: B 185 GLU cc_start: 0.9025 (mp0) cc_final: 0.8348 (pm20) REVERT: B 220 ASN cc_start: 0.9192 (m-40) cc_final: 0.8812 (m-40) REVERT: B 320 MET cc_start: 0.8568 (ttm) cc_final: 0.8297 (ttp) REVERT: B 322 ASP cc_start: 0.8507 (t0) cc_final: 0.8034 (t70) REVERT: B 323 MET cc_start: 0.9133 (tmm) cc_final: 0.8920 (tmm) REVERT: B 327 ARG cc_start: 0.8588 (tpt170) cc_final: 0.8349 (tpt170) REVERT: B 351 MET cc_start: 0.9097 (mmt) cc_final: 0.8851 (mmm) REVERT: B 440 MET cc_start: 0.8574 (tpp) cc_final: 0.8121 (tpp) REVERT: B 461 TYR cc_start: 0.7233 (t80) cc_final: 0.6883 (t80) REVERT: B 506 PHE cc_start: 0.8932 (t80) cc_final: 0.8517 (m-80) REVERT: B 532 LEU cc_start: 0.9564 (mm) cc_final: 0.9174 (mm) REVERT: B 550 CYS cc_start: 0.8894 (p) cc_final: 0.8271 (t) REVERT: B 555 MET cc_start: 0.9048 (mtm) cc_final: 0.8245 (mtt) REVERT: B 652 ILE cc_start: 0.8650 (pt) cc_final: 0.8287 (mm) REVERT: B 682 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7751 (mm-30) REVERT: B 735 ASN cc_start: 0.8136 (m-40) cc_final: 0.7904 (m-40) REVERT: C 139 LEU cc_start: 0.9394 (mm) cc_final: 0.9113 (tp) REVERT: C 159 MET cc_start: 0.8514 (mmm) cc_final: 0.8261 (mmm) REVERT: C 185 GLU cc_start: 0.9043 (mp0) cc_final: 0.8370 (pm20) REVERT: C 220 ASN cc_start: 0.9207 (m-40) cc_final: 0.8984 (m-40) REVERT: C 244 HIS cc_start: 0.8625 (m-70) cc_final: 0.8400 (m-70) REVERT: C 414 ASP cc_start: 0.7933 (m-30) cc_final: 0.7161 (t0) REVERT: C 440 MET cc_start: 0.8596 (tpp) cc_final: 0.8176 (tpp) REVERT: C 461 TYR cc_start: 0.7234 (t80) cc_final: 0.6944 (t80) REVERT: C 506 PHE cc_start: 0.8946 (t80) cc_final: 0.8517 (m-80) REVERT: C 532 LEU cc_start: 0.9564 (mm) cc_final: 0.9199 (mm) REVERT: C 550 CYS cc_start: 0.8910 (p) cc_final: 0.8326 (t) REVERT: C 555 MET cc_start: 0.8790 (mtp) cc_final: 0.8320 (mtt) REVERT: C 565 TYR cc_start: 0.9269 (m-80) cc_final: 0.9012 (m-80) REVERT: C 652 ILE cc_start: 0.8762 (pt) cc_final: 0.8381 (mm) REVERT: C 682 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7815 (mm-30) REVERT: D 139 LEU cc_start: 0.9375 (mm) cc_final: 0.9105 (tp) REVERT: D 159 MET cc_start: 0.8501 (mmm) cc_final: 0.8247 (mmm) REVERT: D 185 GLU cc_start: 0.9031 (mp0) cc_final: 0.8361 (pm20) REVERT: D 220 ASN cc_start: 0.9220 (m-40) cc_final: 0.8976 (m-40) REVERT: D 244 HIS cc_start: 0.8667 (m-70) cc_final: 0.8423 (m-70) REVERT: D 320 MET cc_start: 0.8268 (ttm) cc_final: 0.8063 (ttp) REVERT: D 326 LEU cc_start: 0.9054 (mp) cc_final: 0.8848 (mp) REVERT: D 351 MET cc_start: 0.9115 (mmt) cc_final: 0.8852 (mmm) REVERT: D 440 MET cc_start: 0.8537 (tpp) cc_final: 0.8286 (tpp) REVERT: D 462 ARG cc_start: 0.6484 (mmt90) cc_final: 0.5626 (mtm110) REVERT: D 488 MET cc_start: 0.8845 (ttp) cc_final: 0.8529 (ttm) REVERT: D 506 PHE cc_start: 0.8948 (t80) cc_final: 0.8524 (m-80) REVERT: D 551 LEU cc_start: 0.9599 (tp) cc_final: 0.9330 (tp) REVERT: D 555 MET cc_start: 0.9118 (mtt) cc_final: 0.8693 (mtt) REVERT: D 585 HIS cc_start: 0.8559 (t-90) cc_final: 0.8312 (t-90) REVERT: D 591 LEU cc_start: 0.9067 (tp) cc_final: 0.8394 (tt) REVERT: D 595 ILE cc_start: 0.9275 (mt) cc_final: 0.8838 (mt) REVERT: D 677 MET cc_start: 0.8296 (mmm) cc_final: 0.7844 (tpp) REVERT: D 682 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7817 (mm-30) outliers start: 0 outliers final: 0 residues processed: 618 average time/residue: 0.1129 time to fit residues: 113.1569 Evaluate side-chains 482 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 158 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN C 735 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.078000 restraints weight = 60035.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.080497 restraints weight = 37073.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.082324 restraints weight = 26215.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.083506 restraints weight = 19958.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.084380 restraints weight = 16560.795| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21460 Z= 0.190 Angle : 0.759 8.129 29032 Z= 0.377 Chirality : 0.045 0.196 3308 Planarity : 0.004 0.048 3624 Dihedral : 5.302 22.441 2808 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.36 % Favored : 86.49 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2568 helix: 0.36 (0.13), residues: 1504 sheet: -3.26 (0.43), residues: 68 loop : -3.25 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 147 TYR 0.019 0.002 TYR B 359 PHE 0.022 0.002 PHE A 489 TRP 0.013 0.002 TRP A 380 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00425 (21460) covalent geometry : angle 0.75878 (29032) hydrogen bonds : bond 0.03498 ( 888) hydrogen bonds : angle 4.33037 ( 2580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 602 time to evaluate : 0.723 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: A 139 LEU cc_start: 0.9388 (mm) cc_final: 0.9102 (tp) REVERT: A 185 GLU cc_start: 0.9049 (mp0) cc_final: 0.8361 (pm20) REVERT: A 220 ASN cc_start: 0.9197 (m-40) cc_final: 0.8961 (m-40) REVERT: A 244 HIS cc_start: 0.8647 (m-70) cc_final: 0.8424 (m-70) REVERT: A 255 GLN cc_start: 0.8721 (pm20) cc_final: 0.8450 (pm20) REVERT: A 326 LEU cc_start: 0.9040 (mp) cc_final: 0.8817 (mp) REVERT: A 351 MET cc_start: 0.8962 (mmt) cc_final: 0.8488 (mmm) REVERT: A 440 MET cc_start: 0.8636 (tpp) cc_final: 0.8382 (tpp) REVERT: A 461 TYR cc_start: 0.7360 (t80) cc_final: 0.7029 (t80) REVERT: A 488 MET cc_start: 0.8844 (ttp) cc_final: 0.8540 (ttm) REVERT: A 506 PHE cc_start: 0.9022 (t80) cc_final: 0.8523 (m-80) REVERT: A 555 MET cc_start: 0.9067 (mtm) cc_final: 0.8324 (mtt) REVERT: A 565 TYR cc_start: 0.9235 (m-80) cc_final: 0.8599 (m-80) REVERT: A 585 HIS cc_start: 0.8524 (t-90) cc_final: 0.8244 (t-90) REVERT: A 591 LEU cc_start: 0.9081 (tp) cc_final: 0.8313 (tt) REVERT: A 595 ILE cc_start: 0.9333 (mt) cc_final: 0.8985 (mt) REVERT: B 139 LEU cc_start: 0.9398 (mm) cc_final: 0.9130 (tp) REVERT: B 159 MET cc_start: 0.8506 (mmm) cc_final: 0.8242 (mmm) REVERT: B 185 GLU cc_start: 0.9032 (mp0) cc_final: 0.8348 (pm20) REVERT: B 220 ASN cc_start: 0.9153 (m-40) cc_final: 0.8751 (m-40) REVERT: B 320 MET cc_start: 0.8577 (ttm) cc_final: 0.8241 (ttp) REVERT: B 351 MET cc_start: 0.9082 (mmt) cc_final: 0.8794 (mmm) REVERT: B 414 ASP cc_start: 0.8022 (m-30) cc_final: 0.7272 (t0) REVERT: B 440 MET cc_start: 0.8696 (tpp) cc_final: 0.8357 (tpp) REVERT: B 461 TYR cc_start: 0.7169 (t80) cc_final: 0.6823 (t80) REVERT: B 506 PHE cc_start: 0.9029 (t80) cc_final: 0.8529 (m-80) REVERT: B 532 LEU cc_start: 0.9587 (mm) cc_final: 0.9215 (mm) REVERT: B 550 CYS cc_start: 0.8893 (p) cc_final: 0.8294 (t) REVERT: B 555 MET cc_start: 0.9078 (mtm) cc_final: 0.8288 (mtt) REVERT: B 585 HIS cc_start: 0.8450 (t-90) cc_final: 0.8220 (t-90) REVERT: C 139 LEU cc_start: 0.9382 (mm) cc_final: 0.9112 (tp) REVERT: C 159 MET cc_start: 0.8545 (mmm) cc_final: 0.8282 (mmm) REVERT: C 185 GLU cc_start: 0.9050 (mp0) cc_final: 0.8367 (pm20) REVERT: C 220 ASN cc_start: 0.9190 (m-40) cc_final: 0.8851 (m-40) REVERT: C 244 HIS cc_start: 0.8554 (m-70) cc_final: 0.8342 (m-70) REVERT: C 271 CYS cc_start: 0.9468 (m) cc_final: 0.9250 (m) REVERT: C 322 ASP cc_start: 0.8485 (t0) cc_final: 0.8244 (t0) REVERT: C 327 ARG cc_start: 0.8653 (tpt170) cc_final: 0.8404 (tpt170) REVERT: C 353 LYS cc_start: 0.9677 (mmtt) cc_final: 0.9334 (mmtp) REVERT: C 414 ASP cc_start: 0.7978 (m-30) cc_final: 0.7189 (t0) REVERT: C 440 MET cc_start: 0.8672 (tpp) cc_final: 0.8246 (tpp) REVERT: C 461 TYR cc_start: 0.7197 (t80) cc_final: 0.6889 (t80) REVERT: C 506 PHE cc_start: 0.8968 (t80) cc_final: 0.8513 (m-80) REVERT: C 532 LEU cc_start: 0.9575 (mm) cc_final: 0.9207 (mm) REVERT: C 550 CYS cc_start: 0.8974 (p) cc_final: 0.8309 (t) REVERT: C 555 MET cc_start: 0.8799 (mtp) cc_final: 0.8320 (mtt) REVERT: C 565 TYR cc_start: 0.9327 (m-80) cc_final: 0.8859 (m-80) REVERT: C 585 HIS cc_start: 0.8404 (t-90) cc_final: 0.8163 (t-90) REVERT: C 588 LEU cc_start: 0.8976 (mm) cc_final: 0.8767 (tt) REVERT: C 682 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7835 (mm-30) REVERT: D 139 LEU cc_start: 0.9384 (mm) cc_final: 0.9104 (tp) REVERT: D 159 MET cc_start: 0.8558 (mmm) cc_final: 0.8290 (mmm) REVERT: D 176 LEU cc_start: 0.9645 (mm) cc_final: 0.9416 (mm) REVERT: D 185 GLU cc_start: 0.9034 (mp0) cc_final: 0.8363 (pm20) REVERT: D 220 ASN cc_start: 0.9152 (m-40) cc_final: 0.8806 (m-40) REVERT: D 323 MET cc_start: 0.9208 (tmm) cc_final: 0.8986 (tmm) REVERT: D 326 LEU cc_start: 0.9019 (mp) cc_final: 0.8764 (mp) REVERT: D 351 MET cc_start: 0.9108 (mmt) cc_final: 0.8822 (mmm) REVERT: D 488 MET cc_start: 0.8869 (ttp) cc_final: 0.8548 (ttm) REVERT: D 505 ILE cc_start: 0.9609 (pt) cc_final: 0.9339 (tt) REVERT: D 506 PHE cc_start: 0.9007 (t80) cc_final: 0.8498 (m-80) REVERT: D 532 LEU cc_start: 0.9542 (mm) cc_final: 0.9057 (mm) REVERT: D 550 CYS cc_start: 0.8992 (p) cc_final: 0.8303 (t) REVERT: D 551 LEU cc_start: 0.9597 (tp) cc_final: 0.9349 (tp) REVERT: D 555 MET cc_start: 0.9117 (mtt) cc_final: 0.8707 (mtt) REVERT: D 585 HIS cc_start: 0.8469 (t-90) cc_final: 0.8227 (t-90) REVERT: D 588 LEU cc_start: 0.8998 (mm) cc_final: 0.8797 (tt) REVERT: D 591 LEU cc_start: 0.9060 (tp) cc_final: 0.8249 (tt) REVERT: D 595 ILE cc_start: 0.9268 (mt) cc_final: 0.8844 (mt) REVERT: D 677 MET cc_start: 0.8292 (mmm) cc_final: 0.7874 (tpp) REVERT: D 682 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7844 (mm-30) outliers start: 0 outliers final: 0 residues processed: 602 average time/residue: 0.1205 time to fit residues: 119.2343 Evaluate side-chains 470 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 155 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 116 optimal weight: 0.0870 chunk 74 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 2.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 735 ASN B 244 HIS ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN C 292 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.078418 restraints weight = 59800.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.080560 restraints weight = 36742.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.082583 restraints weight = 26485.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083853 restraints weight = 20320.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.084916 restraints weight = 16765.451| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21460 Z= 0.170 Angle : 0.763 9.693 29032 Z= 0.375 Chirality : 0.044 0.293 3308 Planarity : 0.004 0.062 3624 Dihedral : 5.248 22.651 2808 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.81 % Favored : 87.03 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.17), residues: 2568 helix: 0.38 (0.13), residues: 1512 sheet: -3.20 (0.43), residues: 68 loop : -3.13 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 464 TYR 0.019 0.002 TYR B 359 PHE 0.018 0.001 PHE A 625 TRP 0.015 0.002 TRP B 481 HIS 0.004 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00384 (21460) covalent geometry : angle 0.76341 (29032) hydrogen bonds : bond 0.03424 ( 888) hydrogen bonds : angle 4.29727 ( 2580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5136 Ramachandran restraints generated. 2568 Oldfield, 0 Emsley, 2568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 599 time to evaluate : 0.616 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 139 LEU cc_start: 0.9401 (mm) cc_final: 0.9118 (tp) REVERT: A 159 MET cc_start: 0.8581 (mmt) cc_final: 0.8052 (mmm) REVERT: A 185 GLU cc_start: 0.9033 (mp0) cc_final: 0.8341 (pm20) REVERT: A 323 MET cc_start: 0.9264 (tmm) cc_final: 0.9060 (tmm) REVERT: A 326 LEU cc_start: 0.8961 (mp) cc_final: 0.8684 (mp) REVERT: A 351 MET cc_start: 0.9024 (mmt) cc_final: 0.8523 (mmm) REVERT: A 461 TYR cc_start: 0.7327 (t80) cc_final: 0.7030 (t80) REVERT: A 488 MET cc_start: 0.8835 (ttp) cc_final: 0.8527 (ttm) REVERT: A 506 PHE cc_start: 0.8996 (t80) cc_final: 0.8532 (m-80) REVERT: A 565 TYR cc_start: 0.9182 (m-80) cc_final: 0.8394 (m-80) REVERT: A 585 HIS cc_start: 0.8550 (t-90) cc_final: 0.8273 (t-90) REVERT: A 591 LEU cc_start: 0.9057 (tp) cc_final: 0.8439 (tt) REVERT: A 595 ILE cc_start: 0.9258 (mt) cc_final: 0.8942 (mt) REVERT: B 139 LEU cc_start: 0.9390 (mm) cc_final: 0.9146 (tp) REVERT: B 159 MET cc_start: 0.8617 (mmm) cc_final: 0.8340 (mmm) REVERT: B 185 GLU cc_start: 0.9028 (mp0) cc_final: 0.8352 (pm20) REVERT: B 220 ASN cc_start: 0.9166 (m-40) cc_final: 0.8763 (m-40) REVERT: B 320 MET cc_start: 0.8510 (ttm) cc_final: 0.8202 (ttp) REVERT: B 351 MET cc_start: 0.9091 (mmt) cc_final: 0.8817 (mmm) REVERT: B 410 ASN cc_start: 0.9168 (t0) cc_final: 0.8802 (t0) REVERT: B 414 ASP cc_start: 0.8047 (m-30) cc_final: 0.7294 (t0) REVERT: B 440 MET cc_start: 0.8703 (tpp) cc_final: 0.8345 (tpp) REVERT: B 461 TYR cc_start: 0.7135 (t80) cc_final: 0.6867 (t80) REVERT: B 506 PHE cc_start: 0.9024 (t80) cc_final: 0.8518 (m-80) REVERT: B 555 MET cc_start: 0.9068 (mtm) cc_final: 0.8294 (mtt) REVERT: B 585 HIS cc_start: 0.8458 (t-90) cc_final: 0.8216 (t-90) REVERT: B 688 SER cc_start: 0.8947 (t) cc_final: 0.8721 (t) REVERT: C 159 MET cc_start: 0.8609 (mmm) cc_final: 0.8346 (mmm) REVERT: C 185 GLU cc_start: 0.9042 (mp0) cc_final: 0.8361 (pm20) REVERT: C 220 ASN cc_start: 0.9118 (m-40) cc_final: 0.8851 (m-40) REVERT: C 244 HIS cc_start: 0.8580 (m-70) cc_final: 0.8309 (m-70) REVERT: C 271 CYS cc_start: 0.9451 (m) cc_final: 0.9228 (m) REVERT: C 414 ASP cc_start: 0.7999 (m-30) cc_final: 0.7135 (t0) REVERT: C 440 MET cc_start: 0.8749 (tpp) cc_final: 0.8348 (tpp) REVERT: C 461 TYR cc_start: 0.7236 (t80) cc_final: 0.6959 (t80) REVERT: C 506 PHE cc_start: 0.8978 (t80) cc_final: 0.8521 (m-80) REVERT: C 555 MET cc_start: 0.8810 (mtp) cc_final: 0.8322 (mtt) REVERT: C 565 TYR cc_start: 0.9344 (m-80) cc_final: 0.8840 (m-80) REVERT: C 574 MET cc_start: 0.8932 (tpp) cc_final: 0.8537 (tpp) REVERT: C 585 HIS cc_start: 0.8422 (t-90) cc_final: 0.8192 (t-90) REVERT: C 682 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7843 (mm-30) REVERT: D 159 MET cc_start: 0.8618 (mmm) cc_final: 0.8370 (mmm) REVERT: D 185 GLU cc_start: 0.9037 (mp0) cc_final: 0.8359 (pm20) REVERT: D 220 ASN cc_start: 0.9159 (m-40) cc_final: 0.8823 (m-40) REVERT: D 271 CYS cc_start: 0.9477 (m) cc_final: 0.9226 (m) REVERT: D 351 MET cc_start: 0.9103 (mmt) cc_final: 0.8797 (mmm) REVERT: D 462 ARG cc_start: 0.6637 (mmt90) cc_final: 0.5415 (ptm160) REVERT: D 488 MET cc_start: 0.8839 (ttp) cc_final: 0.8449 (ttm) REVERT: D 505 ILE cc_start: 0.9624 (pt) cc_final: 0.9314 (tt) REVERT: D 506 PHE cc_start: 0.8976 (t80) cc_final: 0.8482 (m-80) REVERT: D 532 LEU cc_start: 0.9550 (mm) cc_final: 0.9088 (mm) REVERT: D 550 CYS cc_start: 0.8969 (p) cc_final: 0.8255 (t) REVERT: D 551 LEU cc_start: 0.9594 (tp) cc_final: 0.9334 (tp) REVERT: D 555 MET cc_start: 0.9116 (mtt) cc_final: 0.8713 (mtt) REVERT: D 574 MET cc_start: 0.8933 (tpp) cc_final: 0.8504 (tpp) REVERT: D 585 HIS cc_start: 0.8484 (t-90) cc_final: 0.8199 (t-90) REVERT: D 591 LEU cc_start: 0.9053 (tp) cc_final: 0.8393 (tt) REVERT: D 595 ILE cc_start: 0.9277 (mt) cc_final: 0.8916 (mt) REVERT: D 677 MET cc_start: 0.8264 (mmm) cc_final: 0.7869 (tpp) REVERT: D 682 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7858 (mm-30) outliers start: 0 outliers final: 0 residues processed: 599 average time/residue: 0.1180 time to fit residues: 116.0989 Evaluate side-chains 484 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 223 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN B 244 HIS B 735 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 561 ASN D 735 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.097822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.079043 restraints weight = 59597.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.081475 restraints weight = 36351.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.083356 restraints weight = 25628.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.084584 restraints weight = 19614.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085628 restraints weight = 16207.473| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21460 Z= 0.153 Angle : 0.739 8.071 29032 Z= 0.363 Chirality : 0.043 0.243 3308 Planarity : 0.004 0.050 3624 Dihedral : 5.139 22.528 2808 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.19 % Favored : 87.66 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2568 helix: 0.42 (0.13), residues: 1512 sheet: -2.97 (0.46), residues: 68 loop : -3.05 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 464 TYR 0.019 0.001 TYR B 359 PHE 0.026 0.001 PHE D 524 TRP 0.012 0.001 TRP B 481 HIS 0.004 0.001 HIS D 523 Details of bonding type rmsd covalent geometry : bond 0.00342 (21460) covalent geometry : angle 0.73916 (29032) hydrogen bonds : bond 0.03383 ( 888) hydrogen bonds : angle 4.26458 ( 2580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3645.84 seconds wall clock time: 63 minutes 43.15 seconds (3823.15 seconds total)