Starting phenix.real_space_refine on Wed Nov 19 04:50:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pvl_20492/11_2025/6pvl_20492.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvl_20492/11_2025/6pvl_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_20492/11_2025/6pvl_20492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvl_20492/11_2025/6pvl_20492.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pvl_20492/11_2025/6pvl_20492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvl_20492/11_2025/6pvl_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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21006 Number of models: 1 Model: "" Number of chains: 2 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: "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} Restraints were copied for chains: B, C, D Time building chain proxies: 5.71, per 1000 atoms: 0.27 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: 1.98 Conformation dependent library (CDL) restraints added in 926.9 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: 3.20 Time building geometry restraints manager: 2.52 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 20.220 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- 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 : 0.836 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: 0.8791 (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: 0.8035 (mmt) REVERT: A 704 GLU cc_start: 0.8644 (mm-30) cc_final: 0.7997 (tp30) REVERT: A 728 PHE cc_start: 0.7573 (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: 0.8879 (tpp) cc_final: 0.8518 (tpp) REVERT: B 322 ASP cc_start: 0.8900 (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: 0.8928 (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: 0.8639 (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: 0.7621 (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: 0.6784 (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: 0.7639 (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: 0.7757 (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: 0.8920 (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: 0.7579 (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: 0.1537 time to fit residues: 200.3338 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 : 0.844 ------------------------------------------------------------------------------- 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 = 0.082223 restraints weight = 36103.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084076 restraints weight = 24826.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.085382 restraints weight = 19101.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.086473 restraints weight = 15378.701| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.846 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: A 139 LEU cc_start: 0.9280 (mm) cc_final: 0.9018 (tp) REVERT: A 173 MET cc_start: 0.8358 (mmt) cc_final: 0.8111 (mmt) REVERT: A 185 GLU cc_start: 0.9015 (mp0) cc_final: 0.8361 (pm20) REVERT: A 220 ASN cc_start: 0.9131 (m-40) cc_final: 0.8742 (m-40) REVERT: A 290 THR cc_start: 0.9377 (m) cc_final: 0.9127 (p) REVERT: A 322 ASP cc_start: 0.8806 (t0) cc_final: 0.8198 (t0) REVERT: A 323 MET cc_start: 0.8925 (ttm) cc_final: 0.8561 (tmm) REVERT: A 326 LEU cc_start: 0.9146 (mp) cc_final: 0.8941 (mp) REVERT: A 351 MET cc_start: 0.9062 (mmt) cc_final: 0.8817 (mmm) REVERT: A 414 ASP cc_start: 0.7714 (m-30) cc_final: 0.6916 (t0) REVERT: A 439 TYR cc_start: 0.8903 (m-80) cc_final: 0.8607 (m-10) REVERT: A 452 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8308 (t0) REVERT: A 461 TYR cc_start: 0.6989 (t80) cc_final: 0.6742 (t80) REVERT: A 501 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7930 (tp30) REVERT: A 506 PHE cc_start: 0.8985 (t80) cc_final: 0.8553 (m-80) REVERT: A 565 TYR cc_start: 0.9186 (m-80) cc_final: 0.8968 (m-80) REVERT: A 567 ARG cc_start: 0.8369 (mtt180) cc_final: 0.7804 (mtm-85) REVERT: A 591 LEU cc_start: 0.8903 (tp) cc_final: 0.8476 (tt) REVERT: A 595 ILE cc_start: 0.9315 (mt) cc_final: 0.9082 (mt) REVERT: A 677 MET cc_start: 0.8344 (mmm) cc_final: 0.7937 (tpp) REVERT: A 688 SER cc_start: 0.8916 (t) cc_final: 0.8573 (t) REVERT: A 699 THR cc_start: 0.9677 (p) cc_final: 0.9376 (t) REVERT: A 704 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8203 (tp30) REVERT: A 717 MET cc_start: 0.7980 (tpp) cc_final: 0.7431 (tmm) REVERT: A 728 PHE cc_start: 0.7678 (m-80) cc_final: 0.7268 (m-80) REVERT: A 742 TRP cc_start: 0.7214 (m-90) cc_final: 0.6907 (m-90) REVERT: A 752 ASP cc_start: 0.8047 (t0) cc_final: 0.7623 (t0) REVERT: B 139 LEU cc_start: 0.9290 (mm) cc_final: 0.9031 (tp) REVERT: B 185 GLU cc_start: 0.8993 (mp0) cc_final: 0.8287 (pm20) REVERT: B 220 ASN cc_start: 0.9148 (m-40) cc_final: 0.8762 (m-40) REVERT: B 290 THR cc_start: 0.9369 (m) cc_final: 0.9122 (p) REVERT: B 322 ASP cc_start: 0.8853 (t0) cc_final: 0.8217 (t0) REVERT: B 323 MET cc_start: 0.8959 (ttm) cc_final: 0.8627 (tmm) REVERT: B 326 LEU cc_start: 0.9144 (mp) cc_final: 0.8929 (mp) REVERT: B 351 MET cc_start: 0.9041 (mmt) cc_final: 0.8801 (mmm) REVERT: B 414 ASP cc_start: 0.7948 (m-30) cc_final: 0.7034 (t0) REVERT: B 439 TYR cc_start: 0.8913 (m-80) cc_final: 0.8628 (m-10) REVERT: B 452 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8393 (t0) REVERT: B 461 TYR cc_start: 0.6962 (t80) cc_final: 0.6733 (t80) REVERT: B 501 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7948 (tp30) REVERT: B 506 PHE cc_start: 0.8986 (t80) cc_final: 0.8536 (m-80) REVERT: B 519 ASP cc_start: 0.8442 (m-30) cc_final: 0.8096 (m-30) REVERT: B 567 ARG cc_start: 0.8333 (mtt180) cc_final: 0.7934 (mtt90) REVERT: B 591 LEU cc_start: 0.8884 (tp) cc_final: 0.8510 (tt) REVERT: B 677 MET cc_start: 0.8371 (mmm) cc_final: 0.8040 (tpp) REVERT: B 682 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 688 SER cc_start: 0.8974 (t) cc_final: 0.8510 (t) REVERT: B 699 THR cc_start: 0.9674 (p) cc_final: 0.9436 (t) REVERT: B 704 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8208 (tp30) REVERT: B 717 MET cc_start: 0.7940 (tpp) cc_final: 0.7404 (tmm) REVERT: B 728 PHE cc_start: 0.7632 (m-80) cc_final: 0.7222 (m-80) REVERT: B 742 TRP cc_start: 0.7170 (m-90) cc_final: 0.6951 (m-90) REVERT: C 139 LEU cc_start: 0.9293 (mm) cc_final: 0.9046 (tp) REVERT: C 185 GLU cc_start: 0.9003 (mp0) cc_final: 0.8291 (pm20) REVERT: C 220 ASN cc_start: 0.9132 (m-40) cc_final: 0.8736 (m-40) REVERT: C 256 HIS cc_start: 0.6944 (p90) cc_final: 0.6204 (p90) REVERT: C 290 THR cc_start: 0.9380 (m) cc_final: 0.9138 (p) REVERT: C 322 ASP cc_start: 0.8847 (t0) cc_final: 0.8210 (t0) REVERT: C 323 MET cc_start: 0.8958 (ttm) cc_final: 0.8645 (tmm) REVERT: C 326 LEU cc_start: 0.9140 (mp) cc_final: 0.8932 (mp) REVERT: C 351 MET cc_start: 0.9051 (mmt) cc_final: 0.8792 (mmm) REVERT: C 414 ASP cc_start: 0.7912 (m-30) cc_final: 0.7029 (t0) REVERT: C 439 TYR cc_start: 0.8910 (m-80) cc_final: 0.8633 (m-10) REVERT: C 452 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8366 (t0) REVERT: C 461 TYR cc_start: 0.6998 (t80) cc_final: 0.6758 (t80) REVERT: C 501 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7942 (tp30) REVERT: C 506 PHE cc_start: 0.8976 (t80) cc_final: 0.8542 (m-80) REVERT: C 567 ARG cc_start: 0.8313 (mtt180) cc_final: 0.7743 (mtm-85) REVERT: C 591 LEU cc_start: 0.8867 (tp) cc_final: 0.8514 (tt) REVERT: C 677 MET cc_start: 0.8369 (mmm) cc_final: 0.8055 (tpp) REVERT: C 688 SER cc_start: 0.9002 (t) cc_final: 0.8532 (t) REVERT: C 699 THR cc_start: 0.9667 (p) cc_final: 0.9371 (t) REVERT: C 704 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8222 (tp30) REVERT: C 717 MET cc_start: 0.7943 (tpp) cc_final: 0.7402 (tmm) REVERT: C 728 PHE cc_start: 0.7669 (m-80) cc_final: 0.7234 (m-80) REVERT: C 742 TRP cc_start: 0.7170 (m-90) cc_final: 0.6918 (m-90) REVERT: D 139 LEU cc_start: 0.9304 (mm) cc_final: 0.9051 (tp) REVERT: D 185 GLU cc_start: 0.9020 (mp0) cc_final: 0.8287 (pm20) REVERT: D 220 ASN cc_start: 0.9150 (m-40) cc_final: 0.8743 (m-40) REVERT: D 256 HIS cc_start: 0.6968 (p90) cc_final: 0.6191 (p90) REVERT: D 282 MET cc_start: 0.8743 (tpp) cc_final: 0.8539 (tpp) REVERT: D 290 THR cc_start: 0.9385 (m) cc_final: 0.9158 (p) REVERT: D 322 ASP cc_start: 0.8830 (t0) cc_final: 0.8199 (t0) REVERT: D 323 MET cc_start: 0.8962 (ttm) cc_final: 0.8634 (tmm) REVERT: D 326 LEU cc_start: 0.9143 (mp) cc_final: 0.8901 (mp) REVERT: D 351 MET cc_start: 0.9077 (mmt) cc_final: 0.8816 (mmm) REVERT: D 414 ASP cc_start: 0.7927 (m-30) cc_final: 0.7024 (t0) REVERT: D 439 TYR cc_start: 0.8896 (m-80) cc_final: 0.8600 (m-10) REVERT: D 440 MET cc_start: 0.8285 (tpp) cc_final: 0.7675 (tpp) REVERT: D 452 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8366 (t0) REVERT: D 501 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7921 (tp30) REVERT: D 506 PHE cc_start: 0.8975 (t80) cc_final: 0.8571 (m-80) REVERT: D 519 ASP cc_start: 0.8467 (m-30) cc_final: 0.8079 (m-30) REVERT: D 532 LEU cc_start: 0.9626 (mt) cc_final: 0.9353 (mm) REVERT: D 550 CYS cc_start: 0.8862 (p) cc_final: 0.8068 (t) REVERT: D 567 ARG cc_start: 0.8345 (mtt180) cc_final: 0.7948 (mtt90) REVERT: D 591 LEU cc_start: 0.8874 (tp) cc_final: 0.8516 (tt) REVERT: D 595 ILE cc_start: 0.9309 (mt) cc_final: 0.9102 (mt) REVERT: D 677 MET cc_start: 0.8346 (mmm) cc_final: 0.8032 (tpp) REVERT: D 688 SER cc_start: 0.9010 (t) cc_final: 0.8520 (t) REVERT: D 699 THR cc_start: 0.9675 (p) cc_final: 0.9444 (t) REVERT: D 704 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8131 (tp30) REVERT: D 717 MET cc_start: 0.7911 (tpp) cc_final: 0.7330 (tmm) REVERT: D 728 PHE cc_start: 0.7652 (m-80) cc_final: 0.7192 (m-80) REVERT: D 742 TRP cc_start: 0.7170 (m-90) cc_final: 0.6944 (m-90) outliers start: 4 outliers final: 0 residues processed: 764 average time/residue: 0.1427 time to fit residues: 174.2204 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 : 0.908 ------------------------------------------------------------------------------- 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: 7.9990 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 = 0.3366 r_free = 0.3366 target = 0.101490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.083711 restraints weight = 59023.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.086155 restraints weight = 35407.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.088005 restraints weight = 24154.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.089263 restraints weight = 18316.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.090269 restraints weight = 14972.886| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21460 Z= 0.127 Angle : 0.687 8.517 29032 Z= 0.342 Chirality : 0.041 0.178 3308 Planarity : 0.004 0.054 3624 Dihedral : 5.660 32.861 2808 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.95 % Favored : 87.89 % Rotamer: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % 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: -2.77 (0.15), residues: 2568 helix: -0.70 (0.12), residues: 1472 sheet: -3.40 (0.46), residues: 68 loop : -3.48 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 118 TYR 0.013 0.001 TYR D 382 PHE 0.010 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 0.00265 (21460) covalent geometry : angle 0.68713 (29032) hydrogen bonds : bond 0.03670 ( 888) hydrogen bonds : angle 4.33660 ( 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 : 0.824 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: A 139 LEU cc_start: 0.9326 (mm) cc_final: 0.8994 (tp) REVERT: A 160 HIS cc_start: 0.8054 (t70) cc_final: 0.7829 (t-90) REVERT: A 176 LEU cc_start: 0.9660 (mm) cc_final: 0.9455 (mm) REVERT: A 185 GLU cc_start: 0.8997 (mp0) cc_final: 0.8363 (pm20) REVERT: A 220 ASN cc_start: 0.9067 (m-40) cc_final: 0.8666 (m-40) REVERT: A 322 ASP cc_start: 0.8963 (t0) cc_final: 0.8693 (t70) REVERT: A 351 MET cc_start: 0.9101 (mmt) cc_final: 0.8855 (mmm) REVERT: A 414 ASP cc_start: 0.7922 (m-30) cc_final: 0.7092 (t0) REVERT: A 440 MET cc_start: 0.8188 (tpp) cc_final: 0.7711 (tpp) REVERT: A 461 TYR cc_start: 0.7175 (t80) cc_final: 0.6798 (t80) REVERT: A 471 HIS cc_start: 0.7322 (p90) cc_final: 0.6973 (p90) REVERT: A 501 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8102 (tp30) REVERT: A 506 PHE cc_start: 0.8871 (t80) cc_final: 0.8523 (m-80) REVERT: A 555 MET cc_start: 0.9118 (mtm) cc_final: 0.8522 (mpp) REVERT: A 561 ASN cc_start: 0.8627 (m110) cc_final: 0.8186 (m110) REVERT: A 567 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8378 (mtt180) REVERT: A 572 MET cc_start: 0.8487 (tmm) cc_final: 0.8164 (tmm) REVERT: A 585 HIS cc_start: 0.8080 (t-90) cc_final: 0.7717 (t-90) REVERT: A 595 ILE cc_start: 0.9215 (mt) cc_final: 0.8998 (mt) REVERT: A 677 MET cc_start: 0.8249 (mmm) cc_final: 0.7888 (tpp) REVERT: A 699 THR cc_start: 0.9626 (p) cc_final: 0.9310 (t) REVERT: A 717 MET cc_start: 0.7761 (tpp) cc_final: 0.7543 (tmm) REVERT: B 139 LEU cc_start: 0.9367 (mm) cc_final: 0.9057 (tp) REVERT: B 176 LEU cc_start: 0.9650 (mm) cc_final: 0.9435 (mm) REVERT: B 185 GLU cc_start: 0.9004 (mp0) cc_final: 0.8337 (pm20) REVERT: B 220 ASN cc_start: 0.9014 (m-40) cc_final: 0.8602 (m-40) REVERT: B 256 HIS cc_start: 0.6698 (p-80) cc_final: 0.6164 (p-80) REVERT: B 290 THR cc_start: 0.9309 (m) cc_final: 0.9091 (p) REVERT: B 308 GLU cc_start: 0.6309 (pm20) cc_final: 0.6079 (pm20) REVERT: B 322 ASP cc_start: 0.8954 (t0) cc_final: 0.8263 (t70) REVERT: B 351 MET cc_start: 0.9123 (mmt) cc_final: 0.8854 (mmm) REVERT: B 414 ASP cc_start: 0.7889 (m-30) cc_final: 0.7050 (t0) REVERT: B 440 MET cc_start: 0.8201 (tpp) cc_final: 0.7760 (tpp) REVERT: B 461 TYR cc_start: 0.7122 (t80) cc_final: 0.6769 (t80) REVERT: B 471 HIS cc_start: 0.7377 (p90) cc_final: 0.7052 (p90) REVERT: B 501 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8049 (tp30) REVERT: B 505 ILE cc_start: 0.9485 (pt) cc_final: 0.9108 (tt) REVERT: B 506 PHE cc_start: 0.8878 (t80) cc_final: 0.8479 (m-80) REVERT: B 517 LEU cc_start: 0.9291 (pt) cc_final: 0.9084 (pt) REVERT: B 555 MET cc_start: 0.9083 (mtm) cc_final: 0.8508 (mpp) REVERT: B 561 ASN cc_start: 0.8605 (m110) cc_final: 0.8182 (m110) REVERT: B 572 MET cc_start: 0.8422 (tmm) cc_final: 0.8105 (tmm) REVERT: B 585 HIS cc_start: 0.8229 (t-90) cc_final: 0.7923 (t-90) REVERT: B 677 MET cc_start: 0.8266 (mmm) cc_final: 0.7897 (tpp) REVERT: B 699 THR cc_start: 0.9639 (p) cc_final: 0.9426 (t) REVERT: C 139 LEU cc_start: 0.9378 (mm) cc_final: 0.9060 (tp) REVERT: C 160 HIS cc_start: 0.8030 (t70) cc_final: 0.7811 (t-90) REVERT: C 185 GLU cc_start: 0.8979 (mp0) cc_final: 0.8267 (pm20) REVERT: C 220 ASN cc_start: 0.9029 (m-40) cc_final: 0.8621 (m-40) REVERT: C 322 ASP cc_start: 0.8935 (t0) cc_final: 0.8239 (t70) REVERT: C 351 MET cc_start: 0.9115 (mmt) cc_final: 0.8866 (mmm) REVERT: C 414 ASP cc_start: 0.7894 (m-30) cc_final: 0.7015 (t0) REVERT: C 440 MET cc_start: 0.8194 (tpp) cc_final: 0.7802 (tpp) REVERT: C 461 TYR cc_start: 0.7143 (t80) cc_final: 0.6781 (t80) REVERT: C 471 HIS cc_start: 0.7358 (p90) cc_final: 0.7017 (p90) REVERT: C 501 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8074 (tp30) REVERT: C 505 ILE cc_start: 0.9468 (pt) cc_final: 0.9106 (tt) REVERT: C 506 PHE cc_start: 0.8864 (t80) cc_final: 0.8485 (m-80) REVERT: C 555 MET cc_start: 0.8826 (mtp) cc_final: 0.8332 (mtt) REVERT: C 561 ASN cc_start: 0.8626 (m110) cc_final: 0.8252 (m110) REVERT: C 567 ARG cc_start: 0.8846 (mtt180) cc_final: 0.8456 (mtt180) REVERT: C 585 HIS cc_start: 0.8205 (t-90) cc_final: 0.7912 (t-90) REVERT: C 677 MET cc_start: 0.8238 (mmm) cc_final: 0.7927 (tpp) REVERT: C 699 THR cc_start: 0.9626 (p) cc_final: 0.9381 (t) REVERT: C 717 MET cc_start: 0.7710 (tpp) cc_final: 0.7504 (tmm) REVERT: D 139 LEU cc_start: 0.9372 (mm) cc_final: 0.9064 (tp) REVERT: D 160 HIS cc_start: 0.8031 (t70) cc_final: 0.7800 (t-90) REVERT: D 185 GLU cc_start: 0.8967 (mp0) cc_final: 0.8264 (pm20) REVERT: D 220 ASN cc_start: 0.9065 (m-40) cc_final: 0.8648 (m-40) REVERT: D 308 GLU cc_start: 0.6270 (pm20) cc_final: 0.6053 (pm20) REVERT: D 322 ASP cc_start: 0.8935 (t0) cc_final: 0.8249 (t70) REVERT: D 351 MET cc_start: 0.9144 (mmt) cc_final: 0.8860 (mmm) REVERT: D 414 ASP cc_start: 0.7893 (m-30) cc_final: 0.7014 (t0) REVERT: D 440 MET cc_start: 0.8167 (tpp) cc_final: 0.7697 (tpp) REVERT: D 471 HIS cc_start: 0.7429 (p90) cc_final: 0.7046 (p90) REVERT: D 501 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8093 (tp30) REVERT: D 506 PHE cc_start: 0.8860 (t80) cc_final: 0.8542 (m-80) REVERT: D 517 LEU cc_start: 0.9273 (pt) cc_final: 0.9057 (pt) REVERT: D 532 LEU cc_start: 0.9592 (mt) cc_final: 0.9270 (mm) REVERT: D 550 CYS cc_start: 0.8815 (p) cc_final: 0.8174 (t) REVERT: D 561 ASN cc_start: 0.8649 (m110) cc_final: 0.8239 (m110) REVERT: D 585 HIS cc_start: 0.8224 (t-90) cc_final: 0.7891 (t-90) REVERT: D 595 ILE cc_start: 0.9216 (mt) cc_final: 0.9002 (mt) REVERT: D 677 MET cc_start: 0.8305 (mmm) cc_final: 0.8074 (tpp) REVERT: D 699 THR cc_start: 0.9633 (p) cc_final: 0.9422 (t) REVERT: D 717 MET cc_start: 0.7747 (tpp) cc_final: 0.7512 (tmm) outliers start: 1 outliers final: 0 residues processed: 745 average time/residue: 0.1331 time to fit residues: 162.2204 Evaluate side-chains 558 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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: 7.9990 chunk 207 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 255 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.082741 restraints weight = 59517.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085370 restraints weight = 36505.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087244 restraints weight = 25412.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088285 restraints weight = 19455.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.089403 restraints weight = 16052.287| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5105 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= 0.125 Angle : 0.682 7.349 29032 Z= 0.340 Chirality : 0.041 0.187 3308 Planarity : 0.004 0.049 3624 Dihedral : 5.375 29.424 2808 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.76 % Favored : 88.08 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % 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: -2.27 (0.16), residues: 2568 helix: -0.16 (0.13), residues: 1476 sheet: -3.10 (0.47), residues: 68 loop : -3.50 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 464 TYR 0.013 0.001 TYR A 359 PHE 0.011 0.001 PHE D 666 TRP 0.009 0.001 TRP C 692 HIS 0.011 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00262 (21460) covalent geometry : angle 0.68231 (29032) hydrogen bonds : bond 0.03360 ( 888) hydrogen bonds : angle 4.18423 ( 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 680 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 680 time to evaluate : 0.829 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: 0.9406 (mm) cc_final: 0.8944 (pp) REVERT: A 220 ASN cc_start: 0.9020 (m-40) cc_final: 0.8676 (m-40) REVERT: A 320 MET cc_start: 0.8557 (ttm) cc_final: 0.8138 (ttp) REVERT: A 322 ASP cc_start: 0.8947 (t0) cc_final: 0.8049 (t70) REVERT: A 351 MET cc_start: 0.9087 (mmt) cc_final: 0.8872 (mmm) REVERT: A 440 MET cc_start: 0.8274 (tpp) cc_final: 0.7840 (tpp) REVERT: A 461 TYR cc_start: 0.7207 (t80) cc_final: 0.6810 (t80) REVERT: A 506 PHE cc_start: 0.8881 (t80) cc_final: 0.8524 (m-80) REVERT: A 519 ASP cc_start: 0.8603 (m-30) cc_final: 0.8129 (m-30) REVERT: A 555 MET cc_start: 0.9092 (mtm) cc_final: 0.8400 (mtt) REVERT: A 585 HIS cc_start: 0.8174 (t-90) cc_final: 0.7847 (t-90) REVERT: A 591 LEU cc_start: 0.8844 (tp) cc_final: 0.8633 (tt) REVERT: A 677 MET cc_start: 0.8163 (mmm) cc_final: 0.7864 (tpp) REVERT: A 699 THR cc_start: 0.9683 (p) cc_final: 0.9457 (t) REVERT: B 139 LEU cc_start: 0.9388 (mm) cc_final: 0.9050 (tp) REVERT: B 220 ASN cc_start: 0.9009 (m-40) cc_final: 0.8635 (m-40) REVERT: B 256 HIS cc_start: 0.6683 (p-80) cc_final: 0.6339 (p-80) REVERT: B 320 MET cc_start: 0.8689 (ttm) cc_final: 0.8319 (ttp) REVERT: B 322 ASP cc_start: 0.8855 (t0) cc_final: 0.8093 (t0) REVERT: B 351 MET cc_start: 0.9090 (mmt) cc_final: 0.8889 (mmm) REVERT: B 440 MET cc_start: 0.8346 (tpp) cc_final: 0.7807 (tpp) REVERT: B 461 TYR cc_start: 0.7173 (t80) cc_final: 0.6794 (t80) REVERT: B 506 PHE cc_start: 0.8881 (t80) cc_final: 0.8518 (m-80) REVERT: B 555 MET cc_start: 0.9093 (mtm) cc_final: 0.8871 (mtm) REVERT: B 585 HIS cc_start: 0.8332 (t-90) cc_final: 0.8087 (t-90) REVERT: B 677 MET cc_start: 0.8299 (mmm) cc_final: 0.8016 (tpp) REVERT: B 682 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7809 (mm-30) REVERT: B 699 THR cc_start: 0.9735 (p) cc_final: 0.9509 (t) REVERT: C 139 LEU cc_start: 0.9366 (mm) cc_final: 0.9017 (tp) REVERT: C 185 GLU cc_start: 0.8988 (mp0) cc_final: 0.8348 (pm20) REVERT: C 220 ASN cc_start: 0.9023 (m-40) cc_final: 0.8679 (m-40) REVERT: C 255 GLN cc_start: 0.8599 (pm20) cc_final: 0.8083 (pp30) REVERT: C 256 HIS cc_start: 0.7015 (p-80) cc_final: 0.5388 (p-80) REVERT: C 320 MET cc_start: 0.8721 (ttm) cc_final: 0.8351 (ttp) REVERT: C 322 ASP cc_start: 0.8856 (t0) cc_final: 0.8069 (t0) REVERT: C 351 MET cc_start: 0.9106 (mmt) cc_final: 0.8887 (mmm) REVERT: C 440 MET cc_start: 0.8347 (tpp) cc_final: 0.7844 (tpp) REVERT: C 461 TYR cc_start: 0.7191 (t80) cc_final: 0.6813 (t80) REVERT: C 506 PHE cc_start: 0.8894 (t80) cc_final: 0.8527 (m-80) REVERT: C 519 ASP cc_start: 0.8625 (m-30) cc_final: 0.8157 (m-30) REVERT: C 551 LEU cc_start: 0.9532 (tp) cc_final: 0.9309 (tp) REVERT: C 555 MET cc_start: 0.8809 (mtp) cc_final: 0.8277 (mtt) REVERT: C 585 HIS cc_start: 0.8331 (t-90) cc_final: 0.8115 (t-90) REVERT: C 677 MET cc_start: 0.8253 (mmm) cc_final: 0.8016 (tpp) REVERT: C 682 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7784 (mm-30) REVERT: C 699 THR cc_start: 0.9683 (p) cc_final: 0.9465 (t) REVERT: D 139 LEU cc_start: 0.9366 (mm) cc_final: 0.9016 (tp) REVERT: D 185 GLU cc_start: 0.8978 (mp0) cc_final: 0.8294 (pm20) REVERT: D 220 ASN cc_start: 0.9040 (m-40) cc_final: 0.8677 (m-40) REVERT: D 255 GLN cc_start: 0.8588 (pm20) cc_final: 0.8049 (pp30) REVERT: D 256 HIS cc_start: 0.6982 (p-80) cc_final: 0.5392 (p-80) REVERT: D 320 MET cc_start: 0.8687 (ttm) cc_final: 0.8319 (ttp) REVERT: D 322 ASP cc_start: 0.8842 (t0) cc_final: 0.8095 (t0) REVERT: D 351 MET cc_start: 0.9084 (mmt) cc_final: 0.8856 (mmm) REVERT: D 414 ASP cc_start: 0.7971 (m-30) cc_final: 0.7042 (t0) REVERT: D 440 MET cc_start: 0.8347 (tpp) cc_final: 0.7797 (tpp) REVERT: D 506 PHE cc_start: 0.8901 (t80) cc_final: 0.8540 (m-80) REVERT: D 532 LEU cc_start: 0.9588 (mt) cc_final: 0.9357 (mm) REVERT: D 550 CYS cc_start: 0.8885 (p) cc_final: 0.8253 (t) REVERT: D 585 HIS cc_start: 0.8343 (t-90) cc_final: 0.8098 (t-90) REVERT: D 591 LEU cc_start: 0.8840 (tp) cc_final: 0.8408 (tt) REVERT: D 595 ILE cc_start: 0.9171 (mt) cc_final: 0.8903 (mt) REVERT: D 677 MET cc_start: 0.8215 (mmm) cc_final: 0.8006 (tpp) REVERT: D 682 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7557 (mm-30) REVERT: D 699 THR cc_start: 0.9717 (p) cc_final: 0.9508 (t) outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.1287 time to fit residues: 144.0924 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 : 0.847 ------------------------------------------------------------------------------- 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: 3.9990 chunk 142 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 GLN A 735 ASN B 273 ASN B 452 ASN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 735 ASN ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 695 GLN C 735 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN D 452 ASN ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN D 735 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.097012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.078112 restraints weight = 60054.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.080493 restraints weight = 36990.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.081807 restraints weight = 26228.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083404 restraints weight = 20974.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084318 restraints weight = 17094.946| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21460 Z= 0.180 Angle : 0.721 8.155 29032 Z= 0.364 Chirality : 0.043 0.186 3308 Planarity : 0.004 0.050 3624 Dihedral : 5.447 24.982 2808 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.31 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: -1.97 (0.16), residues: 2568 helix: 0.16 (0.13), residues: 1484 sheet: -3.34 (0.45), residues: 68 loop : -3.52 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 567 TYR 0.017 0.002 TYR D 565 PHE 0.020 0.001 PHE C 489 TRP 0.018 0.001 TRP C 742 HIS 0.009 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00394 (21460) covalent geometry : angle 0.72135 (29032) hydrogen bonds : bond 0.03501 ( 888) hydrogen bonds : angle 4.32619 ( 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 634 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 0.905 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: 0.9388 (mm) cc_final: 0.9149 (tp) REVERT: A 159 MET cc_start: 0.8557 (mmm) cc_final: 0.8293 (mmm) REVERT: A 185 GLU cc_start: 0.9056 (mp0) cc_final: 0.8389 (pm20) REVERT: A 220 ASN cc_start: 0.9146 (m-40) cc_final: 0.8743 (m-40) REVERT: A 244 HIS cc_start: 0.8793 (m-70) cc_final: 0.8513 (m-70) REVERT: A 256 HIS cc_start: 0.6839 (p-80) cc_final: 0.6579 (p-80) REVERT: A 320 MET cc_start: 0.8597 (ttm) cc_final: 0.8359 (ttp) REVERT: A 322 ASP cc_start: 0.8890 (t0) cc_final: 0.8084 (t0) REVERT: A 351 MET cc_start: 0.9062 (mmt) cc_final: 0.8825 (mmm) REVERT: A 440 MET cc_start: 0.8502 (tpp) cc_final: 0.8038 (tpp) REVERT: A 461 TYR cc_start: 0.7252 (t80) cc_final: 0.6949 (t80) REVERT: A 506 PHE cc_start: 0.8936 (t80) cc_final: 0.8469 (m-80) REVERT: A 555 MET cc_start: 0.9112 (mtm) cc_final: 0.8353 (mtt) REVERT: A 567 ARG cc_start: 0.8500 (mtt180) cc_final: 0.7924 (mtt90) REVERT: A 572 MET cc_start: 0.8604 (tmm) cc_final: 0.8340 (tmm) REVERT: A 585 HIS cc_start: 0.8366 (t-90) cc_final: 0.8097 (t-90) REVERT: A 677 MET cc_start: 0.8289 (mmm) cc_final: 0.8048 (tpp) REVERT: A 695 GLN cc_start: 0.8678 (tt0) cc_final: 0.8472 (tt0) REVERT: A 699 THR cc_start: 0.9758 (p) cc_final: 0.9433 (t) REVERT: A 715 PHE cc_start: 0.7884 (t80) cc_final: 0.7639 (t80) REVERT: A 717 MET cc_start: 0.7954 (tmm) cc_final: 0.7698 (tmm) REVERT: A 722 LYS cc_start: 0.7060 (mttt) cc_final: 0.6730 (tttt) REVERT: B 139 LEU cc_start: 0.9409 (mm) cc_final: 0.9092 (tp) REVERT: B 159 MET cc_start: 0.8615 (mmm) cc_final: 0.8349 (mmm) REVERT: B 185 GLU cc_start: 0.9040 (mp0) cc_final: 0.8294 (pm20) REVERT: B 220 ASN cc_start: 0.9148 (m-40) cc_final: 0.8755 (m-40) REVERT: B 256 HIS cc_start: 0.6858 (p-80) cc_final: 0.6429 (p-80) REVERT: B 320 MET cc_start: 0.8656 (ttm) cc_final: 0.8176 (ttp) REVERT: B 322 ASP cc_start: 0.8834 (t0) cc_final: 0.8219 (t0) REVERT: B 351 MET cc_start: 0.9081 (mmt) cc_final: 0.8834 (mmm) REVERT: B 440 MET cc_start: 0.8461 (tpp) cc_final: 0.7956 (tpp) REVERT: B 461 TYR cc_start: 0.7240 (t80) cc_final: 0.6950 (t80) REVERT: B 506 PHE cc_start: 0.8938 (t80) cc_final: 0.8453 (m-80) REVERT: B 555 MET cc_start: 0.9097 (mtm) cc_final: 0.8342 (mtt) REVERT: B 567 ARG cc_start: 0.8283 (mtm-85) cc_final: 0.7871 (mpt-90) REVERT: B 677 MET cc_start: 0.8248 (mmm) cc_final: 0.8012 (tpp) REVERT: B 682 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 699 THR cc_start: 0.9791 (p) cc_final: 0.9413 (t) REVERT: B 715 PHE cc_start: 0.7868 (t80) cc_final: 0.7618 (t80) REVERT: C 139 LEU cc_start: 0.9381 (mm) cc_final: 0.9061 (tp) REVERT: C 159 MET cc_start: 0.8593 (mmm) cc_final: 0.8333 (mmm) REVERT: C 185 GLU cc_start: 0.9029 (mp0) cc_final: 0.8297 (pm20) REVERT: C 220 ASN cc_start: 0.9159 (m-40) cc_final: 0.8775 (m-40) REVERT: C 244 HIS cc_start: 0.8750 (m-70) cc_final: 0.8473 (m-70) REVERT: C 320 MET cc_start: 0.8671 (ttm) cc_final: 0.8385 (ttp) REVERT: C 322 ASP cc_start: 0.8842 (t0) cc_final: 0.8306 (t0) REVERT: C 323 MET cc_start: 0.9077 (tmm) cc_final: 0.8853 (tmm) REVERT: C 326 LEU cc_start: 0.9119 (mp) cc_final: 0.8895 (pp) REVERT: C 351 MET cc_start: 0.9058 (mmt) cc_final: 0.8797 (mmm) REVERT: C 440 MET cc_start: 0.8487 (tpp) cc_final: 0.7963 (tpp) REVERT: C 461 TYR cc_start: 0.7245 (t80) cc_final: 0.6999 (t80) REVERT: C 506 PHE cc_start: 0.8985 (t80) cc_final: 0.8511 (m-80) REVERT: C 555 MET cc_start: 0.8819 (mtp) cc_final: 0.8321 (mtt) REVERT: C 567 ARG cc_start: 0.8542 (mtt180) cc_final: 0.8035 (mtt90) REVERT: C 572 MET cc_start: 0.8689 (tmm) cc_final: 0.8452 (tmm) REVERT: C 682 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7702 (mm-30) REVERT: C 699 THR cc_start: 0.9742 (p) cc_final: 0.9431 (t) REVERT: C 715 PHE cc_start: 0.7896 (t80) cc_final: 0.7671 (t80) REVERT: C 717 MET cc_start: 0.8007 (tmm) cc_final: 0.7765 (tmm) REVERT: D 139 LEU cc_start: 0.9359 (mm) cc_final: 0.9061 (tp) REVERT: D 159 MET cc_start: 0.8591 (mmm) cc_final: 0.8339 (mmm) REVERT: D 185 GLU cc_start: 0.9040 (mp0) cc_final: 0.8330 (pm20) REVERT: D 220 ASN cc_start: 0.9132 (m-40) cc_final: 0.8757 (m-40) REVERT: D 244 HIS cc_start: 0.8776 (m-70) cc_final: 0.8543 (m-70) REVERT: D 320 MET cc_start: 0.8668 (ttm) cc_final: 0.8262 (ttp) REVERT: D 322 ASP cc_start: 0.8808 (t0) cc_final: 0.8196 (t0) REVERT: D 351 MET cc_start: 0.9105 (mmt) cc_final: 0.8846 (mmm) REVERT: D 440 MET cc_start: 0.8525 (tpp) cc_final: 0.8292 (tpp) REVERT: D 506 PHE cc_start: 0.8985 (t80) cc_final: 0.8529 (m-80) REVERT: D 551 LEU cc_start: 0.9586 (tp) cc_final: 0.9320 (tp) REVERT: D 555 MET cc_start: 0.9113 (mtt) cc_final: 0.8677 (mtt) REVERT: D 567 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.7896 (mpt-90) REVERT: D 572 MET cc_start: 0.8591 (tmm) cc_final: 0.8322 (tmm) REVERT: D 585 HIS cc_start: 0.8389 (t-90) cc_final: 0.8169 (t-90) REVERT: D 591 LEU cc_start: 0.8955 (tp) cc_final: 0.8423 (tt) REVERT: D 595 ILE cc_start: 0.9203 (mt) cc_final: 0.8866 (mt) REVERT: D 677 MET cc_start: 0.8268 (mmm) cc_final: 0.8066 (tpp) REVERT: D 682 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7735 (mm-30) REVERT: D 699 THR cc_start: 0.9786 (p) cc_final: 0.9418 (t) REVERT: D 715 PHE cc_start: 0.7871 (t80) cc_final: 0.7640 (t80) REVERT: D 717 MET cc_start: 0.7997 (tmm) cc_final: 0.7743 (tmm) REVERT: D 745 HIS cc_start: 0.8163 (m-70) cc_final: 0.7690 (m90) outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.1332 time to fit residues: 137.4130 Evaluate side-chains 479 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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: 0.8980 chunk 136 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 452 ASN A 671 ASN B 452 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN C 273 ASN C 452 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN D 452 ASN ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.078914 restraints weight = 60053.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.081247 restraints weight = 37021.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.083018 restraints weight = 26055.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.084247 restraints weight = 20307.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.085083 restraints weight = 16850.975| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.5471 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= 0.149 Angle : 0.699 8.227 29032 Z= 0.348 Chirality : 0.042 0.192 3308 Planarity : 0.004 0.049 3624 Dihedral : 5.339 22.703 2808 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.27 % Favored : 87.58 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.13), residues: 1476 sheet: -3.53 (0.43), residues: 68 loop : -3.38 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 464 TYR 0.019 0.001 TYR C 565 PHE 0.017 0.001 PHE D 203 TRP 0.019 0.001 TRP A 742 HIS 0.006 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00331 (21460) covalent geometry : angle 0.69935 (29032) hydrogen bonds : bond 0.03393 ( 888) hydrogen bonds : angle 4.23923 ( 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 : 1.028 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: 0.9396 (mm) cc_final: 0.9108 (tp) REVERT: A 185 GLU cc_start: 0.9050 (mp0) cc_final: 0.8384 (pm20) REVERT: A 220 ASN cc_start: 0.9140 (m-40) cc_final: 0.8766 (m-40) REVERT: A 244 HIS cc_start: 0.8812 (m-70) cc_final: 0.8593 (m90) REVERT: A 322 ASP cc_start: 0.8823 (t0) cc_final: 0.8365 (t0) REVERT: A 326 LEU cc_start: 0.9145 (mp) cc_final: 0.8905 (pp) REVERT: A 351 MET cc_start: 0.9112 (mmt) cc_final: 0.8863 (mmm) REVERT: A 440 MET cc_start: 0.8554 (tpp) cc_final: 0.8066 (tpp) REVERT: A 461 TYR cc_start: 0.7304 (t80) cc_final: 0.7012 (t80) REVERT: A 506 PHE cc_start: 0.8962 (t80) cc_final: 0.8531 (m-80) REVERT: A 555 MET cc_start: 0.9108 (mtm) cc_final: 0.8305 (mtt) REVERT: A 567 ARG cc_start: 0.8357 (mtt180) cc_final: 0.8099 (mtt180) REVERT: A 585 HIS cc_start: 0.8446 (t-90) cc_final: 0.8210 (t-90) REVERT: A 672 MET cc_start: 0.9140 (tmm) cc_final: 0.8844 (tmm) REVERT: A 699 THR cc_start: 0.9722 (p) cc_final: 0.9454 (t) REVERT: B 139 LEU cc_start: 0.9431 (mm) cc_final: 0.9160 (tp) REVERT: B 185 GLU cc_start: 0.9042 (mp0) cc_final: 0.8295 (pm20) REVERT: B 220 ASN cc_start: 0.9138 (m-40) cc_final: 0.8761 (m-40) REVERT: B 256 HIS cc_start: 0.6737 (p-80) cc_final: 0.6314 (p-80) REVERT: B 308 GLU cc_start: 0.6860 (pm20) cc_final: 0.6177 (pm20) REVERT: B 320 MET cc_start: 0.8696 (ttm) cc_final: 0.8369 (ttp) REVERT: B 351 MET cc_start: 0.9031 (mmt) cc_final: 0.8828 (mmm) REVERT: B 440 MET cc_start: 0.8532 (tpp) cc_final: 0.8034 (tpp) REVERT: B 461 TYR cc_start: 0.7311 (t80) cc_final: 0.7008 (t80) REVERT: B 506 PHE cc_start: 0.8984 (t80) cc_final: 0.8494 (m-80) REVERT: B 555 MET cc_start: 0.9104 (mtm) cc_final: 0.8320 (mtt) REVERT: B 677 MET cc_start: 0.8162 (mmm) cc_final: 0.7951 (tpp) REVERT: B 682 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7787 (mm-30) REVERT: B 715 PHE cc_start: 0.7679 (t80) cc_final: 0.7419 (t80) REVERT: B 722 LYS cc_start: 0.7079 (mttt) cc_final: 0.6752 (tttt) REVERT: C 139 LEU cc_start: 0.9398 (mm) cc_final: 0.9113 (tp) REVERT: C 185 GLU cc_start: 0.9023 (mp0) cc_final: 0.8300 (pm20) REVERT: C 220 ASN cc_start: 0.9160 (m-40) cc_final: 0.8793 (m-40) REVERT: C 244 HIS cc_start: 0.8803 (m-70) cc_final: 0.8573 (m90) REVERT: C 256 HIS cc_start: 0.6744 (p-80) cc_final: 0.6430 (p-80) REVERT: C 320 MET cc_start: 0.8732 (ttm) cc_final: 0.8247 (ttp) REVERT: C 322 ASP cc_start: 0.8825 (t0) cc_final: 0.8188 (t0) REVERT: C 323 MET cc_start: 0.9151 (tmm) cc_final: 0.8875 (tmm) REVERT: C 351 MET cc_start: 0.9110 (mmt) cc_final: 0.8840 (mmm) REVERT: C 414 ASP cc_start: 0.8050 (m-30) cc_final: 0.7187 (t0) REVERT: C 440 MET cc_start: 0.8516 (tpp) cc_final: 0.8038 (tpp) REVERT: C 461 TYR cc_start: 0.7316 (t80) cc_final: 0.7047 (t80) REVERT: C 506 PHE cc_start: 0.8981 (t80) cc_final: 0.8521 (m-80) REVERT: C 555 MET cc_start: 0.8837 (mtp) cc_final: 0.8334 (mtt) REVERT: C 567 ARG cc_start: 0.8551 (mtt180) cc_final: 0.8235 (mtt180) REVERT: C 585 HIS cc_start: 0.8406 (t-90) cc_final: 0.8189 (t-90) REVERT: C 652 ILE cc_start: 0.8744 (pt) cc_final: 0.8372 (mm) REVERT: C 682 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7597 (mm-30) REVERT: C 699 THR cc_start: 0.9734 (p) cc_final: 0.9458 (t) REVERT: C 745 HIS cc_start: 0.8152 (m-70) cc_final: 0.7681 (m90) REVERT: D 139 LEU cc_start: 0.9373 (mm) cc_final: 0.9097 (tp) REVERT: D 185 GLU cc_start: 0.9036 (mp0) cc_final: 0.8304 (pm20) REVERT: D 220 ASN cc_start: 0.9147 (m-40) cc_final: 0.8781 (m-40) REVERT: D 244 HIS cc_start: 0.8725 (m-70) cc_final: 0.8525 (m-70) REVERT: D 256 HIS cc_start: 0.6715 (p-80) cc_final: 0.6401 (p-80) REVERT: D 271 CYS cc_start: 0.9561 (m) cc_final: 0.9343 (m) REVERT: D 308 GLU cc_start: 0.6772 (pm20) cc_final: 0.6115 (pm20) REVERT: D 320 MET cc_start: 0.8630 (ttm) cc_final: 0.8258 (ttp) REVERT: D 351 MET cc_start: 0.9100 (mmt) cc_final: 0.8846 (mmm) REVERT: D 506 PHE cc_start: 0.8987 (t80) cc_final: 0.8532 (m-80) REVERT: D 551 LEU cc_start: 0.9609 (tp) cc_final: 0.9309 (tp) REVERT: D 555 MET cc_start: 0.9090 (mtt) cc_final: 0.8710 (mtt) REVERT: D 591 LEU cc_start: 0.8950 (tp) cc_final: 0.8476 (tt) REVERT: D 595 ILE cc_start: 0.9278 (mt) cc_final: 0.8963 (mt) REVERT: D 682 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7779 (mm-30) REVERT: D 745 HIS cc_start: 0.8143 (m-70) cc_final: 0.7643 (m90) outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 0.1384 time to fit residues: 143.5118 Evaluate side-chains 481 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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: 0.9990 chunk 150 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 213 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN B 735 ASN C 523 HIS C 695 GLN C 735 ASN D 452 ASN D 523 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 ASN D 735 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.081340 restraints weight = 59959.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.083344 restraints weight = 37420.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.085437 restraints weight = 27236.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.086523 restraints weight = 21139.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.087755 restraints weight = 17800.493| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5677 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= 0.134 Angle : 0.683 7.747 29032 Z= 0.337 Chirality : 0.042 0.190 3308 Planarity : 0.004 0.045 3624 Dihedral : 5.207 23.212 2808 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.11 % Favored : 87.73 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: 0.34 (0.13), residues: 1496 sheet: -3.58 (0.41), residues: 68 loop : -3.46 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.017 0.001 TYR C 382 PHE 0.023 0.001 PHE D 489 TRP 0.011 0.001 TRP D 742 HIS 0.006 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00292 (21460) covalent geometry : angle 0.68345 (29032) hydrogen bonds : bond 0.03307 ( 888) hydrogen bonds : angle 4.21689 ( 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 658 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9382 (mm) cc_final: 0.9068 (tp) REVERT: A 159 MET cc_start: 0.8495 (mmm) cc_final: 0.8248 (mmm) REVERT: A 185 GLU cc_start: 0.9025 (mp0) cc_final: 0.8371 (pm20) REVERT: A 256 HIS cc_start: 0.6554 (p-80) cc_final: 0.6241 (p-80) REVERT: A 322 ASP cc_start: 0.8732 (t0) cc_final: 0.8122 (t0) REVERT: A 323 MET cc_start: 0.9296 (ppp) cc_final: 0.9092 (tmm) REVERT: A 326 LEU cc_start: 0.9098 (mp) cc_final: 0.8873 (pp) REVERT: A 351 MET cc_start: 0.9088 (mmt) cc_final: 0.8869 (mmm) REVERT: A 440 MET cc_start: 0.8457 (tpp) cc_final: 0.8106 (tpp) REVERT: A 461 TYR cc_start: 0.7376 (t80) cc_final: 0.7125 (t80) REVERT: A 506 PHE cc_start: 0.8932 (t80) cc_final: 0.8562 (m-80) REVERT: A 532 LEU cc_start: 0.9519 (mm) cc_final: 0.9113 (mm) REVERT: A 550 CYS cc_start: 0.8952 (p) cc_final: 0.8242 (t) REVERT: A 555 MET cc_start: 0.9061 (mtm) cc_final: 0.8287 (mtt) REVERT: A 572 MET cc_start: 0.8589 (tmm) cc_final: 0.8295 (tmm) REVERT: A 699 THR cc_start: 0.9709 (p) cc_final: 0.9376 (t) REVERT: A 745 HIS cc_start: 0.8016 (m-70) cc_final: 0.7469 (m-70) REVERT: B 139 LEU cc_start: 0.9394 (mm) cc_final: 0.9100 (tp) REVERT: B 159 MET cc_start: 0.8500 (mmm) cc_final: 0.8243 (mmm) REVERT: B 185 GLU cc_start: 0.8994 (mp0) cc_final: 0.8301 (pm20) REVERT: B 220 ASN cc_start: 0.9089 (m-40) cc_final: 0.8732 (m-40) REVERT: B 440 MET cc_start: 0.8454 (tpp) cc_final: 0.8123 (tpp) REVERT: B 461 TYR cc_start: 0.7368 (t80) cc_final: 0.7124 (t80) REVERT: B 506 PHE cc_start: 0.8874 (t80) cc_final: 0.8482 (m-80) REVERT: B 532 LEU cc_start: 0.9474 (mm) cc_final: 0.9031 (mm) REVERT: B 550 CYS cc_start: 0.8922 (p) cc_final: 0.8192 (t) REVERT: B 555 MET cc_start: 0.9065 (mtm) cc_final: 0.8249 (mtt) REVERT: B 585 HIS cc_start: 0.8397 (t-90) cc_final: 0.8154 (t-90) REVERT: B 722 LYS cc_start: 0.7020 (mttt) cc_final: 0.6749 (mttt) REVERT: B 745 HIS cc_start: 0.8062 (m-70) cc_final: 0.7436 (m-70) REVERT: C 139 LEU cc_start: 0.9371 (mm) cc_final: 0.9063 (tp) REVERT: C 159 MET cc_start: 0.8479 (mmm) cc_final: 0.8233 (mmm) REVERT: C 185 GLU cc_start: 0.8994 (mp0) cc_final: 0.8301 (pm20) REVERT: C 220 ASN cc_start: 0.9122 (m-40) cc_final: 0.8761 (m-40) REVERT: C 256 HIS cc_start: 0.6656 (p-80) cc_final: 0.6243 (p-80) REVERT: C 271 CYS cc_start: 0.9550 (m) cc_final: 0.9336 (m) REVERT: C 320 MET cc_start: 0.8565 (ttm) cc_final: 0.8212 (ttp) REVERT: C 351 MET cc_start: 0.9096 (mmt) cc_final: 0.8851 (mmm) REVERT: C 414 ASP cc_start: 0.7963 (m-30) cc_final: 0.7135 (t0) REVERT: C 440 MET cc_start: 0.8440 (tpp) cc_final: 0.8120 (tpp) REVERT: C 461 TYR cc_start: 0.7353 (t80) cc_final: 0.7136 (t80) REVERT: C 506 PHE cc_start: 0.8939 (t80) cc_final: 0.8508 (m-80) REVERT: C 532 LEU cc_start: 0.9456 (mm) cc_final: 0.8993 (mm) REVERT: C 550 CYS cc_start: 0.8869 (p) cc_final: 0.8224 (t) REVERT: C 551 LEU cc_start: 0.9549 (tp) cc_final: 0.9348 (tp) REVERT: C 555 MET cc_start: 0.8798 (mtp) cc_final: 0.8263 (mtt) REVERT: C 567 ARG cc_start: 0.8553 (mtt180) cc_final: 0.8120 (mtt90) REVERT: C 572 MET cc_start: 0.8502 (tmm) cc_final: 0.8200 (tmm) REVERT: C 574 MET cc_start: 0.8775 (tpp) cc_final: 0.8270 (tpp) REVERT: C 652 ILE cc_start: 0.8492 (pt) cc_final: 0.8111 (mm) REVERT: C 682 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7698 (mm-30) REVERT: C 699 THR cc_start: 0.9732 (p) cc_final: 0.9436 (t) REVERT: C 745 HIS cc_start: 0.7988 (m-70) cc_final: 0.7436 (m-70) REVERT: D 139 LEU cc_start: 0.9387 (mm) cc_final: 0.9090 (tp) REVERT: D 159 MET cc_start: 0.8488 (mmm) cc_final: 0.8237 (mmm) REVERT: D 176 LEU cc_start: 0.9619 (mm) cc_final: 0.9410 (mm) REVERT: D 185 GLU cc_start: 0.8996 (mp0) cc_final: 0.8318 (pm20) REVERT: D 220 ASN cc_start: 0.9067 (m-40) cc_final: 0.8696 (m-40) REVERT: D 271 CYS cc_start: 0.9513 (m) cc_final: 0.9259 (m) REVERT: D 308 GLU cc_start: 0.6672 (pm20) cc_final: 0.6216 (pm20) REVERT: D 351 MET cc_start: 0.9075 (mmt) cc_final: 0.8813 (mmm) REVERT: D 440 MET cc_start: 0.8367 (tpp) cc_final: 0.7976 (tpp) REVERT: D 506 PHE cc_start: 0.8919 (t80) cc_final: 0.8516 (m-80) REVERT: D 551 LEU cc_start: 0.9576 (tp) cc_final: 0.9290 (tp) REVERT: D 555 MET cc_start: 0.9103 (mtt) cc_final: 0.8679 (mtt) REVERT: D 572 MET cc_start: 0.8611 (tmm) cc_final: 0.8367 (tmm) REVERT: D 585 HIS cc_start: 0.8386 (t-90) cc_final: 0.8183 (t-90) REVERT: D 591 LEU cc_start: 0.8949 (tp) cc_final: 0.8429 (tt) REVERT: D 595 ILE cc_start: 0.9246 (mt) cc_final: 0.8799 (mt) REVERT: D 682 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7584 (mm-30) REVERT: D 745 HIS cc_start: 0.8016 (m-70) cc_final: 0.7441 (m-70) outliers start: 0 outliers final: 0 residues processed: 658 average time/residue: 0.1372 time to fit residues: 145.8451 Evaluate side-chains 498 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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: 5.9990 chunk 79 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 207 optimal weight: 0.7980 chunk 192 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 452 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN B 292 GLN B 452 ASN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN C 292 GLN C 452 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN C 695 GLN C 735 ASN D 292 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.095719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.077360 restraints weight = 59996.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.079734 restraints weight = 37765.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.081545 restraints weight = 26520.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.082775 restraints weight = 20823.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.083715 restraints weight = 16928.629| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21460 Z= 0.197 Angle : 0.752 8.270 29032 Z= 0.374 Chirality : 0.045 0.222 3308 Planarity : 0.004 0.057 3624 Dihedral : 5.365 22.041 2808 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.32 % Favored : 86.53 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -1.83 (0.16), residues: 2568 helix: 0.20 (0.13), residues: 1524 sheet: -3.71 (0.40), residues: 68 loop : -3.43 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 567 TYR 0.021 0.002 TYR A 382 PHE 0.017 0.001 PHE D 526 TRP 0.014 0.002 TRP B 742 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00437 (21460) covalent geometry : angle 0.75158 (29032) hydrogen bonds : bond 0.03524 ( 888) hydrogen bonds : angle 4.36683 ( 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 623 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 0.714 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: 0.9389 (mm) cc_final: 0.9097 (tp) REVERT: A 159 MET cc_start: 0.8513 (mmm) cc_final: 0.8248 (mmm) REVERT: A 185 GLU cc_start: 0.9023 (mp0) cc_final: 0.8310 (pm20) REVERT: A 220 ASN cc_start: 0.9191 (m-40) cc_final: 0.8972 (m-40) REVERT: A 244 HIS cc_start: 0.8733 (m-70) cc_final: 0.8415 (m-70) REVERT: A 322 ASP cc_start: 0.8626 (t0) cc_final: 0.8071 (t0) REVERT: A 323 MET cc_start: 0.9339 (ppp) cc_final: 0.9122 (tmm) REVERT: A 351 MET cc_start: 0.9063 (mmt) cc_final: 0.8820 (mmm) REVERT: A 440 MET cc_start: 0.8602 (tpp) cc_final: 0.8292 (tpp) REVERT: A 461 TYR cc_start: 0.7407 (t80) cc_final: 0.7156 (t80) REVERT: A 506 PHE cc_start: 0.8915 (t80) cc_final: 0.8498 (m-80) REVERT: A 555 MET cc_start: 0.9148 (mtm) cc_final: 0.8339 (mtt) REVERT: A 585 HIS cc_start: 0.8371 (t-90) cc_final: 0.8121 (t-90) REVERT: A 588 LEU cc_start: 0.8935 (mm) cc_final: 0.8712 (tt) REVERT: A 699 THR cc_start: 0.9627 (p) cc_final: 0.9406 (t) REVERT: A 745 HIS cc_start: 0.8019 (m-70) cc_final: 0.7534 (m-70) REVERT: B 139 LEU cc_start: 0.9375 (mm) cc_final: 0.9126 (tp) REVERT: B 159 MET cc_start: 0.8475 (mmm) cc_final: 0.8223 (mmm) REVERT: B 185 GLU cc_start: 0.9018 (mp0) cc_final: 0.8306 (pm20) REVERT: B 220 ASN cc_start: 0.9144 (m-40) cc_final: 0.8778 (m-40) REVERT: B 440 MET cc_start: 0.8509 (tpp) cc_final: 0.8181 (tpp) REVERT: B 461 TYR cc_start: 0.7417 (t80) cc_final: 0.7156 (t80) REVERT: B 506 PHE cc_start: 0.8920 (t80) cc_final: 0.8499 (m-80) REVERT: B 532 LEU cc_start: 0.9573 (mm) cc_final: 0.9152 (mm) REVERT: B 550 CYS cc_start: 0.8965 (p) cc_final: 0.8268 (t) REVERT: B 555 MET cc_start: 0.9076 (mtm) cc_final: 0.8254 (mtt) REVERT: B 585 HIS cc_start: 0.8500 (t-90) cc_final: 0.8258 (t-90) REVERT: B 735 ASN cc_start: 0.8286 (m-40) cc_final: 0.8083 (m110) REVERT: B 745 HIS cc_start: 0.8101 (m-70) cc_final: 0.7523 (m-70) REVERT: C 139 LEU cc_start: 0.9362 (mm) cc_final: 0.9099 (tp) REVERT: C 159 MET cc_start: 0.8460 (mmm) cc_final: 0.8207 (mmm) REVERT: C 185 GLU cc_start: 0.9008 (mp0) cc_final: 0.8304 (pm20) REVERT: C 220 ASN cc_start: 0.9138 (m-40) cc_final: 0.8785 (m-40) REVERT: C 244 HIS cc_start: 0.8733 (m-70) cc_final: 0.8391 (m-70) REVERT: C 351 MET cc_start: 0.9067 (mmt) cc_final: 0.8786 (mmm) REVERT: C 414 ASP cc_start: 0.7923 (m-30) cc_final: 0.7130 (t0) REVERT: C 440 MET cc_start: 0.8516 (tpp) cc_final: 0.8277 (tpp) REVERT: C 461 TYR cc_start: 0.7409 (t80) cc_final: 0.7156 (t80) REVERT: C 506 PHE cc_start: 0.8940 (t80) cc_final: 0.8490 (m-80) REVERT: C 532 LEU cc_start: 0.9564 (mm) cc_final: 0.9139 (mm) REVERT: C 550 CYS cc_start: 0.8957 (p) cc_final: 0.8289 (t) REVERT: C 555 MET cc_start: 0.8775 (mtp) cc_final: 0.8307 (mtt) REVERT: C 567 ARG cc_start: 0.8616 (mtt180) cc_final: 0.8154 (mtt90) REVERT: C 572 MET cc_start: 0.8569 (tmm) cc_final: 0.8232 (tmm) REVERT: C 585 HIS cc_start: 0.8413 (t-90) cc_final: 0.8207 (t-90) REVERT: C 588 LEU cc_start: 0.9011 (mm) cc_final: 0.8809 (tt) REVERT: C 677 MET cc_start: 0.8262 (mmm) cc_final: 0.7915 (tpp) REVERT: C 682 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7746 (mm-30) REVERT: C 695 GLN cc_start: 0.8748 (tt0) cc_final: 0.8421 (tt0) REVERT: C 699 THR cc_start: 0.9745 (p) cc_final: 0.9448 (t) REVERT: C 745 HIS cc_start: 0.8075 (m-70) cc_final: 0.7511 (m-70) REVERT: D 139 LEU cc_start: 0.9367 (mm) cc_final: 0.9119 (tp) REVERT: D 159 MET cc_start: 0.8469 (mmm) cc_final: 0.8217 (mmm) REVERT: D 185 GLU cc_start: 0.9009 (mp0) cc_final: 0.8312 (pm20) REVERT: D 220 ASN cc_start: 0.9125 (m-40) cc_final: 0.8801 (m-40) REVERT: D 320 MET cc_start: 0.8418 (ttm) cc_final: 0.7994 (ttp) REVERT: D 323 MET cc_start: 0.9124 (tmm) cc_final: 0.8903 (tmm) REVERT: D 351 MET cc_start: 0.9056 (mmt) cc_final: 0.8793 (mmm) REVERT: D 414 ASP cc_start: 0.7896 (m-30) cc_final: 0.7092 (t0) REVERT: D 440 MET cc_start: 0.8450 (tpp) cc_final: 0.8191 (tpp) REVERT: D 501 GLU cc_start: 0.8216 (tp30) cc_final: 0.8009 (tp30) REVERT: D 506 PHE cc_start: 0.8924 (t80) cc_final: 0.8466 (m-80) REVERT: D 555 MET cc_start: 0.9120 (mtt) cc_final: 0.8779 (mtt) REVERT: D 572 MET cc_start: 0.8638 (tmm) cc_final: 0.8281 (tmm) REVERT: D 585 HIS cc_start: 0.8420 (t-90) cc_final: 0.8189 (t-90) REVERT: D 591 LEU cc_start: 0.9001 (tp) cc_final: 0.8510 (tt) REVERT: D 595 ILE cc_start: 0.9286 (mt) cc_final: 0.8957 (mt) REVERT: D 682 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7664 (mm-30) REVERT: D 745 HIS cc_start: 0.8037 (m-70) cc_final: 0.7534 (m-70) outliers start: 0 outliers final: 0 residues processed: 623 average time/residue: 0.1395 time to fit residues: 138.0264 Evaluate side-chains 480 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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: 0.4980 chunk 48 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 99 optimal weight: 0.0870 chunk 229 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.9164 ------------------------------------------------------------------------------- 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 ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN B 452 ASN B 523 HIS C 452 ASN ** 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 = 0.3351 r_free = 0.3351 target = 0.100027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081903 restraints weight = 58928.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.084421 restraints weight = 36052.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.086047 restraints weight = 25906.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.087345 restraints weight = 20094.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088297 restraints weight = 16088.271| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21460 Z= 0.133 Angle : 0.719 7.602 29032 Z= 0.351 Chirality : 0.042 0.189 3308 Planarity : 0.004 0.042 3624 Dihedral : 5.151 22.932 2808 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.11 % Favored : 87.73 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: -1.65 (0.16), residues: 2568 helix: 0.33 (0.13), residues: 1516 sheet: -3.32 (0.46), residues: 68 loop : -3.32 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 147 TYR 0.018 0.001 TYR D 382 PHE 0.023 0.001 PHE D 489 TRP 0.009 0.001 TRP C 739 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00289 (21460) covalent geometry : angle 0.71938 (29032) hydrogen bonds : bond 0.03363 ( 888) hydrogen bonds : angle 4.26379 ( 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 642 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 642 time to evaluate : 0.866 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: 0.9367 (mm) cc_final: 0.9060 (tp) REVERT: A 159 MET cc_start: 0.8472 (mmm) cc_final: 0.8201 (mmm) REVERT: A 185 GLU cc_start: 0.8961 (mp0) cc_final: 0.8279 (pm20) REVERT: A 220 ASN cc_start: 0.9065 (m-40) cc_final: 0.8857 (m-40) REVERT: A 351 MET cc_start: 0.8967 (mmt) cc_final: 0.8765 (mmm) REVERT: A 461 TYR cc_start: 0.7299 (t80) cc_final: 0.7045 (t80) REVERT: A 505 ILE cc_start: 0.9573 (pt) cc_final: 0.9167 (tt) REVERT: A 506 PHE cc_start: 0.8872 (t80) cc_final: 0.8439 (m-80) REVERT: A 555 MET cc_start: 0.9096 (mtm) cc_final: 0.8298 (mtt) REVERT: A 565 TYR cc_start: 0.8968 (m-80) cc_final: 0.8259 (m-80) REVERT: A 572 MET cc_start: 0.8680 (tmm) cc_final: 0.8364 (tmm) REVERT: A 574 MET cc_start: 0.8721 (tpp) cc_final: 0.8514 (tpp) REVERT: A 585 HIS cc_start: 0.8349 (t-90) cc_final: 0.8120 (t-90) REVERT: A 682 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7369 (mm-30) REVERT: A 699 THR cc_start: 0.9606 (p) cc_final: 0.9375 (t) REVERT: A 745 HIS cc_start: 0.7930 (m-70) cc_final: 0.7369 (m-70) REVERT: B 139 LEU cc_start: 0.9357 (mm) cc_final: 0.9064 (tp) REVERT: B 159 MET cc_start: 0.8428 (mmm) cc_final: 0.8164 (mmm) REVERT: B 185 GLU cc_start: 0.8941 (mp0) cc_final: 0.8265 (pm20) REVERT: B 320 MET cc_start: 0.7951 (ttp) cc_final: 0.7709 (ttp) REVERT: B 461 TYR cc_start: 0.7331 (t80) cc_final: 0.7048 (t80) REVERT: B 505 ILE cc_start: 0.9578 (pt) cc_final: 0.9198 (tt) REVERT: B 506 PHE cc_start: 0.8864 (t80) cc_final: 0.8420 (m-80) REVERT: B 555 MET cc_start: 0.9040 (mtm) cc_final: 0.8237 (mtt) REVERT: B 585 HIS cc_start: 0.8498 (t-90) cc_final: 0.8286 (t-90) REVERT: B 611 LYS cc_start: 0.6433 (tptt) cc_final: 0.6219 (tppt) REVERT: B 745 HIS cc_start: 0.7966 (m-70) cc_final: 0.7377 (m-70) REVERT: C 139 LEU cc_start: 0.9340 (mm) cc_final: 0.9028 (tp) REVERT: C 159 MET cc_start: 0.8438 (mmm) cc_final: 0.8192 (mmm) REVERT: C 185 GLU cc_start: 0.8922 (mp0) cc_final: 0.8283 (pm20) REVERT: C 220 ASN cc_start: 0.8987 (m-40) cc_final: 0.8646 (m-40) REVERT: C 244 HIS cc_start: 0.8642 (m-70) cc_final: 0.8421 (m-70) REVERT: C 320 MET cc_start: 0.8088 (ttp) cc_final: 0.7717 (ttp) REVERT: C 351 MET cc_start: 0.8995 (mmt) cc_final: 0.8773 (mmm) REVERT: C 410 ASN cc_start: 0.9022 (t0) cc_final: 0.8802 (t0) REVERT: C 414 ASP cc_start: 0.7822 (m-30) cc_final: 0.7066 (t0) REVERT: C 461 TYR cc_start: 0.7304 (t80) cc_final: 0.7087 (t80) REVERT: C 505 ILE cc_start: 0.9572 (pt) cc_final: 0.9218 (tt) REVERT: C 506 PHE cc_start: 0.8860 (t80) cc_final: 0.8432 (m-80) REVERT: C 572 MET cc_start: 0.8629 (tmm) cc_final: 0.8304 (tmm) REVERT: C 574 MET cc_start: 0.8659 (tpp) cc_final: 0.8429 (tpp) REVERT: C 585 HIS cc_start: 0.8435 (t-90) cc_final: 0.8219 (t-90) REVERT: C 677 MET cc_start: 0.8192 (mmm) cc_final: 0.7761 (tpp) REVERT: C 682 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7703 (mm-30) REVERT: C 699 THR cc_start: 0.9709 (p) cc_final: 0.9411 (t) REVERT: C 745 HIS cc_start: 0.7905 (m-70) cc_final: 0.7367 (m-70) REVERT: D 139 LEU cc_start: 0.9333 (mm) cc_final: 0.9035 (tp) REVERT: D 159 MET cc_start: 0.8424 (mmm) cc_final: 0.8177 (mmm) REVERT: D 185 GLU cc_start: 0.8942 (mp0) cc_final: 0.8286 (pm20) REVERT: D 220 ASN cc_start: 0.9013 (m-40) cc_final: 0.8667 (m-40) REVERT: D 255 GLN cc_start: 0.8808 (pm20) cc_final: 0.8596 (pm20) REVERT: D 308 GLU cc_start: 0.6784 (pm20) cc_final: 0.5922 (pm20) REVERT: D 320 MET cc_start: 0.8111 (ttm) cc_final: 0.7909 (ttp) REVERT: D 351 MET cc_start: 0.8998 (mmt) cc_final: 0.8791 (mmm) REVERT: D 501 GLU cc_start: 0.8071 (tp30) cc_final: 0.7838 (tp30) REVERT: D 505 ILE cc_start: 0.9583 (pt) cc_final: 0.9158 (tt) REVERT: D 506 PHE cc_start: 0.8859 (t80) cc_final: 0.8412 (m-80) REVERT: D 551 LEU cc_start: 0.9589 (tp) cc_final: 0.9334 (tp) REVERT: D 555 MET cc_start: 0.9056 (mtt) cc_final: 0.8696 (mtt) REVERT: D 572 MET cc_start: 0.8656 (tmm) cc_final: 0.8333 (tmm) REVERT: D 574 MET cc_start: 0.8758 (tpp) cc_final: 0.8531 (tpp) REVERT: D 585 HIS cc_start: 0.8390 (t-90) cc_final: 0.8177 (t-90) REVERT: D 591 LEU cc_start: 0.9015 (tp) cc_final: 0.8430 (tt) REVERT: D 595 ILE cc_start: 0.9248 (mt) cc_final: 0.8950 (mt) REVERT: D 611 LYS cc_start: 0.6443 (tptt) cc_final: 0.6222 (tppt) REVERT: D 682 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7665 (mm-30) REVERT: D 745 HIS cc_start: 0.7923 (m-70) cc_final: 0.7339 (m-70) outliers start: 0 outliers final: 0 residues processed: 642 average time/residue: 0.1364 time to fit residues: 141.3441 Evaluate side-chains 498 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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: 0.9980 chunk 77 optimal weight: 0.1980 chunk 131 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN A 735 ASN B 292 GLN B 452 ASN B 735 ASN C 452 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 735 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.079735 restraints weight = 59939.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.082101 restraints weight = 37490.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.083944 restraints weight = 26290.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.085235 restraints weight = 20773.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.086243 restraints weight = 16813.155| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21460 Z= 0.157 Angle : 0.726 8.519 29032 Z= 0.359 Chirality : 0.043 0.192 3308 Planarity : 0.004 0.046 3624 Dihedral : 5.141 22.290 2808 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.62 % Favored : 87.23 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.17), residues: 2568 helix: 0.37 (0.13), residues: 1516 sheet: -3.17 (0.47), residues: 68 loop : -3.20 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 147 TYR 0.017 0.001 TYR B 359 PHE 0.016 0.001 PHE C 590 TRP 0.011 0.001 TRP B 742 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00352 (21460) covalent geometry : angle 0.72612 (29032) hydrogen bonds : bond 0.03391 ( 888) hydrogen bonds : angle 4.28672 ( 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 632 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 0.913 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: 0.9373 (mm) cc_final: 0.9068 (tp) REVERT: A 159 MET cc_start: 0.8559 (mmm) cc_final: 0.8308 (mmm) REVERT: A 185 GLU cc_start: 0.8969 (mp0) cc_final: 0.8291 (pm20) REVERT: A 244 HIS cc_start: 0.8657 (m-70) cc_final: 0.8455 (m-70) REVERT: A 461 TYR cc_start: 0.7322 (t80) cc_final: 0.7038 (t80) REVERT: A 506 PHE cc_start: 0.8923 (t80) cc_final: 0.8492 (m-80) REVERT: A 555 MET cc_start: 0.9101 (mtm) cc_final: 0.8305 (mtt) REVERT: A 565 TYR cc_start: 0.9046 (m-80) cc_final: 0.8394 (m-80) REVERT: A 572 MET cc_start: 0.8721 (tmm) cc_final: 0.8399 (tmm) REVERT: A 574 MET cc_start: 0.8786 (tpp) cc_final: 0.8391 (tpp) REVERT: A 585 HIS cc_start: 0.8371 (t-90) cc_final: 0.8157 (t-90) REVERT: A 682 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 699 THR cc_start: 0.9599 (p) cc_final: 0.9391 (t) REVERT: A 722 LYS cc_start: 0.7172 (mttt) cc_final: 0.6952 (mttt) REVERT: A 735 ASN cc_start: 0.8170 (m-40) cc_final: 0.7958 (m110) REVERT: A 745 HIS cc_start: 0.7897 (m-70) cc_final: 0.7385 (m-70) REVERT: B 159 MET cc_start: 0.8557 (mmm) cc_final: 0.8295 (mmm) REVERT: B 185 GLU cc_start: 0.8945 (mp0) cc_final: 0.8272 (pm20) REVERT: B 220 ASN cc_start: 0.9077 (m-40) cc_final: 0.8814 (m-40) REVERT: B 308 GLU cc_start: 0.6966 (pm20) cc_final: 0.6390 (pm20) REVERT: B 410 ASN cc_start: 0.9134 (t0) cc_final: 0.8816 (t0) REVERT: B 461 TYR cc_start: 0.7331 (t80) cc_final: 0.7050 (t80) REVERT: B 505 ILE cc_start: 0.9598 (pt) cc_final: 0.9205 (tt) REVERT: B 506 PHE cc_start: 0.8919 (t80) cc_final: 0.8437 (m-80) REVERT: B 555 MET cc_start: 0.9020 (mtm) cc_final: 0.8237 (mtt) REVERT: B 585 HIS cc_start: 0.8561 (t-90) cc_final: 0.8340 (t-90) REVERT: B 611 LYS cc_start: 0.6505 (tptt) cc_final: 0.6282 (tppt) REVERT: B 743 LYS cc_start: 0.8405 (pttt) cc_final: 0.8099 (pttm) REVERT: B 745 HIS cc_start: 0.7928 (m-70) cc_final: 0.7487 (m-70) REVERT: C 159 MET cc_start: 0.8566 (mmm) cc_final: 0.8300 (mmm) REVERT: C 185 GLU cc_start: 0.8923 (mp0) cc_final: 0.8283 (pm20) REVERT: C 220 ASN cc_start: 0.8962 (m-40) cc_final: 0.8694 (m-40) REVERT: C 244 HIS cc_start: 0.8707 (m-70) cc_final: 0.8501 (m-70) REVERT: C 320 MET cc_start: 0.8247 (ttp) cc_final: 0.7912 (ttp) REVERT: C 351 MET cc_start: 0.8998 (mmt) cc_final: 0.8760 (mmm) REVERT: C 410 ASN cc_start: 0.9142 (t0) cc_final: 0.8849 (t0) REVERT: C 414 ASP cc_start: 0.7830 (m-30) cc_final: 0.7113 (t0) REVERT: C 461 TYR cc_start: 0.7312 (t80) cc_final: 0.7073 (t80) REVERT: C 501 GLU cc_start: 0.8347 (tp30) cc_final: 0.8001 (tp30) REVERT: C 505 ILE cc_start: 0.9590 (pt) cc_final: 0.9215 (tt) REVERT: C 506 PHE cc_start: 0.8910 (t80) cc_final: 0.8458 (m-80) REVERT: C 532 LEU cc_start: 0.9459 (mm) cc_final: 0.8975 (mm) REVERT: C 550 CYS cc_start: 0.8957 (p) cc_final: 0.8215 (t) REVERT: C 555 MET cc_start: 0.8797 (mtp) cc_final: 0.8360 (mtt) REVERT: C 572 MET cc_start: 0.8641 (tmm) cc_final: 0.8302 (tmm) REVERT: C 574 MET cc_start: 0.8801 (tpp) cc_final: 0.8037 (tpp) REVERT: C 689 GLU cc_start: 0.9196 (tt0) cc_final: 0.8732 (tp30) REVERT: C 735 ASN cc_start: 0.8241 (m-40) cc_final: 0.8025 (m110) REVERT: C 745 HIS cc_start: 0.7942 (m-70) cc_final: 0.7375 (m-70) REVERT: D 159 MET cc_start: 0.8533 (mmm) cc_final: 0.8277 (mmm) REVERT: D 185 GLU cc_start: 0.8971 (mp0) cc_final: 0.8299 (pm20) REVERT: D 220 ASN cc_start: 0.9040 (m-40) cc_final: 0.8726 (m-40) REVERT: D 351 MET cc_start: 0.8981 (mmt) cc_final: 0.8742 (mmm) REVERT: D 410 ASN cc_start: 0.8976 (t0) cc_final: 0.8745 (t0) REVERT: D 414 ASP cc_start: 0.7875 (m-30) cc_final: 0.7104 (t0) REVERT: D 506 PHE cc_start: 0.8939 (t80) cc_final: 0.8497 (m-80) REVERT: D 532 LEU cc_start: 0.9505 (mm) cc_final: 0.8944 (mm) REVERT: D 550 CYS cc_start: 0.8932 (p) cc_final: 0.8127 (t) REVERT: D 551 LEU cc_start: 0.9598 (tp) cc_final: 0.9313 (tp) REVERT: D 555 MET cc_start: 0.9068 (mtt) cc_final: 0.8727 (mtt) REVERT: D 572 MET cc_start: 0.8660 (tmm) cc_final: 0.8307 (tmm) REVERT: D 574 MET cc_start: 0.8818 (tpp) cc_final: 0.8411 (tpp) REVERT: D 585 HIS cc_start: 0.8487 (t-90) cc_final: 0.8259 (t-90) REVERT: D 591 LEU cc_start: 0.9059 (tp) cc_final: 0.8450 (tt) REVERT: D 595 ILE cc_start: 0.9300 (mt) cc_final: 0.8952 (mt) REVERT: D 611 LYS cc_start: 0.6577 (tptt) cc_final: 0.6336 (tppt) REVERT: D 682 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7761 (mm-30) REVERT: D 735 ASN cc_start: 0.8224 (m-40) cc_final: 0.8000 (m110) REVERT: D 745 HIS cc_start: 0.7892 (m-70) cc_final: 0.7346 (m-70) outliers start: 0 outliers final: 0 residues processed: 632 average time/residue: 0.1348 time to fit residues: 137.6833 Evaluate side-chains 498 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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: 3.9990 chunk 35 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 125 optimal weight: 0.0870 chunk 111 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN B 292 GLN B 452 ASN B 735 ASN C 452 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.078677 restraints weight = 60084.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.081013 restraints weight = 37615.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.082542 restraints weight = 27000.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.083793 restraints weight = 21288.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084745 restraints weight = 17745.316| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.6188 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= 0.177 Angle : 0.747 8.516 29032 Z= 0.368 Chirality : 0.044 0.284 3308 Planarity : 0.004 0.048 3624 Dihedral : 5.193 21.853 2808 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.27 % Favored : 87.58 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -1.49 (0.17), residues: 2568 helix: 0.35 (0.13), residues: 1524 sheet: -3.20 (0.48), residues: 68 loop : -3.09 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 147 TYR 0.019 0.002 TYR B 359 PHE 0.024 0.002 PHE B 489 TRP 0.011 0.002 TRP B 742 HIS 0.005 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00398 (21460) covalent geometry : angle 0.74684 (29032) hydrogen bonds : bond 0.03434 ( 888) hydrogen bonds : angle 4.35656 ( 2580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3899.61 seconds wall clock time: 68 minutes 7.57 seconds (4087.57 seconds total)