Starting phenix.real_space_refine on Wed Jun 18 07:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pvl_20492/06_2025/6pvl_20492.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pvl_20492/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6pvl_20492/06_2025/6pvl_20492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pvl_20492/06_2025/6pvl_20492.map" model { file = "/net/cci-nas-00/data/ceres_data/6pvl_20492/06_2025/6pvl_20492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pvl_20492/06_2025/6pvl_20492.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.00, per 1000 atoms: 0.57 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: 4.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.96 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: 5.33 Time building geometry restraints manager: 5.56 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 42.780 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.960 ------------------------------------------------------------------------------- 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 : 6.80 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.003 TRP A 380 HIS 0.005 0.002 HIS C 301 PHE 0.018 0.002 PHE A 715 TYR 0.013 0.002 TYR D 382 ARG 0.008 0.001 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.28589 ( 888) hydrogen bonds : angle 9.34867 ( 2580) covalent geometry : bond 0.00757 (21460) covalent geometry : angle 1.13053 (29032) *********************** 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 : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.7541 (t0) REVERT: A 248 VAL cc_start: 0.9188 (t) cc_final: 0.8980 (m) REVERT: A 282 MET cc_start: 0.8867 (tpp) cc_final: 0.8525 (tpp) REVERT: A 322 ASP cc_start: 0.8908 (t0) cc_final: 0.8587 (t0) REVERT: A 326 LEU cc_start: 0.9262 (mp) cc_final: 0.9022 (mp) REVERT: A 335 THR cc_start: 0.9298 (p) cc_final: 0.9046 (m) REVERT: A 351 MET cc_start: 0.8940 (mmt) cc_final: 0.8671 (mmm) REVERT: A 414 ASP cc_start: 0.7711 (m-30) cc_final: 0.6797 (t0) REVERT: A 506 PHE cc_start: 0.9026 (t80) cc_final: 0.8519 (m-80) REVERT: A 565 TYR cc_start: 0.9059 (m-80) cc_final: 0.8853 (m-80) REVERT: A 630 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8790 (tm) REVERT: A 634 LYS cc_start: 0.9074 (mttt) cc_final: 0.8815 (mmmt) REVERT: A 677 MET cc_start: 0.8461 (mmm) cc_final: 0.8037 (mmt) REVERT: A 704 GLU cc_start: 0.8644 (mm-30) cc_final: 0.7999 (tp30) REVERT: A 728 PHE cc_start: 0.7573 (m-80) cc_final: 0.7249 (m-80) REVERT: A 735 ASN cc_start: 0.8835 (m-40) cc_final: 0.8331 (m110) REVERT: B 144 ASP cc_start: 0.9212 (t70) cc_final: 0.8719 (t0) REVERT: B 198 ASP cc_start: 0.7797 (m-30) cc_final: 0.7584 (t0) REVERT: B 282 MET cc_start: 0.8879 (tpp) cc_final: 0.8510 (tpp) REVERT: B 322 ASP cc_start: 0.8900 (t0) cc_final: 0.8602 (t0) REVERT: B 326 LEU cc_start: 0.9288 (mp) cc_final: 0.9076 (mp) REVERT: B 351 MET cc_start: 0.8928 (mmt) cc_final: 0.8663 (mmm) REVERT: B 414 ASP cc_start: 0.7691 (m-30) cc_final: 0.6834 (t0) REVERT: B 506 PHE cc_start: 0.9032 (t80) cc_final: 0.8516 (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: 0.8107 (mmt) REVERT: B 688 SER cc_start: 0.8727 (t) cc_final: 0.8519 (t) REVERT: B 704 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8009 (tp30) REVERT: B 728 PHE cc_start: 0.7566 (m-80) cc_final: 0.7240 (m-80) REVERT: B 735 ASN cc_start: 0.8837 (m-40) cc_final: 0.8335 (m110) REVERT: B 752 ASP cc_start: 0.7853 (m-30) cc_final: 0.7609 (m-30) REVERT: C 144 ASP cc_start: 0.9200 (t70) cc_final: 0.8728 (t0) REVERT: C 198 ASP cc_start: 0.7782 (m-30) cc_final: 0.7571 (t0) REVERT: C 256 HIS cc_start: 0.6784 (p90) cc_final: 0.6076 (p90) REVERT: C 282 MET cc_start: 0.8876 (tpp) cc_final: 0.8503 (tpp) REVERT: C 322 ASP cc_start: 0.8893 (t0) cc_final: 0.8587 (t0) REVERT: C 326 LEU cc_start: 0.9282 (mp) cc_final: 0.9073 (mp) REVERT: C 351 MET cc_start: 0.8906 (mmt) cc_final: 0.8641 (mmm) REVERT: C 414 ASP cc_start: 0.7639 (m-30) cc_final: 0.6784 (t0) REVERT: C 506 PHE cc_start: 0.9045 (t80) cc_final: 0.8518 (m-80) REVERT: C 627 ASP cc_start: 0.9215 (t0) cc_final: 0.8985 (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: 0.8085 (mmt) REVERT: C 704 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7964 (tp30) REVERT: C 728 PHE cc_start: 0.7581 (m-80) cc_final: 0.7237 (m-80) REVERT: C 735 ASN cc_start: 0.8840 (m-40) cc_final: 0.8361 (m110) REVERT: C 752 ASP cc_start: 0.7757 (m-30) cc_final: 0.7539 (m-30) REVERT: D 144 ASP cc_start: 0.9181 (t70) cc_final: 0.8716 (t0) REVERT: D 198 ASP cc_start: 0.7789 (m-30) cc_final: 0.7579 (t0) REVERT: D 256 HIS cc_start: 0.6755 (p90) cc_final: 0.6072 (p90) REVERT: D 282 MET cc_start: 0.8900 (tpp) cc_final: 0.8518 (tpp) REVERT: D 322 ASP cc_start: 0.8897 (t0) cc_final: 0.8546 (t0) REVERT: D 326 LEU cc_start: 0.9287 (mp) cc_final: 0.9078 (mp) REVERT: D 351 MET cc_start: 0.8920 (mmt) cc_final: 0.8657 (mmm) REVERT: D 414 ASP cc_start: 0.7621 (m-30) cc_final: 0.6760 (t0) REVERT: D 506 PHE cc_start: 0.9039 (t80) cc_final: 0.8544 (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: 0.8939 (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: 0.8088 (mmt) REVERT: D 704 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7939 (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: 0.8395 (m110) REVERT: D 752 ASP cc_start: 0.7811 (m-30) cc_final: 0.7543 (m-30) outliers start: 32 outliers final: 12 residues processed: 841 average time/residue: 0.3205 time to fit residues: 413.7867 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 : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 232 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 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 452 ASN B 585 HIS ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 HIS C 452 ASN C 585 HIS C 695 GLN D 417 HIS D 452 ASN D 585 HIS D 695 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.095277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.077091 restraints weight = 59751.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.079064 restraints weight = 35912.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.081009 restraints weight = 25760.240| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21460 Z= 0.194 Angle : 0.785 11.377 29032 Z= 0.400 Chirality : 0.044 0.214 3308 Planarity : 0.006 0.092 3624 Dihedral : 6.482 33.538 2808 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.81 % Favored : 87.03 % Rotamer: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.15), residues: 2568 helix: -1.61 (0.11), residues: 1496 sheet: -3.61 (0.44), residues: 68 loop : -3.73 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 742 HIS 0.003 0.001 HIS B 471 PHE 0.044 0.002 PHE D 633 TYR 0.015 0.002 TYR A 622 ARG 0.005 0.001 ARG A 733 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 888) hydrogen bonds : angle 4.92156 ( 2580) covalent geometry : bond 0.00413 (21460) covalent geometry : angle 0.78514 (29032) *********************** 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 724 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 724 time to evaluate : 2.500 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: 0.9303 (mm) cc_final: 0.9046 (tp) REVERT: A 220 ASN cc_start: 0.9151 (m-40) cc_final: 0.8746 (m-40) REVERT: A 256 HIS cc_start: 0.6935 (p90) cc_final: 0.6649 (p-80) REVERT: A 282 MET cc_start: 0.8853 (tpp) cc_final: 0.8642 (tpp) REVERT: A 290 THR cc_start: 0.9396 (m) cc_final: 0.9149 (p) REVERT: A 322 ASP cc_start: 0.8890 (t0) cc_final: 0.8294 (t0) REVERT: A 323 MET cc_start: 0.8988 (ttm) cc_final: 0.8604 (tmm) REVERT: A 326 LEU cc_start: 0.9206 (mp) cc_final: 0.8997 (mp) REVERT: A 351 MET cc_start: 0.9120 (mmt) cc_final: 0.8899 (mmm) REVERT: A 364 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 414 ASP cc_start: 0.8123 (m-30) cc_final: 0.7186 (t0) REVERT: A 439 TYR cc_start: 0.8996 (m-80) cc_final: 0.8751 (m-10) REVERT: A 461 TYR cc_start: 0.6952 (t80) cc_final: 0.6722 (t80) REVERT: A 501 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8003 (tp30) REVERT: A 506 PHE cc_start: 0.9065 (t80) cc_final: 0.8575 (m-80) REVERT: A 539 LEU cc_start: 0.9398 (tp) cc_final: 0.9038 (pp) REVERT: A 565 TYR cc_start: 0.9244 (m-80) cc_final: 0.8959 (m-80) REVERT: A 567 ARG cc_start: 0.8392 (mtt180) cc_final: 0.8106 (mtt90) REVERT: A 591 LEU cc_start: 0.8960 (tp) cc_final: 0.8502 (tt) REVERT: A 595 ILE cc_start: 0.9335 (mt) cc_final: 0.9055 (mt) REVERT: A 677 MET cc_start: 0.8453 (mmm) cc_final: 0.8175 (tpp) REVERT: A 699 THR cc_start: 0.9717 (p) cc_final: 0.9438 (t) REVERT: A 704 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8157 (tp30) REVERT: A 728 PHE cc_start: 0.7726 (m-80) cc_final: 0.7313 (m-80) REVERT: A 742 TRP cc_start: 0.7339 (m-90) cc_final: 0.7057 (m-90) REVERT: B 139 LEU cc_start: 0.9322 (mm) cc_final: 0.9066 (tp) REVERT: B 196 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8912 (tm-30) REVERT: B 220 ASN cc_start: 0.9176 (m-40) cc_final: 0.8778 (m-40) REVERT: B 256 HIS cc_start: 0.6886 (p90) cc_final: 0.6644 (p-80) REVERT: B 290 THR cc_start: 0.9398 (m) cc_final: 0.9150 (p) REVERT: B 322 ASP cc_start: 0.8921 (t0) cc_final: 0.8322 (t0) REVERT: B 323 MET cc_start: 0.9034 (ttm) cc_final: 0.8671 (tmm) REVERT: B 326 LEU cc_start: 0.9223 (mp) cc_final: 0.9012 (mp) REVERT: B 351 MET cc_start: 0.9128 (mmt) cc_final: 0.8914 (mmm) REVERT: B 414 ASP cc_start: 0.8109 (m-30) cc_final: 0.7162 (t0) REVERT: B 439 TYR cc_start: 0.9005 (m-80) cc_final: 0.8673 (m-10) REVERT: B 461 TYR cc_start: 0.6846 (t80) cc_final: 0.6616 (t80) REVERT: B 501 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8016 (tp30) REVERT: B 506 PHE cc_start: 0.9063 (t80) cc_final: 0.8563 (m-80) REVERT: B 539 LEU cc_start: 0.9382 (tp) cc_final: 0.9017 (pp) REVERT: B 567 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8155 (mtt90) REVERT: B 591 LEU cc_start: 0.8955 (tp) cc_final: 0.8491 (tt) REVERT: B 595 ILE cc_start: 0.9320 (mt) cc_final: 0.9028 (mt) REVERT: B 682 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8192 (mm-30) REVERT: B 688 SER cc_start: 0.9024 (t) cc_final: 0.8529 (t) REVERT: B 699 THR cc_start: 0.9714 (p) cc_final: 0.9437 (t) REVERT: B 704 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8148 (tp30) REVERT: B 728 PHE cc_start: 0.7747 (m-80) cc_final: 0.7294 (m-80) REVERT: B 742 TRP cc_start: 0.7469 (m-90) cc_final: 0.7245 (m-90) REVERT: C 139 LEU cc_start: 0.9329 (mm) cc_final: 0.9079 (tp) REVERT: C 196 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8910 (tm-30) REVERT: C 220 ASN cc_start: 0.9167 (m-40) cc_final: 0.8761 (m-40) REVERT: C 256 HIS cc_start: 0.6974 (p90) cc_final: 0.6249 (p90) REVERT: C 282 MET cc_start: 0.8823 (tpp) cc_final: 0.8614 (tpp) REVERT: C 322 ASP cc_start: 0.8906 (t0) cc_final: 0.8299 (t0) REVERT: C 323 MET cc_start: 0.9038 (ttm) cc_final: 0.8703 (tmm) REVERT: C 326 LEU cc_start: 0.9233 (mp) cc_final: 0.9024 (mp) REVERT: C 351 MET cc_start: 0.9129 (mmt) cc_final: 0.8906 (mmm) REVERT: C 414 ASP cc_start: 0.8085 (m-30) cc_final: 0.7141 (t0) REVERT: C 439 TYR cc_start: 0.9001 (m-80) cc_final: 0.8667 (m-10) REVERT: C 440 MET cc_start: 0.8409 (tpp) cc_final: 0.8195 (tpp) REVERT: C 461 TYR cc_start: 0.6877 (t80) cc_final: 0.6634 (t80) REVERT: C 501 GLU cc_start: 0.8629 (mm-30) cc_final: 0.7982 (tp30) REVERT: C 506 PHE cc_start: 0.9050 (t80) cc_final: 0.8561 (m-80) REVERT: C 539 LEU cc_start: 0.9381 (tp) cc_final: 0.9018 (pp) REVERT: C 555 MET cc_start: 0.8821 (mtp) cc_final: 0.8312 (mtt) REVERT: C 567 ARG cc_start: 0.8364 (mtt180) cc_final: 0.8090 (mtt90) REVERT: C 591 LEU cc_start: 0.8938 (tp) cc_final: 0.8482 (tt) REVERT: C 595 ILE cc_start: 0.9329 (mt) cc_final: 0.9036 (mt) REVERT: C 677 MET cc_start: 0.8483 (mmm) cc_final: 0.8243 (tpp) REVERT: C 688 SER cc_start: 0.9045 (t) cc_final: 0.8517 (t) REVERT: C 699 THR cc_start: 0.9711 (p) cc_final: 0.9435 (t) REVERT: C 704 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8150 (tp30) REVERT: C 728 PHE cc_start: 0.7755 (m-80) cc_final: 0.7308 (m-80) REVERT: D 139 LEU cc_start: 0.9327 (mm) cc_final: 0.9080 (tp) REVERT: D 196 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8909 (tm-30) REVERT: D 220 ASN cc_start: 0.9194 (m-40) cc_final: 0.8767 (m-40) REVERT: D 256 HIS cc_start: 0.6989 (p90) cc_final: 0.6232 (p90) REVERT: D 282 MET cc_start: 0.8849 (tpp) cc_final: 0.8632 (tpp) REVERT: D 322 ASP cc_start: 0.8888 (t0) cc_final: 0.8286 (t0) REVERT: D 323 MET cc_start: 0.9026 (ttm) cc_final: 0.8703 (tmm) REVERT: D 326 LEU cc_start: 0.9225 (mp) cc_final: 0.9020 (mp) REVERT: D 351 MET cc_start: 0.9128 (mmt) cc_final: 0.8898 (mmm) REVERT: D 414 ASP cc_start: 0.8100 (m-30) cc_final: 0.7142 (t0) REVERT: D 439 TYR cc_start: 0.8991 (m-80) cc_final: 0.8698 (m-10) REVERT: D 461 TYR cc_start: 0.6756 (t80) cc_final: 0.6545 (t80) REVERT: D 501 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7915 (tp30) REVERT: D 506 PHE cc_start: 0.9046 (t80) cc_final: 0.8580 (m-80) REVERT: D 539 LEU cc_start: 0.9399 (tp) cc_final: 0.9054 (pp) REVERT: D 565 TYR cc_start: 0.9237 (m-80) cc_final: 0.8953 (m-80) REVERT: D 567 ARG cc_start: 0.8358 (mtt180) cc_final: 0.8098 (mtt90) REVERT: D 591 LEU cc_start: 0.8939 (tp) cc_final: 0.8499 (tt) REVERT: D 595 ILE cc_start: 0.9323 (mt) cc_final: 0.9034 (mt) REVERT: D 677 MET cc_start: 0.8487 (mmm) cc_final: 0.8258 (tpp) REVERT: D 688 SER cc_start: 0.9077 (t) cc_final: 0.8551 (t) REVERT: D 699 THR cc_start: 0.9717 (p) cc_final: 0.9441 (t) REVERT: D 704 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8078 (tp30) REVERT: D 717 MET cc_start: 0.7987 (tpp) cc_final: 0.7399 (tmm) REVERT: D 728 PHE cc_start: 0.7708 (m-80) cc_final: 0.7291 (m-80) outliers start: 0 outliers final: 0 residues processed: 724 average time/residue: 0.3028 time to fit residues: 345.2093 Evaluate side-chains 537 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 250 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS B 452 ASN B 735 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN C 735 ASN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.077661 restraints weight = 59773.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.079997 restraints weight = 35612.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.081834 restraints weight = 24336.161| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21460 Z= 0.190 Angle : 0.750 10.439 29032 Z= 0.382 Chirality : 0.044 0.216 3308 Planarity : 0.005 0.056 3624 Dihedral : 6.077 32.427 2808 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.28 % Favored : 86.53 % Rotamer: Outliers : 0.17 % Allowed : 4.87 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.16), residues: 2568 helix: -0.56 (0.13), residues: 1468 sheet: -3.71 (0.43), residues: 68 loop : -3.61 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 742 HIS 0.009 0.001 HIS D 301 PHE 0.014 0.001 PHE D 715 TYR 0.012 0.001 TYR D 575 ARG 0.005 0.001 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 888) hydrogen bonds : angle 4.56293 ( 2580) covalent geometry : bond 0.00413 (21460) covalent geometry : angle 0.74973 (29032) *********************** 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 705 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 701 time to evaluate : 2.514 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 122 ARG cc_start: 0.8276 (tpt-90) cc_final: 0.7910 (mmm160) REVERT: A 139 LEU cc_start: 0.9357 (mm) cc_final: 0.9080 (tp) REVERT: A 220 ASN cc_start: 0.9064 (m-40) cc_final: 0.8680 (m-40) REVERT: A 322 ASP cc_start: 0.9047 (t0) cc_final: 0.8410 (t70) REVERT: A 351 MET cc_start: 0.9076 (mmt) cc_final: 0.8867 (mmm) REVERT: A 440 MET cc_start: 0.8397 (tpp) cc_final: 0.7757 (tpp) REVERT: A 461 TYR cc_start: 0.7154 (t80) cc_final: 0.6811 (t80) REVERT: A 471 HIS cc_start: 0.7531 (p90) cc_final: 0.7152 (p90) REVERT: A 501 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8003 (tp30) REVERT: A 506 PHE cc_start: 0.9012 (t80) cc_final: 0.8506 (m-80) REVERT: A 517 LEU cc_start: 0.9303 (pt) cc_final: 0.9086 (pt) REVERT: A 555 MET cc_start: 0.9120 (mtt) cc_final: 0.8754 (mtt) REVERT: A 561 ASN cc_start: 0.8709 (m110) cc_final: 0.8314 (m110) REVERT: A 565 TYR cc_start: 0.9333 (m-80) cc_final: 0.8962 (m-80) REVERT: A 585 HIS cc_start: 0.8131 (t-90) cc_final: 0.7755 (t-90) REVERT: A 591 LEU cc_start: 0.8965 (tp) cc_final: 0.8492 (tt) REVERT: A 595 ILE cc_start: 0.9307 (mt) cc_final: 0.8997 (mt) REVERT: A 672 MET cc_start: 0.9146 (ttp) cc_final: 0.8931 (tmm) REVERT: A 677 MET cc_start: 0.8393 (mmm) cc_final: 0.8013 (tpp) REVERT: A 699 THR cc_start: 0.9676 (p) cc_final: 0.9305 (t) REVERT: A 717 MET cc_start: 0.7834 (tpp) cc_final: 0.7132 (tmm) REVERT: A 722 LYS cc_start: 0.7464 (mttt) cc_final: 0.7186 (tttt) REVERT: A 728 PHE cc_start: 0.7552 (m-80) cc_final: 0.7150 (m-80) REVERT: B 139 LEU cc_start: 0.9385 (mm) cc_final: 0.9104 (tp) REVERT: B 220 ASN cc_start: 0.9082 (m-40) cc_final: 0.8709 (m-40) REVERT: B 282 MET cc_start: 0.9147 (tpp) cc_final: 0.8661 (tpp) REVERT: B 322 ASP cc_start: 0.9052 (t0) cc_final: 0.8370 (t70) REVERT: B 351 MET cc_start: 0.9100 (mmt) cc_final: 0.8867 (mmm) REVERT: B 414 ASP cc_start: 0.8181 (m-30) cc_final: 0.7222 (t0) REVERT: B 440 MET cc_start: 0.8343 (tpp) cc_final: 0.7735 (tpp) REVERT: B 461 TYR cc_start: 0.7113 (t80) cc_final: 0.6783 (t80) REVERT: B 471 HIS cc_start: 0.7602 (p90) cc_final: 0.7268 (p90) REVERT: B 501 GLU cc_start: 0.8675 (mm-30) cc_final: 0.7980 (tp30) REVERT: B 506 PHE cc_start: 0.9029 (t80) cc_final: 0.8507 (m-80) REVERT: B 517 LEU cc_start: 0.9341 (pt) cc_final: 0.9125 (pt) REVERT: B 555 MET cc_start: 0.9117 (mtt) cc_final: 0.8751 (mtt) REVERT: B 561 ASN cc_start: 0.8777 (m110) cc_final: 0.8370 (m110) REVERT: B 585 HIS cc_start: 0.8219 (t-90) cc_final: 0.7934 (t-90) REVERT: B 591 LEU cc_start: 0.8968 (tp) cc_final: 0.8524 (tt) REVERT: B 595 ILE cc_start: 0.9314 (mt) cc_final: 0.9031 (mt) REVERT: B 699 THR cc_start: 0.9698 (p) cc_final: 0.9316 (t) REVERT: B 728 PHE cc_start: 0.7557 (m-80) cc_final: 0.7141 (m-80) REVERT: B 742 TRP cc_start: 0.7521 (m-90) cc_final: 0.6923 (m-90) REVERT: C 139 LEU cc_start: 0.9381 (mm) cc_final: 0.9099 (tp) REVERT: C 220 ASN cc_start: 0.9090 (m-40) cc_final: 0.8717 (m-40) REVERT: C 322 ASP cc_start: 0.9006 (t0) cc_final: 0.8339 (t70) REVERT: C 351 MET cc_start: 0.9078 (mmt) cc_final: 0.8860 (mmm) REVERT: C 414 ASP cc_start: 0.8141 (m-30) cc_final: 0.7216 (t0) REVERT: C 440 MET cc_start: 0.8361 (tpp) cc_final: 0.7770 (tpp) REVERT: C 461 TYR cc_start: 0.7148 (t80) cc_final: 0.6817 (t80) REVERT: C 471 HIS cc_start: 0.7572 (p90) cc_final: 0.7238 (p90) REVERT: C 501 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8073 (tp30) REVERT: C 506 PHE cc_start: 0.9033 (t80) cc_final: 0.8514 (m-80) REVERT: C 517 LEU cc_start: 0.9321 (pt) cc_final: 0.9108 (pt) REVERT: C 555 MET cc_start: 0.8794 (mtp) cc_final: 0.8275 (mtt) REVERT: C 561 ASN cc_start: 0.8797 (m110) cc_final: 0.8393 (m110) REVERT: C 585 HIS cc_start: 0.8242 (t-90) cc_final: 0.7954 (t-90) REVERT: C 591 LEU cc_start: 0.8970 (tp) cc_final: 0.8522 (tt) REVERT: C 595 ILE cc_start: 0.9322 (mt) cc_final: 0.9041 (mt) REVERT: C 677 MET cc_start: 0.8405 (mmm) cc_final: 0.8091 (tpp) REVERT: C 699 THR cc_start: 0.9704 (p) cc_final: 0.9311 (t) REVERT: C 728 PHE cc_start: 0.7517 (m-80) cc_final: 0.7149 (m-80) REVERT: C 742 TRP cc_start: 0.7468 (m-90) cc_final: 0.7091 (m-90) REVERT: D 139 LEU cc_start: 0.9377 (mm) cc_final: 0.9098 (tp) REVERT: D 185 GLU cc_start: 0.9050 (mp0) cc_final: 0.8370 (pm20) REVERT: D 220 ASN cc_start: 0.9083 (m-40) cc_final: 0.8720 (m-40) REVERT: D 256 HIS cc_start: 0.7026 (p90) cc_final: 0.6185 (p90) REVERT: D 322 ASP cc_start: 0.9012 (t0) cc_final: 0.8351 (t70) REVERT: D 351 MET cc_start: 0.9089 (mmt) cc_final: 0.8875 (mmm) REVERT: D 414 ASP cc_start: 0.8143 (m-30) cc_final: 0.7236 (t0) REVERT: D 440 MET cc_start: 0.8357 (tpp) cc_final: 0.7757 (tpp) REVERT: D 461 TYR cc_start: 0.7122 (t80) cc_final: 0.6819 (t80) REVERT: D 471 HIS cc_start: 0.7525 (p90) cc_final: 0.7206 (p90) REVERT: D 501 GLU cc_start: 0.8684 (mm-30) cc_final: 0.7993 (tp30) REVERT: D 506 PHE cc_start: 0.9028 (t80) cc_final: 0.8531 (m-80) REVERT: D 517 LEU cc_start: 0.9316 (pt) cc_final: 0.9087 (pt) REVERT: D 532 LEU cc_start: 0.9594 (mm) cc_final: 0.9223 (mm) REVERT: D 550 CYS cc_start: 0.8936 (p) cc_final: 0.8283 (t) REVERT: D 551 LEU cc_start: 0.9623 (tp) cc_final: 0.9291 (tp) REVERT: D 555 MET cc_start: 0.9138 (mtt) cc_final: 0.8727 (mtt) REVERT: D 561 ASN cc_start: 0.8718 (m110) cc_final: 0.8363 (m110) REVERT: D 565 TYR cc_start: 0.9313 (m-80) cc_final: 0.8966 (m-80) REVERT: D 585 HIS cc_start: 0.8247 (t-90) cc_final: 0.7916 (t-90) REVERT: D 591 LEU cc_start: 0.8942 (tp) cc_final: 0.8413 (tt) REVERT: D 595 ILE cc_start: 0.9307 (mt) cc_final: 0.8977 (mt) REVERT: D 677 MET cc_start: 0.8413 (mmm) cc_final: 0.8068 (tpp) REVERT: D 699 THR cc_start: 0.9676 (p) cc_final: 0.9302 (t) REVERT: D 728 PHE cc_start: 0.7506 (m-80) cc_final: 0.7135 (m-80) REVERT: D 742 TRP cc_start: 0.7495 (m-90) cc_final: 0.7042 (m-90) outliers start: 4 outliers final: 1 residues processed: 705 average time/residue: 0.2869 time to fit residues: 322.8879 Evaluate side-chains 512 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 511 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 B 273 ASN B 452 ASN B 643 ASN B 671 ASN B 735 ASN C 256 HIS C 273 ASN C 452 ASN C 643 ASN C 671 ASN C 735 ASN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN D 452 ASN D 643 ASN D 735 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.079473 restraints weight = 60222.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.081941 restraints weight = 36088.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.083551 restraints weight = 24983.597| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21460 Z= 0.147 Angle : 0.718 9.908 29032 Z= 0.361 Chirality : 0.043 0.228 3308 Planarity : 0.004 0.046 3624 Dihedral : 5.692 29.148 2808 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.23 % Favored : 87.62 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.16), residues: 2568 helix: -0.07 (0.13), residues: 1472 sheet: -3.65 (0.43), residues: 68 loop : -3.57 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 493 HIS 0.006 0.001 HIS D 301 PHE 0.021 0.001 PHE C 489 TYR 0.016 0.001 TYR B 565 ARG 0.007 0.001 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 888) hydrogen bonds : angle 4.20499 ( 2580) covalent geometry : bond 0.00317 (21460) covalent geometry : angle 0.71832 (29032) *********************** 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 666 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 2.312 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: 0.9355 (mm) cc_final: 0.9055 (tp) REVERT: A 159 MET cc_start: 0.8545 (mmm) cc_final: 0.8267 (tpt) REVERT: A 220 ASN cc_start: 0.9035 (m-40) cc_final: 0.8692 (m-40) REVERT: A 320 MET cc_start: 0.8661 (ttm) cc_final: 0.8440 (ttp) REVERT: A 322 ASP cc_start: 0.8979 (t0) cc_final: 0.8433 (t70) REVERT: A 351 MET cc_start: 0.9105 (mmt) cc_final: 0.8870 (mmm) REVERT: A 440 MET cc_start: 0.8435 (tpp) cc_final: 0.7911 (tpp) REVERT: A 461 TYR cc_start: 0.7359 (t80) cc_final: 0.6922 (t80) REVERT: A 501 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7880 (tp30) REVERT: A 506 PHE cc_start: 0.9022 (t80) cc_final: 0.8474 (m-80) REVERT: A 555 MET cc_start: 0.9124 (mtt) cc_final: 0.8740 (mtt) REVERT: A 565 TYR cc_start: 0.9244 (m-80) cc_final: 0.8766 (m-80) REVERT: A 578 MET cc_start: 0.8799 (mtm) cc_final: 0.8579 (mmt) REVERT: A 585 HIS cc_start: 0.8280 (t-90) cc_final: 0.7966 (t-90) REVERT: A 591 LEU cc_start: 0.8936 (tp) cc_final: 0.8425 (tt) REVERT: A 595 ILE cc_start: 0.9249 (mt) cc_final: 0.8944 (mt) REVERT: A 677 MET cc_start: 0.8359 (mmm) cc_final: 0.7970 (tpp) REVERT: A 699 THR cc_start: 0.9665 (p) cc_final: 0.9447 (t) REVERT: A 722 LYS cc_start: 0.7478 (mttt) cc_final: 0.7234 (tttt) REVERT: A 728 PHE cc_start: 0.7525 (m-80) cc_final: 0.7153 (m-80) REVERT: B 139 LEU cc_start: 0.9380 (mm) cc_final: 0.9052 (tp) REVERT: B 220 ASN cc_start: 0.9062 (m-40) cc_final: 0.8716 (m-40) REVERT: B 322 ASP cc_start: 0.8973 (t0) cc_final: 0.8479 (t70) REVERT: B 351 MET cc_start: 0.9079 (mmt) cc_final: 0.8818 (mmm) REVERT: B 440 MET cc_start: 0.8408 (tpp) cc_final: 0.7898 (tpp) REVERT: B 461 TYR cc_start: 0.7319 (t80) cc_final: 0.6914 (t80) REVERT: B 501 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7875 (tp30) REVERT: B 506 PHE cc_start: 0.9017 (t80) cc_final: 0.8512 (m-80) REVERT: B 532 LEU cc_start: 0.9566 (mm) cc_final: 0.9183 (mm) REVERT: B 550 CYS cc_start: 0.8891 (p) cc_final: 0.8245 (t) REVERT: B 555 MET cc_start: 0.9102 (mtt) cc_final: 0.8741 (mtt) REVERT: B 585 HIS cc_start: 0.8286 (t-90) cc_final: 0.7997 (t-90) REVERT: B 591 LEU cc_start: 0.8986 (tp) cc_final: 0.8468 (tt) REVERT: B 595 ILE cc_start: 0.9250 (mt) cc_final: 0.8953 (mt) REVERT: B 682 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 699 THR cc_start: 0.9673 (p) cc_final: 0.9430 (t) REVERT: B 722 LYS cc_start: 0.7557 (tttt) cc_final: 0.7348 (mttt) REVERT: B 728 PHE cc_start: 0.7507 (m-80) cc_final: 0.7184 (m-80) REVERT: C 139 LEU cc_start: 0.9378 (mm) cc_final: 0.9044 (tp) REVERT: C 220 ASN cc_start: 0.9055 (m-40) cc_final: 0.8703 (m-40) REVERT: C 320 MET cc_start: 0.8668 (ttm) cc_final: 0.8386 (ttp) REVERT: C 322 ASP cc_start: 0.8966 (t0) cc_final: 0.8414 (t70) REVERT: C 323 MET cc_start: 0.8992 (tmm) cc_final: 0.8692 (tmm) REVERT: C 351 MET cc_start: 0.9134 (mmt) cc_final: 0.8900 (mmm) REVERT: C 414 ASP cc_start: 0.8212 (m-30) cc_final: 0.7211 (t0) REVERT: C 440 MET cc_start: 0.8329 (tpp) cc_final: 0.7799 (tpp) REVERT: C 461 TYR cc_start: 0.7342 (t80) cc_final: 0.6882 (t80) REVERT: C 501 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7913 (tp30) REVERT: C 506 PHE cc_start: 0.9053 (t80) cc_final: 0.8522 (m-80) REVERT: C 555 MET cc_start: 0.8805 (mtp) cc_final: 0.8271 (mtt) REVERT: C 585 HIS cc_start: 0.8342 (t-90) cc_final: 0.8057 (t-90) REVERT: C 591 LEU cc_start: 0.8972 (tp) cc_final: 0.8454 (tt) REVERT: C 595 ILE cc_start: 0.9259 (mt) cc_final: 0.8956 (mt) REVERT: C 677 MET cc_start: 0.8312 (mmm) cc_final: 0.8012 (tpp) REVERT: C 699 THR cc_start: 0.9636 (p) cc_final: 0.9393 (t) REVERT: C 722 LYS cc_start: 0.7549 (tttt) cc_final: 0.7308 (tttt) REVERT: C 728 PHE cc_start: 0.7497 (m-80) cc_final: 0.7169 (m-80) REVERT: D 139 LEU cc_start: 0.9391 (mm) cc_final: 0.9075 (tp) REVERT: D 220 ASN cc_start: 0.9075 (m-40) cc_final: 0.8710 (m-40) REVERT: D 322 ASP cc_start: 0.8958 (t0) cc_final: 0.8434 (t70) REVERT: D 351 MET cc_start: 0.9092 (mmt) cc_final: 0.8831 (mmm) REVERT: D 414 ASP cc_start: 0.8251 (m-30) cc_final: 0.7201 (t0) REVERT: D 440 MET cc_start: 0.8435 (tpp) cc_final: 0.7949 (tpp) REVERT: D 461 TYR cc_start: 0.7318 (t80) cc_final: 0.6903 (t80) REVERT: D 501 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7880 (tp30) REVERT: D 506 PHE cc_start: 0.9031 (t80) cc_final: 0.8485 (m-80) REVERT: D 551 LEU cc_start: 0.9618 (tp) cc_final: 0.9288 (tp) REVERT: D 555 MET cc_start: 0.9133 (mtt) cc_final: 0.8701 (mtt) REVERT: D 565 TYR cc_start: 0.9254 (m-80) cc_final: 0.8888 (m-80) REVERT: D 585 HIS cc_start: 0.8397 (t-90) cc_final: 0.8125 (t-90) REVERT: D 591 LEU cc_start: 0.8990 (tp) cc_final: 0.8578 (tt) REVERT: D 595 ILE cc_start: 0.9258 (mt) cc_final: 0.8958 (mt) REVERT: D 677 MET cc_start: 0.8325 (mmm) cc_final: 0.8070 (tpp) REVERT: D 699 THR cc_start: 0.9661 (p) cc_final: 0.9422 (t) REVERT: D 722 LYS cc_start: 0.7465 (mttt) cc_final: 0.7157 (tttt) REVERT: D 728 PHE cc_start: 0.7480 (m-80) cc_final: 0.7146 (m-80) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.2843 time to fit residues: 300.7828 Evaluate side-chains 514 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 204 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 245 optimal weight: 0.4980 chunk 248 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN B 273 ASN B 683 ASN B 735 ASN C 273 ASN C 735 ASN D 523 HIS D 735 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.082589 restraints weight = 59166.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.085052 restraints weight = 35685.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.086774 restraints weight = 24858.389| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21460 Z= 0.130 Angle : 0.706 9.536 29032 Z= 0.354 Chirality : 0.042 0.224 3308 Planarity : 0.004 0.050 3624 Dihedral : 5.424 27.053 2808 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.31 % Favored : 87.54 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.16), residues: 2568 helix: 0.23 (0.13), residues: 1492 sheet: -3.13 (0.51), residues: 68 loop : -3.55 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 493 HIS 0.004 0.001 HIS B 301 PHE 0.013 0.001 PHE B 666 TYR 0.018 0.001 TYR B 382 ARG 0.008 0.001 ARG D 464 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 888) hydrogen bonds : angle 4.17028 ( 2580) covalent geometry : bond 0.00277 (21460) covalent geometry : angle 0.70639 (29032) *********************** 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 695 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 695 time to evaluate : 2.497 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: 0.9215 (mm) cc_final: 0.8830 (tp) REVERT: A 159 MET cc_start: 0.8470 (mmm) cc_final: 0.8172 (tpt) REVERT: A 191 LEU cc_start: 0.9627 (mt) cc_final: 0.9347 (mt) REVERT: A 220 ASN cc_start: 0.9069 (m-40) cc_final: 0.8678 (m-40) REVERT: A 244 HIS cc_start: 0.8726 (m-70) cc_final: 0.8483 (m170) REVERT: A 263 GLU cc_start: 0.6381 (pp20) cc_final: 0.6117 (pp20) REVERT: A 308 GLU cc_start: 0.6719 (pm20) cc_final: 0.6037 (pm20) REVERT: A 322 ASP cc_start: 0.8897 (t0) cc_final: 0.8198 (t70) REVERT: A 351 MET cc_start: 0.9069 (mmt) cc_final: 0.8863 (mmm) REVERT: A 440 MET cc_start: 0.8523 (tpp) cc_final: 0.8027 (tpp) REVERT: A 461 TYR cc_start: 0.7322 (t80) cc_final: 0.7011 (t80) REVERT: A 501 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7785 (tp30) REVERT: A 506 PHE cc_start: 0.8897 (t80) cc_final: 0.8435 (m-80) REVERT: A 555 MET cc_start: 0.9080 (mtt) cc_final: 0.8777 (mtm) REVERT: A 565 TYR cc_start: 0.9176 (m-80) cc_final: 0.8525 (m-80) REVERT: A 572 MET cc_start: 0.8672 (tmm) cc_final: 0.8316 (tmm) REVERT: A 585 HIS cc_start: 0.8386 (t-90) cc_final: 0.8028 (t-90) REVERT: A 591 LEU cc_start: 0.8965 (tp) cc_final: 0.8390 (tt) REVERT: A 595 ILE cc_start: 0.9226 (mt) cc_final: 0.8819 (mt) REVERT: A 677 MET cc_start: 0.8319 (mmm) cc_final: 0.7720 (tpp) REVERT: B 139 LEU cc_start: 0.9341 (mm) cc_final: 0.9020 (tp) REVERT: B 159 MET cc_start: 0.8476 (mmm) cc_final: 0.8219 (mmm) REVERT: B 191 LEU cc_start: 0.9645 (mt) cc_final: 0.9407 (mt) REVERT: B 220 ASN cc_start: 0.9109 (m-40) cc_final: 0.8735 (m-40) REVERT: B 244 HIS cc_start: 0.8742 (m-70) cc_final: 0.8484 (m170) REVERT: B 322 ASP cc_start: 0.8671 (t0) cc_final: 0.8088 (t0) REVERT: B 440 MET cc_start: 0.8394 (tpp) cc_final: 0.7965 (tpp) REVERT: B 461 TYR cc_start: 0.7263 (t80) cc_final: 0.6974 (t80) REVERT: B 501 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7809 (tp30) REVERT: B 506 PHE cc_start: 0.8919 (t80) cc_final: 0.8445 (m-80) REVERT: B 555 MET cc_start: 0.9058 (mtt) cc_final: 0.8773 (mtm) REVERT: B 585 HIS cc_start: 0.8450 (t-90) cc_final: 0.8247 (t-90) REVERT: B 591 LEU cc_start: 0.8963 (tp) cc_final: 0.8483 (tt) REVERT: B 595 ILE cc_start: 0.9221 (mt) cc_final: 0.8921 (mt) REVERT: B 682 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 699 THR cc_start: 0.9688 (p) cc_final: 0.9481 (t) REVERT: B 715 PHE cc_start: 0.7593 (t80) cc_final: 0.6198 (t80) REVERT: C 139 LEU cc_start: 0.9336 (mm) cc_final: 0.9017 (tp) REVERT: C 159 MET cc_start: 0.8479 (mmm) cc_final: 0.8217 (mmm) REVERT: C 191 LEU cc_start: 0.9651 (mt) cc_final: 0.9413 (mt) REVERT: C 220 ASN cc_start: 0.9110 (m-40) cc_final: 0.8709 (m-40) REVERT: C 244 HIS cc_start: 0.8761 (m-70) cc_final: 0.8477 (m170) REVERT: C 308 GLU cc_start: 0.6669 (pm20) cc_final: 0.5806 (pm20) REVERT: C 322 ASP cc_start: 0.8934 (t0) cc_final: 0.8245 (t70) REVERT: C 351 MET cc_start: 0.9038 (mmt) cc_final: 0.8834 (mmm) REVERT: C 414 ASP cc_start: 0.8136 (m-30) cc_final: 0.7040 (t0) REVERT: C 440 MET cc_start: 0.8155 (tpp) cc_final: 0.7744 (tpp) REVERT: C 461 TYR cc_start: 0.7283 (t80) cc_final: 0.6986 (t80) REVERT: C 501 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7810 (tp30) REVERT: C 506 PHE cc_start: 0.8932 (t80) cc_final: 0.8468 (m-80) REVERT: C 551 LEU cc_start: 0.9524 (tp) cc_final: 0.9102 (tp) REVERT: C 555 MET cc_start: 0.8803 (mtp) cc_final: 0.8286 (mtm) REVERT: C 585 HIS cc_start: 0.8486 (t-90) cc_final: 0.8234 (t-90) REVERT: C 591 LEU cc_start: 0.8966 (tp) cc_final: 0.8428 (tt) REVERT: C 595 ILE cc_start: 0.9228 (mt) cc_final: 0.8841 (mt) REVERT: C 677 MET cc_start: 0.8192 (mmm) cc_final: 0.7738 (tpp) REVERT: C 699 THR cc_start: 0.9625 (p) cc_final: 0.9410 (t) REVERT: C 742 TRP cc_start: 0.7022 (m-90) cc_final: 0.6775 (m-90) REVERT: D 139 LEU cc_start: 0.9349 (mm) cc_final: 0.9011 (tp) REVERT: D 159 MET cc_start: 0.8474 (mmm) cc_final: 0.8214 (mmm) REVERT: D 176 LEU cc_start: 0.9615 (mm) cc_final: 0.9413 (mm) REVERT: D 191 LEU cc_start: 0.9651 (mt) cc_final: 0.9416 (mt) REVERT: D 220 ASN cc_start: 0.9112 (m-40) cc_final: 0.8751 (m-40) REVERT: D 244 HIS cc_start: 0.8763 (m-70) cc_final: 0.8519 (m170) REVERT: D 322 ASP cc_start: 0.8780 (t0) cc_final: 0.7993 (t0) REVERT: D 351 MET cc_start: 0.9045 (mmt) cc_final: 0.8819 (mmm) REVERT: D 440 MET cc_start: 0.8512 (tpp) cc_final: 0.8027 (tpp) REVERT: D 461 TYR cc_start: 0.7300 (t80) cc_final: 0.6985 (t80) REVERT: D 501 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7767 (tp30) REVERT: D 506 PHE cc_start: 0.8931 (t80) cc_final: 0.8443 (m-80) REVERT: D 551 LEU cc_start: 0.9592 (tp) cc_final: 0.9259 (tp) REVERT: D 555 MET cc_start: 0.9101 (mtt) cc_final: 0.8706 (mtt) REVERT: D 565 TYR cc_start: 0.9165 (m-80) cc_final: 0.8558 (m-80) REVERT: D 585 HIS cc_start: 0.8422 (t-90) cc_final: 0.8203 (t-90) REVERT: D 591 LEU cc_start: 0.8968 (tp) cc_final: 0.8445 (tt) REVERT: D 595 ILE cc_start: 0.9234 (mt) cc_final: 0.8901 (mt) REVERT: D 677 MET cc_start: 0.8290 (mmm) cc_final: 0.7755 (tpp) REVERT: D 715 PHE cc_start: 0.7555 (t80) cc_final: 0.6102 (t80) REVERT: D 742 TRP cc_start: 0.7000 (m-90) cc_final: 0.6700 (m-90) outliers start: 0 outliers final: 0 residues processed: 695 average time/residue: 0.2848 time to fit residues: 314.6713 Evaluate side-chains 507 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 211 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 683 ASN A 735 ASN B 452 ASN B 580 GLN B 735 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 580 GLN D 735 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.081237 restraints weight = 59569.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083801 restraints weight = 35580.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.085544 restraints weight = 24625.250| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21460 Z= 0.138 Angle : 0.707 9.306 29032 Z= 0.351 Chirality : 0.042 0.222 3308 Planarity : 0.004 0.044 3624 Dihedral : 5.294 23.595 2808 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.42 % Favored : 87.42 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.17), residues: 2568 helix: 0.31 (0.13), residues: 1488 sheet: -3.07 (0.53), residues: 68 loop : -3.38 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 742 HIS 0.003 0.001 HIS B 301 PHE 0.022 0.001 PHE A 489 TYR 0.017 0.001 TYR A 382 ARG 0.008 0.001 ARG D 464 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 888) hydrogen bonds : angle 4.14598 ( 2580) covalent geometry : bond 0.00297 (21460) covalent geometry : angle 0.70677 (29032) *********************** 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 633 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 633 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9244 (mm) cc_final: 0.8880 (tp) REVERT: A 159 MET cc_start: 0.8547 (mmm) cc_final: 0.8230 (tpt) REVERT: A 185 GLU cc_start: 0.9108 (mp0) cc_final: 0.8407 (pm20) REVERT: A 220 ASN cc_start: 0.9162 (m-40) cc_final: 0.8797 (m-40) REVERT: A 244 HIS cc_start: 0.8809 (m-70) cc_final: 0.8511 (m170) REVERT: A 322 ASP cc_start: 0.8708 (t0) cc_final: 0.7954 (t0) REVERT: A 351 MET cc_start: 0.9120 (mmt) cc_final: 0.8873 (mmm) REVERT: A 440 MET cc_start: 0.8628 (tpp) cc_final: 0.8136 (tpp) REVERT: A 461 TYR cc_start: 0.7349 (t80) cc_final: 0.7054 (t80) REVERT: A 501 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7734 (tp30) REVERT: A 506 PHE cc_start: 0.8931 (t80) cc_final: 0.8405 (m-80) REVERT: A 555 MET cc_start: 0.9021 (mtt) cc_final: 0.8664 (mtt) REVERT: A 565 TYR cc_start: 0.9204 (m-80) cc_final: 0.8552 (m-80) REVERT: A 585 HIS cc_start: 0.8315 (t-90) cc_final: 0.8023 (t-90) REVERT: A 591 LEU cc_start: 0.8987 (tp) cc_final: 0.8438 (tt) REVERT: A 595 ILE cc_start: 0.9216 (mt) cc_final: 0.8806 (mt) REVERT: B 139 LEU cc_start: 0.9394 (mm) cc_final: 0.9090 (tp) REVERT: B 185 GLU cc_start: 0.9085 (mp0) cc_final: 0.8388 (pm20) REVERT: B 220 ASN cc_start: 0.9161 (m-40) cc_final: 0.8812 (m-40) REVERT: B 244 HIS cc_start: 0.8760 (m-70) cc_final: 0.8541 (m90) REVERT: B 308 GLU cc_start: 0.6763 (pm20) cc_final: 0.6092 (pm20) REVERT: B 322 ASP cc_start: 0.8697 (t0) cc_final: 0.8031 (t0) REVERT: B 440 MET cc_start: 0.8562 (tpp) cc_final: 0.8133 (tpp) REVERT: B 461 TYR cc_start: 0.7285 (t80) cc_final: 0.7001 (t80) REVERT: B 501 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7799 (tp30) REVERT: B 506 PHE cc_start: 0.8947 (t80) cc_final: 0.8410 (m-80) REVERT: B 555 MET cc_start: 0.9019 (mtt) cc_final: 0.8677 (mtt) REVERT: B 585 HIS cc_start: 0.8437 (t-90) cc_final: 0.8218 (t-90) REVERT: B 591 LEU cc_start: 0.8963 (tp) cc_final: 0.8407 (tt) REVERT: B 595 ILE cc_start: 0.9202 (mt) cc_final: 0.8765 (mt) REVERT: B 677 MET cc_start: 0.8295 (mmm) cc_final: 0.7679 (tmm) REVERT: B 715 PHE cc_start: 0.7702 (t80) cc_final: 0.6885 (t80) REVERT: C 139 LEU cc_start: 0.9380 (mm) cc_final: 0.9069 (tp) REVERT: C 185 GLU cc_start: 0.9092 (mp0) cc_final: 0.8410 (pm20) REVERT: C 220 ASN cc_start: 0.9182 (m-40) cc_final: 0.8817 (m-40) REVERT: C 244 HIS cc_start: 0.8743 (m-70) cc_final: 0.8466 (m170) REVERT: C 322 ASP cc_start: 0.8810 (t0) cc_final: 0.8091 (t0) REVERT: C 351 MET cc_start: 0.9154 (mmt) cc_final: 0.8928 (mmm) REVERT: C 440 MET cc_start: 0.8318 (tpp) cc_final: 0.7823 (tpp) REVERT: C 461 TYR cc_start: 0.7290 (t80) cc_final: 0.6978 (t80) REVERT: C 506 PHE cc_start: 0.8953 (t80) cc_final: 0.8464 (m-80) REVERT: C 551 LEU cc_start: 0.9525 (tp) cc_final: 0.9319 (tp) REVERT: C 555 MET cc_start: 0.8775 (mtp) cc_final: 0.8240 (mtt) REVERT: C 561 ASN cc_start: 0.8868 (m-40) cc_final: 0.8352 (m110) REVERT: C 585 HIS cc_start: 0.8481 (t-90) cc_final: 0.8198 (t-90) REVERT: C 591 LEU cc_start: 0.8941 (tp) cc_final: 0.8494 (tt) REVERT: C 595 ILE cc_start: 0.9208 (mt) cc_final: 0.8925 (mt) REVERT: C 677 MET cc_start: 0.8084 (mmm) cc_final: 0.7727 (tpp) REVERT: C 699 THR cc_start: 0.9645 (p) cc_final: 0.9442 (t) REVERT: D 139 LEU cc_start: 0.9394 (mm) cc_final: 0.9079 (tp) REVERT: D 220 ASN cc_start: 0.9129 (m-40) cc_final: 0.8777 (m-40) REVERT: D 244 HIS cc_start: 0.8787 (m-70) cc_final: 0.8475 (m170) REVERT: D 256 HIS cc_start: 0.6728 (p-80) cc_final: 0.6435 (p-80) REVERT: D 308 GLU cc_start: 0.6739 (pm20) cc_final: 0.6007 (pm20) REVERT: D 322 ASP cc_start: 0.8771 (t0) cc_final: 0.8063 (t0) REVERT: D 326 LEU cc_start: 0.9130 (mp) cc_final: 0.8896 (pp) REVERT: D 351 MET cc_start: 0.9111 (mmt) cc_final: 0.8866 (mmm) REVERT: D 440 MET cc_start: 0.8603 (tpp) cc_final: 0.8114 (tpp) REVERT: D 461 TYR cc_start: 0.7317 (t80) cc_final: 0.7012 (t80) REVERT: D 501 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7735 (tp30) REVERT: D 506 PHE cc_start: 0.8991 (t80) cc_final: 0.8491 (m-80) REVERT: D 551 LEU cc_start: 0.9585 (tp) cc_final: 0.9248 (tp) REVERT: D 555 MET cc_start: 0.9084 (mtt) cc_final: 0.8681 (mtt) REVERT: D 565 TYR cc_start: 0.9249 (m-80) cc_final: 0.8628 (m-80) REVERT: D 591 LEU cc_start: 0.8962 (tp) cc_final: 0.8445 (tt) REVERT: D 595 ILE cc_start: 0.9229 (mt) cc_final: 0.8897 (mt) REVERT: D 715 PHE cc_start: 0.7766 (t80) cc_final: 0.6497 (t80) REVERT: D 745 HIS cc_start: 0.8039 (m-70) cc_final: 0.7479 (m-70) outliers start: 0 outliers final: 0 residues processed: 633 average time/residue: 0.2954 time to fit residues: 296.6290 Evaluate side-chains 496 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 65 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 13 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 580 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN C 523 HIS ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN D 452 ASN ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.101378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083023 restraints weight = 59520.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.085613 restraints weight = 35802.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.087409 restraints weight = 24886.775| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21460 Z= 0.128 Angle : 0.703 8.915 29032 Z= 0.346 Chirality : 0.042 0.220 3308 Planarity : 0.004 0.046 3624 Dihedral : 5.166 24.186 2808 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.11 % Favored : 87.77 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.17), residues: 2568 helix: 0.36 (0.13), residues: 1504 sheet: -2.75 (0.55), residues: 60 loop : -3.41 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 742 HIS 0.004 0.001 HIS B 745 PHE 0.017 0.001 PHE A 203 TYR 0.018 0.001 TYR B 359 ARG 0.006 0.000 ARG C 733 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 888) hydrogen bonds : angle 4.16555 ( 2580) covalent geometry : bond 0.00272 (21460) covalent geometry : angle 0.70349 (29032) *********************** 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 667 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 667 time to evaluate : 2.399 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: 0.9233 (mm) cc_final: 0.8826 (tp) REVERT: A 159 MET cc_start: 0.8560 (mmm) cc_final: 0.8270 (tpt) REVERT: A 220 ASN cc_start: 0.9128 (m-40) cc_final: 0.8788 (m-40) REVERT: A 322 ASP cc_start: 0.8546 (t0) cc_final: 0.7895 (t0) REVERT: A 351 MET cc_start: 0.9104 (mmt) cc_final: 0.8901 (mmm) REVERT: A 440 MET cc_start: 0.8601 (tpp) cc_final: 0.8168 (tpp) REVERT: A 461 TYR cc_start: 0.7361 (t80) cc_final: 0.7085 (t80) REVERT: A 501 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7672 (tp30) REVERT: A 506 PHE cc_start: 0.8928 (t80) cc_final: 0.8422 (m-80) REVERT: A 532 LEU cc_start: 0.9499 (mm) cc_final: 0.9045 (mm) REVERT: A 550 CYS cc_start: 0.8958 (p) cc_final: 0.8272 (t) REVERT: A 551 LEU cc_start: 0.9598 (tp) cc_final: 0.9304 (tp) REVERT: A 555 MET cc_start: 0.9060 (mtt) cc_final: 0.8657 (mtt) REVERT: A 561 ASN cc_start: 0.8625 (m110) cc_final: 0.8099 (m110) REVERT: A 565 TYR cc_start: 0.9135 (m-80) cc_final: 0.8488 (m-80) REVERT: A 585 HIS cc_start: 0.8363 (t-90) cc_final: 0.8105 (t-90) REVERT: A 591 LEU cc_start: 0.8976 (tp) cc_final: 0.8438 (tt) REVERT: A 595 ILE cc_start: 0.9194 (mt) cc_final: 0.8765 (mt) REVERT: A 745 HIS cc_start: 0.7921 (m-70) cc_final: 0.7390 (m-70) REVERT: B 139 LEU cc_start: 0.9374 (mm) cc_final: 0.9016 (tp) REVERT: B 159 MET cc_start: 0.8522 (mmm) cc_final: 0.8294 (mmm) REVERT: B 220 ASN cc_start: 0.9131 (m-40) cc_final: 0.8776 (m-40) REVERT: B 256 HIS cc_start: 0.7235 (p-80) cc_final: 0.7021 (p-80) REVERT: B 440 MET cc_start: 0.8565 (tpp) cc_final: 0.8155 (tpp) REVERT: B 461 TYR cc_start: 0.7326 (t80) cc_final: 0.7053 (t80) REVERT: B 501 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7807 (tp30) REVERT: B 506 PHE cc_start: 0.8953 (t80) cc_final: 0.8440 (m-80) REVERT: B 526 PHE cc_start: 0.8297 (m-10) cc_final: 0.8028 (m-10) REVERT: B 532 LEU cc_start: 0.9495 (mm) cc_final: 0.9051 (mm) REVERT: B 550 CYS cc_start: 0.8919 (p) cc_final: 0.8229 (t) REVERT: B 551 LEU cc_start: 0.9576 (tp) cc_final: 0.9305 (tp) REVERT: B 555 MET cc_start: 0.9027 (mtt) cc_final: 0.8700 (mtt) REVERT: B 585 HIS cc_start: 0.8459 (t-90) cc_final: 0.8243 (t-90) REVERT: B 595 ILE cc_start: 0.9194 (mt) cc_final: 0.8941 (mt) REVERT: B 715 PHE cc_start: 0.7544 (t80) cc_final: 0.6414 (t80) REVERT: C 139 LEU cc_start: 0.9366 (mm) cc_final: 0.9011 (tp) REVERT: C 159 MET cc_start: 0.8522 (mmm) cc_final: 0.8299 (mmm) REVERT: C 185 GLU cc_start: 0.9068 (mp0) cc_final: 0.8398 (pm20) REVERT: C 220 ASN cc_start: 0.9155 (m-40) cc_final: 0.8795 (m-40) REVERT: C 244 HIS cc_start: 0.8735 (m-70) cc_final: 0.8420 (m170) REVERT: C 256 HIS cc_start: 0.6565 (p-80) cc_final: 0.6197 (p-80) REVERT: C 308 GLU cc_start: 0.6455 (pm20) cc_final: 0.6121 (pm20) REVERT: C 322 ASP cc_start: 0.8485 (t0) cc_final: 0.7926 (t0) REVERT: C 351 MET cc_start: 0.9139 (mmt) cc_final: 0.8916 (mmm) REVERT: C 440 MET cc_start: 0.8317 (tpp) cc_final: 0.7771 (tpp) REVERT: C 461 TYR cc_start: 0.7296 (t80) cc_final: 0.7039 (t80) REVERT: C 505 ILE cc_start: 0.9548 (pt) cc_final: 0.9256 (tt) REVERT: C 506 PHE cc_start: 0.8936 (t80) cc_final: 0.8448 (m-80) REVERT: C 532 LEU cc_start: 0.9493 (mm) cc_final: 0.9064 (mm) REVERT: C 550 CYS cc_start: 0.8866 (p) cc_final: 0.8181 (t) REVERT: C 551 LEU cc_start: 0.9530 (tp) cc_final: 0.9312 (tp) REVERT: C 555 MET cc_start: 0.8745 (mtp) cc_final: 0.8263 (mtt) REVERT: C 561 ASN cc_start: 0.8879 (m-40) cc_final: 0.7839 (m110) REVERT: C 574 MET cc_start: 0.8844 (tpp) cc_final: 0.8540 (tpp) REVERT: C 585 HIS cc_start: 0.8451 (t-90) cc_final: 0.8216 (t-90) REVERT: C 595 ILE cc_start: 0.9210 (mt) cc_final: 0.8952 (mt) REVERT: C 677 MET cc_start: 0.8068 (mmm) cc_final: 0.7643 (tpp) REVERT: C 682 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8101 (mm-30) REVERT: C 715 PHE cc_start: 0.7348 (t80) cc_final: 0.6319 (t80) REVERT: C 743 LYS cc_start: 0.8203 (pttt) cc_final: 0.7972 (pttm) REVERT: C 745 HIS cc_start: 0.7959 (m-70) cc_final: 0.7506 (m-70) REVERT: D 139 LEU cc_start: 0.9382 (mm) cc_final: 0.9023 (tp) REVERT: D 159 MET cc_start: 0.8526 (mmm) cc_final: 0.8301 (mmm) REVERT: D 176 LEU cc_start: 0.9610 (mm) cc_final: 0.9409 (mm) REVERT: D 220 ASN cc_start: 0.9126 (m-40) cc_final: 0.8808 (m-40) REVERT: D 271 CYS cc_start: 0.9475 (m) cc_final: 0.9228 (m) REVERT: D 322 ASP cc_start: 0.8445 (t0) cc_final: 0.7941 (t0) REVERT: D 351 MET cc_start: 0.9105 (mmt) cc_final: 0.8904 (mmm) REVERT: D 440 MET cc_start: 0.8604 (tpp) cc_final: 0.8177 (tpp) REVERT: D 461 TYR cc_start: 0.7389 (t80) cc_final: 0.7072 (t80) REVERT: D 501 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7677 (tp30) REVERT: D 506 PHE cc_start: 0.8961 (t80) cc_final: 0.8444 (m-80) REVERT: D 532 LEU cc_start: 0.9499 (mm) cc_final: 0.9033 (mm) REVERT: D 550 CYS cc_start: 0.8866 (p) cc_final: 0.8206 (t) REVERT: D 551 LEU cc_start: 0.9585 (tp) cc_final: 0.9235 (tp) REVERT: D 555 MET cc_start: 0.9063 (mtt) cc_final: 0.8624 (mtt) REVERT: D 565 TYR cc_start: 0.9207 (m-80) cc_final: 0.8626 (m-80) REVERT: D 574 MET cc_start: 0.8870 (tpp) cc_final: 0.8575 (tpp) REVERT: D 585 HIS cc_start: 0.8277 (t-90) cc_final: 0.8019 (t-90) REVERT: D 595 ILE cc_start: 0.9209 (mt) cc_final: 0.8908 (mt) REVERT: D 715 PHE cc_start: 0.7727 (t80) cc_final: 0.6344 (t80) REVERT: D 743 LYS cc_start: 0.8186 (pttt) cc_final: 0.7941 (pttm) REVERT: D 745 HIS cc_start: 0.7934 (m-70) cc_final: 0.7452 (m-70) outliers start: 0 outliers final: 0 residues processed: 667 average time/residue: 0.2898 time to fit residues: 306.8653 Evaluate side-chains 532 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 219 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 52 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN B 745 HIS C 561 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084016 restraints weight = 59518.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086632 restraints weight = 35836.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088462 restraints weight = 24945.450| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21460 Z= 0.132 Angle : 0.725 9.508 29032 Z= 0.354 Chirality : 0.043 0.218 3308 Planarity : 0.005 0.065 3624 Dihedral : 5.078 23.809 2808 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.72 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.17), residues: 2568 helix: 0.44 (0.13), residues: 1500 sheet: -3.10 (0.49), residues: 68 loop : -3.36 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 742 HIS 0.004 0.001 HIS B 745 PHE 0.024 0.001 PHE C 489 TYR 0.018 0.001 TYR A 382 ARG 0.010 0.001 ARG B 464 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 888) hydrogen bonds : angle 4.17771 ( 2580) covalent geometry : bond 0.00287 (21460) covalent geometry : angle 0.72486 (29032) *********************** 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 662 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 2.366 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: 0.9216 (mm) cc_final: 0.8822 (tp) REVERT: A 159 MET cc_start: 0.8535 (mmm) cc_final: 0.8251 (tpt) REVERT: A 185 GLU cc_start: 0.9030 (mp0) cc_final: 0.8402 (pm20) REVERT: A 220 ASN cc_start: 0.9109 (m-40) cc_final: 0.8785 (m-40) REVERT: A 320 MET cc_start: 0.8518 (ttm) cc_final: 0.8146 (ttp) REVERT: A 322 ASP cc_start: 0.8686 (t0) cc_final: 0.8162 (t0) REVERT: A 326 LEU cc_start: 0.9117 (mp) cc_final: 0.8801 (pp) REVERT: A 440 MET cc_start: 0.8583 (tpp) cc_final: 0.8272 (tpp) REVERT: A 461 TYR cc_start: 0.7449 (t80) cc_final: 0.7204 (t80) REVERT: A 462 ARG cc_start: 0.6479 (mmt90) cc_final: 0.5494 (mtm110) REVERT: A 506 PHE cc_start: 0.8931 (t80) cc_final: 0.8425 (m-80) REVERT: A 532 LEU cc_start: 0.9502 (mm) cc_final: 0.9049 (mm) REVERT: A 550 CYS cc_start: 0.8944 (p) cc_final: 0.8212 (t) REVERT: A 551 LEU cc_start: 0.9598 (tp) cc_final: 0.9347 (tp) REVERT: A 555 MET cc_start: 0.9060 (mtt) cc_final: 0.8689 (mtt) REVERT: A 565 TYR cc_start: 0.9147 (m-80) cc_final: 0.8517 (m-80) REVERT: A 585 HIS cc_start: 0.8383 (t-90) cc_final: 0.8171 (t-90) REVERT: A 591 LEU cc_start: 0.8963 (tp) cc_final: 0.8422 (tt) REVERT: A 595 ILE cc_start: 0.9157 (mt) cc_final: 0.8824 (mt) REVERT: A 677 MET cc_start: 0.7905 (tpp) cc_final: 0.7696 (mmm) REVERT: A 743 LYS cc_start: 0.8165 (pttt) cc_final: 0.7825 (pttm) REVERT: A 745 HIS cc_start: 0.7937 (m-70) cc_final: 0.7495 (m-70) REVERT: B 139 LEU cc_start: 0.9334 (mm) cc_final: 0.8969 (tp) REVERT: B 159 MET cc_start: 0.8537 (mmm) cc_final: 0.8311 (mmm) REVERT: B 185 GLU cc_start: 0.9042 (mp0) cc_final: 0.8404 (pm20) REVERT: B 220 ASN cc_start: 0.9102 (m-40) cc_final: 0.8766 (m-40) REVERT: B 271 CYS cc_start: 0.9315 (m) cc_final: 0.9103 (m) REVERT: B 353 LYS cc_start: 0.9666 (mmtt) cc_final: 0.9280 (mmtp) REVERT: B 440 MET cc_start: 0.8585 (tpp) cc_final: 0.8345 (tpp) REVERT: B 461 TYR cc_start: 0.7313 (t80) cc_final: 0.7003 (t80) REVERT: B 462 ARG cc_start: 0.6412 (mmt90) cc_final: 0.5434 (mtm110) REVERT: B 501 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 506 PHE cc_start: 0.8931 (t80) cc_final: 0.8408 (m-80) REVERT: B 532 LEU cc_start: 0.9495 (mm) cc_final: 0.9007 (mm) REVERT: B 550 CYS cc_start: 0.8924 (p) cc_final: 0.8167 (t) REVERT: B 551 LEU cc_start: 0.9584 (tp) cc_final: 0.9334 (tp) REVERT: B 555 MET cc_start: 0.9063 (mtt) cc_final: 0.8695 (mtt) REVERT: B 595 ILE cc_start: 0.9159 (mt) cc_final: 0.8894 (mt) REVERT: B 677 MET cc_start: 0.8278 (mmm) cc_final: 0.7789 (tpp) REVERT: B 715 PHE cc_start: 0.7393 (t80) cc_final: 0.6896 (t80) REVERT: B 735 ASN cc_start: 0.8196 (m-40) cc_final: 0.7968 (m-40) REVERT: C 139 LEU cc_start: 0.9341 (mm) cc_final: 0.8986 (tp) REVERT: C 159 MET cc_start: 0.8536 (mmm) cc_final: 0.8305 (mmm) REVERT: C 185 GLU cc_start: 0.9045 (mp0) cc_final: 0.8403 (pm20) REVERT: C 220 ASN cc_start: 0.9122 (m-40) cc_final: 0.8799 (m-40) REVERT: C 440 MET cc_start: 0.8322 (tpp) cc_final: 0.7863 (tpp) REVERT: C 461 TYR cc_start: 0.7322 (t80) cc_final: 0.7004 (t80) REVERT: C 462 ARG cc_start: 0.6423 (mmt90) cc_final: 0.5417 (mtm110) REVERT: C 506 PHE cc_start: 0.8942 (t80) cc_final: 0.8505 (m-80) REVERT: C 532 LEU cc_start: 0.9492 (mm) cc_final: 0.9022 (mm) REVERT: C 550 CYS cc_start: 0.8877 (p) cc_final: 0.8142 (t) REVERT: C 585 HIS cc_start: 0.8430 (t-90) cc_final: 0.8222 (t-90) REVERT: C 595 ILE cc_start: 0.9172 (mt) cc_final: 0.8906 (mt) REVERT: C 677 MET cc_start: 0.8002 (mmm) cc_final: 0.7697 (tpp) REVERT: C 706 MET cc_start: 0.8689 (ttt) cc_final: 0.8399 (tpt) REVERT: C 715 PHE cc_start: 0.7287 (t80) cc_final: 0.6572 (t80) REVERT: C 745 HIS cc_start: 0.7863 (m-70) cc_final: 0.7455 (m-70) REVERT: D 139 LEU cc_start: 0.9357 (mm) cc_final: 0.8878 (pp) REVERT: D 159 MET cc_start: 0.8570 (mmm) cc_final: 0.8357 (mmm) REVERT: D 220 ASN cc_start: 0.9085 (m-40) cc_final: 0.8766 (m-40) REVERT: D 271 CYS cc_start: 0.9234 (m) cc_final: 0.8976 (m) REVERT: D 351 MET cc_start: 0.9093 (mmt) cc_final: 0.8885 (mmm) REVERT: D 440 MET cc_start: 0.8589 (tpp) cc_final: 0.8322 (tpp) REVERT: D 461 TYR cc_start: 0.7288 (t80) cc_final: 0.6990 (t80) REVERT: D 462 ARG cc_start: 0.6423 (mmt90) cc_final: 0.5405 (mtm110) REVERT: D 506 PHE cc_start: 0.8950 (t80) cc_final: 0.8428 (m-80) REVERT: D 532 LEU cc_start: 0.9500 (mm) cc_final: 0.9029 (mm) REVERT: D 550 CYS cc_start: 0.8865 (p) cc_final: 0.8179 (t) REVERT: D 551 LEU cc_start: 0.9580 (tp) cc_final: 0.9239 (tp) REVERT: D 555 MET cc_start: 0.9046 (mtt) cc_final: 0.8632 (mtt) REVERT: D 565 TYR cc_start: 0.9167 (m-80) cc_final: 0.8577 (m-80) REVERT: D 585 HIS cc_start: 0.8319 (t-90) cc_final: 0.8088 (t-90) REVERT: D 595 ILE cc_start: 0.9178 (mt) cc_final: 0.8878 (mt) REVERT: D 715 PHE cc_start: 0.7499 (t80) cc_final: 0.6467 (t80) REVERT: D 745 HIS cc_start: 0.7845 (m-70) cc_final: 0.7479 (m-70) outliers start: 0 outliers final: 0 residues processed: 662 average time/residue: 0.2988 time to fit residues: 309.5453 Evaluate side-chains 545 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 207 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 ASN C 580 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN C 745 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 745 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.084002 restraints weight = 58953.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086617 restraints weight = 35741.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.088426 restraints weight = 24949.929| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21460 Z= 0.128 Angle : 0.719 10.239 29032 Z= 0.350 Chirality : 0.042 0.215 3308 Planarity : 0.004 0.053 3624 Dihedral : 5.025 24.293 2808 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.72 % Favored : 88.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 2568 helix: 0.47 (0.13), residues: 1504 sheet: -2.87 (0.51), residues: 68 loop : -3.32 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 739 HIS 0.004 0.001 HIS D 745 PHE 0.016 0.001 PHE D 590 TYR 0.018 0.001 TYR D 382 ARG 0.011 0.001 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 888) hydrogen bonds : angle 4.20946 ( 2580) covalent geometry : bond 0.00278 (21460) covalent geometry : angle 0.71862 (29032) *********************** 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 651 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 651 time to evaluate : 2.401 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: 0.9269 (mm) cc_final: 0.8887 (tp) REVERT: A 159 MET cc_start: 0.8557 (mmm) cc_final: 0.8241 (tpt) REVERT: A 185 GLU cc_start: 0.9047 (mp0) cc_final: 0.8419 (pm20) REVERT: A 220 ASN cc_start: 0.9101 (m-40) cc_final: 0.8773 (m-40) REVERT: A 320 MET cc_start: 0.8483 (ttm) cc_final: 0.8200 (ttp) REVERT: A 322 ASP cc_start: 0.8546 (t0) cc_final: 0.8071 (t0) REVERT: A 423 GLU cc_start: 0.7462 (tp30) cc_final: 0.7183 (mm-30) REVERT: A 461 TYR cc_start: 0.7504 (t80) cc_final: 0.7269 (t80) REVERT: A 506 PHE cc_start: 0.8922 (t80) cc_final: 0.8450 (m-80) REVERT: A 532 LEU cc_start: 0.9490 (mm) cc_final: 0.9023 (mm) REVERT: A 550 CYS cc_start: 0.8928 (p) cc_final: 0.8161 (t) REVERT: A 551 LEU cc_start: 0.9584 (tp) cc_final: 0.9321 (tp) REVERT: A 555 MET cc_start: 0.9016 (mtt) cc_final: 0.8669 (mtt) REVERT: A 565 TYR cc_start: 0.9137 (m-80) cc_final: 0.8506 (m-80) REVERT: A 585 HIS cc_start: 0.8358 (t-90) cc_final: 0.8150 (t-90) REVERT: A 595 ILE cc_start: 0.9177 (mt) cc_final: 0.8861 (mt) REVERT: A 715 PHE cc_start: 0.6729 (t80) cc_final: 0.6286 (t80) REVERT: A 735 ASN cc_start: 0.8028 (m-40) cc_final: 0.7553 (m110) REVERT: A 743 LYS cc_start: 0.8158 (pttt) cc_final: 0.7745 (pttm) REVERT: A 745 HIS cc_start: 0.7833 (m-70) cc_final: 0.7398 (m-70) REVERT: B 139 LEU cc_start: 0.9356 (mm) cc_final: 0.8984 (tp) REVERT: B 159 MET cc_start: 0.8586 (mmm) cc_final: 0.8333 (mmm) REVERT: B 185 GLU cc_start: 0.9033 (mp0) cc_final: 0.8402 (pm20) REVERT: B 220 ASN cc_start: 0.9083 (m-40) cc_final: 0.8708 (m-40) REVERT: B 308 GLU cc_start: 0.6469 (pm20) cc_final: 0.6161 (pm20) REVERT: B 353 LYS cc_start: 0.9652 (mmtt) cc_final: 0.9255 (mmtp) REVERT: B 461 TYR cc_start: 0.7520 (t80) cc_final: 0.7293 (t80) REVERT: B 501 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7634 (mm-30) REVERT: B 506 PHE cc_start: 0.8921 (t80) cc_final: 0.8455 (m-80) REVERT: B 551 LEU cc_start: 0.9567 (tp) cc_final: 0.9344 (tp) REVERT: B 555 MET cc_start: 0.9054 (mtt) cc_final: 0.8714 (mtt) REVERT: B 574 MET cc_start: 0.8603 (tpp) cc_final: 0.8312 (tpp) REVERT: B 585 HIS cc_start: 0.8521 (t-90) cc_final: 0.8267 (t-90) REVERT: B 595 ILE cc_start: 0.9172 (mt) cc_final: 0.8897 (mt) REVERT: B 677 MET cc_start: 0.8304 (mmm) cc_final: 0.7844 (tpp) REVERT: B 715 PHE cc_start: 0.7589 (t80) cc_final: 0.6927 (t80) REVERT: C 139 LEU cc_start: 0.9366 (mm) cc_final: 0.8984 (tp) REVERT: C 159 MET cc_start: 0.8574 (mmm) cc_final: 0.8329 (mmm) REVERT: C 185 GLU cc_start: 0.9040 (mp0) cc_final: 0.8400 (pm20) REVERT: C 220 ASN cc_start: 0.9090 (m-40) cc_final: 0.8743 (m-40) REVERT: C 308 GLU cc_start: 0.6761 (pm20) cc_final: 0.6531 (pm20) REVERT: C 353 LYS cc_start: 0.9590 (mmtt) cc_final: 0.9342 (mmtp) REVERT: C 440 MET cc_start: 0.8303 (tpp) cc_final: 0.7879 (tpp) REVERT: C 461 TYR cc_start: 0.7460 (t80) cc_final: 0.7228 (t80) REVERT: C 506 PHE cc_start: 0.8954 (t80) cc_final: 0.8513 (m-80) REVERT: C 585 HIS cc_start: 0.8451 (t-90) cc_final: 0.8230 (t-90) REVERT: C 595 ILE cc_start: 0.9183 (mt) cc_final: 0.8916 (mt) REVERT: C 677 MET cc_start: 0.7951 (mmm) cc_final: 0.7744 (tpp) REVERT: C 706 MET cc_start: 0.8663 (ttt) cc_final: 0.8353 (tpt) REVERT: D 139 LEU cc_start: 0.9374 (mm) cc_final: 0.8889 (pp) REVERT: D 159 MET cc_start: 0.8556 (mmm) cc_final: 0.8323 (mmm) REVERT: D 185 GLU cc_start: 0.9015 (mp0) cc_final: 0.8400 (pm20) REVERT: D 220 ASN cc_start: 0.9138 (m-40) cc_final: 0.8804 (m-40) REVERT: D 308 GLU cc_start: 0.6796 (pm20) cc_final: 0.6083 (pm20) REVERT: D 351 MET cc_start: 0.9143 (mmt) cc_final: 0.8912 (mmm) REVERT: D 461 TYR cc_start: 0.7512 (t80) cc_final: 0.7286 (t80) REVERT: D 506 PHE cc_start: 0.8932 (t80) cc_final: 0.8451 (m-80) REVERT: D 532 LEU cc_start: 0.9495 (mm) cc_final: 0.9029 (mm) REVERT: D 550 CYS cc_start: 0.8896 (p) cc_final: 0.8189 (t) REVERT: D 551 LEU cc_start: 0.9585 (tp) cc_final: 0.9314 (tp) REVERT: D 555 MET cc_start: 0.9039 (mtt) cc_final: 0.8673 (mtt) REVERT: D 565 TYR cc_start: 0.9163 (m-80) cc_final: 0.8542 (m-80) REVERT: D 595 ILE cc_start: 0.9164 (mt) cc_final: 0.8895 (mt) REVERT: D 715 PHE cc_start: 0.7319 (t80) cc_final: 0.6963 (t80) outliers start: 0 outliers final: 0 residues processed: 651 average time/residue: 0.2862 time to fit residues: 296.1004 Evaluate side-chains 528 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 92 optimal weight: 0.0270 chunk 236 optimal weight: 0.4980 chunk 212 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 220 optimal weight: 0.0980 chunk 121 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 0.0170 chunk 28 optimal weight: 0.0060 chunk 208 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 overall best weight: 0.1292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 HIS ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 HIS B 561 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087764 restraints weight = 58263.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.090441 restraints weight = 36103.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.092393 restraints weight = 25707.904| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.6607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21460 Z= 0.130 Angle : 0.739 9.115 29032 Z= 0.357 Chirality : 0.042 0.211 3308 Planarity : 0.005 0.093 3624 Dihedral : 4.944 24.396 2808 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.41 % Favored : 88.43 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2568 helix: 0.49 (0.13), residues: 1504 sheet: -1.94 (0.57), residues: 60 loop : -3.20 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 493 HIS 0.004 0.000 HIS B 301 PHE 0.028 0.001 PHE C 526 TYR 0.023 0.001 TYR C 622 ARG 0.009 0.001 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 888) hydrogen bonds : angle 4.22663 ( 2580) covalent geometry : bond 0.00273 (21460) covalent geometry : angle 0.73915 (29032) ********************** 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 680 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 680 time to evaluate : 2.525 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 135 LEU cc_start: 0.9441 (tp) cc_final: 0.9221 (pp) REVERT: A 139 LEU cc_start: 0.9209 (mm) cc_final: 0.8639 (tp) REVERT: A 159 MET cc_start: 0.8611 (mmm) cc_final: 0.8317 (tpt) REVERT: A 185 GLU cc_start: 0.8957 (mp0) cc_final: 0.8345 (pm20) REVERT: A 220 ASN cc_start: 0.9037 (m-40) cc_final: 0.8733 (m-40) REVERT: A 297 ASN cc_start: 0.8150 (t0) cc_final: 0.7909 (t0) REVERT: A 320 MET cc_start: 0.8280 (ttm) cc_final: 0.8039 (ttp) REVERT: A 322 ASP cc_start: 0.8594 (t0) cc_final: 0.8162 (t0) REVERT: A 506 PHE cc_start: 0.8831 (t80) cc_final: 0.8432 (m-80) REVERT: A 532 LEU cc_start: 0.9431 (mm) cc_final: 0.8941 (mm) REVERT: A 550 CYS cc_start: 0.8880 (p) cc_final: 0.7848 (t) REVERT: A 551 LEU cc_start: 0.9565 (tp) cc_final: 0.9339 (tp) REVERT: A 555 MET cc_start: 0.8950 (mtt) cc_final: 0.8670 (mtt) REVERT: A 565 TYR cc_start: 0.8954 (m-80) cc_final: 0.8494 (m-80) REVERT: A 595 ILE cc_start: 0.9140 (mt) cc_final: 0.8874 (mt) REVERT: A 647 ASN cc_start: 0.7325 (t0) cc_final: 0.7112 (t0) REVERT: A 715 PHE cc_start: 0.6627 (t80) cc_final: 0.5881 (t80) REVERT: A 735 ASN cc_start: 0.8135 (m-40) cc_final: 0.7644 (m110) REVERT: A 743 LYS cc_start: 0.8096 (pttt) cc_final: 0.7887 (pttm) REVERT: A 745 HIS cc_start: 0.7701 (m-70) cc_final: 0.7459 (m-70) REVERT: B 139 LEU cc_start: 0.9305 (mm) cc_final: 0.8817 (tp) REVERT: B 159 MET cc_start: 0.8539 (mmm) cc_final: 0.8328 (mmm) REVERT: B 220 ASN cc_start: 0.9014 (m-40) cc_final: 0.8658 (m-40) REVERT: B 308 GLU cc_start: 0.6118 (pm20) cc_final: 0.5880 (pm20) REVERT: B 506 PHE cc_start: 0.8813 (t80) cc_final: 0.8421 (m-80) REVERT: B 551 LEU cc_start: 0.9542 (tp) cc_final: 0.9332 (tp) REVERT: B 555 MET cc_start: 0.9018 (mtt) cc_final: 0.8712 (mtt) REVERT: B 574 MET cc_start: 0.8551 (tpp) cc_final: 0.8269 (tpp) REVERT: B 585 HIS cc_start: 0.8482 (t-90) cc_final: 0.8247 (t-90) REVERT: B 595 ILE cc_start: 0.9153 (mt) cc_final: 0.8904 (mt) REVERT: B 677 MET cc_start: 0.8392 (mmm) cc_final: 0.7982 (tpp) REVERT: C 139 LEU cc_start: 0.9312 (mm) cc_final: 0.8814 (tp) REVERT: C 159 MET cc_start: 0.8501 (mmm) cc_final: 0.8286 (mmm) REVERT: C 185 GLU cc_start: 0.8947 (mp0) cc_final: 0.8324 (pm20) REVERT: C 220 ASN cc_start: 0.9063 (m-40) cc_final: 0.8717 (m-40) REVERT: C 440 MET cc_start: 0.8079 (tpp) cc_final: 0.7877 (tpp) REVERT: C 506 PHE cc_start: 0.8889 (t80) cc_final: 0.8469 (m-80) REVERT: C 532 LEU cc_start: 0.9424 (mm) cc_final: 0.9021 (mm) REVERT: C 550 CYS cc_start: 0.8900 (p) cc_final: 0.7921 (t) REVERT: C 551 LEU cc_start: 0.9564 (tp) cc_final: 0.9333 (tp) REVERT: C 555 MET cc_start: 0.8804 (mtp) cc_final: 0.8298 (mtt) REVERT: C 595 ILE cc_start: 0.9129 (mt) cc_final: 0.8860 (mt) REVERT: C 706 MET cc_start: 0.8613 (ttt) cc_final: 0.8344 (tpt) REVERT: D 139 LEU cc_start: 0.9316 (mm) cc_final: 0.8824 (tp) REVERT: D 159 MET cc_start: 0.8531 (mmm) cc_final: 0.8292 (mmm) REVERT: D 220 ASN cc_start: 0.9024 (m-40) cc_final: 0.8655 (m-40) REVERT: D 297 ASN cc_start: 0.8020 (t0) cc_final: 0.7673 (t0) REVERT: D 351 MET cc_start: 0.9112 (mmt) cc_final: 0.8833 (mmm) REVERT: D 353 LYS cc_start: 0.9633 (mmtt) cc_final: 0.9197 (mmtp) REVERT: D 440 MET cc_start: 0.8243 (tpp) cc_final: 0.7835 (tpp) REVERT: D 506 PHE cc_start: 0.8832 (t80) cc_final: 0.8456 (m-80) REVERT: D 532 LEU cc_start: 0.9422 (mm) cc_final: 0.8893 (mm) REVERT: D 550 CYS cc_start: 0.8859 (p) cc_final: 0.7899 (t) REVERT: D 551 LEU cc_start: 0.9572 (tp) cc_final: 0.9273 (tp) REVERT: D 555 MET cc_start: 0.8987 (mtt) cc_final: 0.8655 (mtt) REVERT: D 565 TYR cc_start: 0.9000 (m-80) cc_final: 0.8487 (m-80) REVERT: D 595 ILE cc_start: 0.9110 (mt) cc_final: 0.8822 (mt) outliers start: 0 outliers final: 0 residues processed: 680 average time/residue: 0.2920 time to fit residues: 314.9392 Evaluate side-chains 548 residues out of total 2300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 172 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 251 optimal weight: 0.0070 chunk 165 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 0.0670 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN A 643 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087632 restraints weight = 58691.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.090319 restraints weight = 36641.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092095 restraints weight = 26009.965| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21460 Z= 0.128 Angle : 0.738 9.279 29032 Z= 0.354 Chirality : 0.042 0.208 3308 Planarity : 0.005 0.086 3624 Dihedral : 4.851 23.986 2808 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.72 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2568 helix: 0.56 (0.14), residues: 1488 sheet: -2.20 (0.54), residues: 68 loop : -3.06 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 331 HIS 0.008 0.001 HIS B 301 PHE 0.017 0.001 PHE A 590 TYR 0.017 0.001 TYR D 382 ARG 0.008 0.001 ARG A 733 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 888) hydrogen bonds : angle 4.12509 ( 2580) covalent geometry : bond 0.00275 (21460) covalent geometry : angle 0.73818 (29032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7699.21 seconds wall clock time: 133 minutes 28.19 seconds (8008.19 seconds total)