Starting phenix.real_space_refine on Mon Mar 18 12:56:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvl_20492/03_2024/6pvl_20492.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvl_20492/03_2024/6pvl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvl_20492/03_2024/6pvl_20492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvl_20492/03_2024/6pvl_20492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvl_20492/03_2024/6pvl_20492.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pvl_20492/03_2024/6pvl_20492.pdb" } 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 Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 758": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 758": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21006 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "B" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "C" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "D" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5251 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 17, 'TRANS': 626} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.55, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 7.22 Conformation dependent library (CDL) restraints added in 3.5 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: 1.84 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: 5.96 Time building geometry restraints manager: 7.92 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: 98.30 - 105.47: 324 105.47 - 112.64: 10970 112.64 - 119.82: 7862 119.82 - 126.99: 9602 126.99 - 134.16: 274 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 2.440 nonbonded pdb=" OH TYR B 260 " pdb=" OD1 ASN B 297 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR D 260 " pdb=" OD1 ASN D 297 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR A 260 " pdb=" OD1 ASN A 297 " model vdw 2.202 2.440 nonbonded pdb=" OG SER A 620 " pdb=" O GLY A 623 " model vdw 2.242 2.440 ... (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 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.500 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 50.640 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.700 ------------------------------------------------------------------------------- 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= 0.484 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 *********************** 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 fitting. rotamer outliers: 32 poor density : 825 time to evaluate : 2.325 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: 0.3097 time to fit residues: 398.4574 Evaluate side-chains 560 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 547 time to evaluate : 2.366 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 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 178 ASN A 220 ASN ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS A 643 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 GLN B 178 ASN B 220 ASN ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 GLN B 585 HIS ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 ASN C 220 ASN ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 ASN ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN C 585 HIS ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN D 178 ASN D 220 ASN D 452 ASN ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21460 Z= 0.258 Angle : 0.771 10.956 29032 Z= 0.392 Chirality : 0.044 0.216 3308 Planarity : 0.005 0.064 3624 Dihedral : 6.454 33.665 2808 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % 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: -3.64 (0.15), residues: 2568 helix: -1.54 (0.11), residues: 1496 sheet: -3.73 (0.43), residues: 68 loop : -3.67 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 742 HIS 0.003 0.001 HIS A 417 PHE 0.042 0.002 PHE D 633 TYR 0.013 0.002 TYR A 622 ARG 0.006 0.001 ARG B 416 *********************** 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 740 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 740 time to evaluate : 2.310 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: A 139 LEU cc_start: 0.9354 (mm) cc_final: 0.9078 (tp) REVERT: A 196 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8908 (tm-30) REVERT: A 220 ASN cc_start: 0.9118 (m110) cc_final: 0.8704 (m110) REVERT: A 256 HIS cc_start: 0.7041 (p-80) cc_final: 0.6588 (p-80) REVERT: A 282 MET cc_start: 0.8869 (tpp) cc_final: 0.8653 (tpp) REVERT: A 322 ASP cc_start: 0.8871 (t0) cc_final: 0.8294 (t0) REVERT: A 323 MET cc_start: 0.8985 (ttm) cc_final: 0.8650 (tmm) REVERT: A 351 MET cc_start: 0.9069 (mmt) cc_final: 0.8852 (mmm) REVERT: A 364 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7779 (tp30) REVERT: A 414 ASP cc_start: 0.7863 (m-30) cc_final: 0.7092 (t0) REVERT: A 439 TYR cc_start: 0.9000 (m-80) cc_final: 0.8766 (m-10) REVERT: A 440 MET cc_start: 0.8426 (tpp) cc_final: 0.7744 (tpp) REVERT: A 461 TYR cc_start: 0.6735 (t80) cc_final: 0.6476 (t80) REVERT: A 506 PHE cc_start: 0.9045 (t80) cc_final: 0.8579 (m-80) REVERT: A 561 ASN cc_start: 0.8906 (m-40) cc_final: 0.7968 (m110) REVERT: A 565 TYR cc_start: 0.9275 (m-80) cc_final: 0.8967 (m-80) REVERT: A 591 LEU cc_start: 0.8934 (tp) cc_final: 0.8489 (tt) REVERT: A 595 ILE cc_start: 0.9309 (mt) cc_final: 0.9018 (mt) REVERT: A 677 MET cc_start: 0.8403 (mmm) cc_final: 0.8201 (tpp) REVERT: A 688 SER cc_start: 0.8869 (t) cc_final: 0.8630 (t) REVERT: A 704 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8137 (tp30) REVERT: A 728 PHE cc_start: 0.7693 (m-80) cc_final: 0.7290 (m-80) REVERT: A 742 TRP cc_start: 0.7380 (m-90) cc_final: 0.7124 (m-90) REVERT: A 752 ASP cc_start: 0.8249 (t0) cc_final: 0.7989 (t0) REVERT: B 139 LEU cc_start: 0.9351 (mm) cc_final: 0.9097 (tp) REVERT: B 196 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8921 (tm-30) REVERT: B 220 ASN cc_start: 0.9151 (m110) cc_final: 0.8743 (m110) REVERT: B 256 HIS cc_start: 0.6979 (p-80) cc_final: 0.6564 (p-80) REVERT: B 290 THR cc_start: 0.9390 (m) cc_final: 0.9112 (p) REVERT: B 320 MET cc_start: 0.8865 (ttm) cc_final: 0.8491 (ttm) REVERT: B 322 ASP cc_start: 0.8911 (t0) cc_final: 0.8258 (t0) REVERT: B 323 MET cc_start: 0.9014 (ttm) cc_final: 0.8802 (tmm) REVERT: B 326 LEU cc_start: 0.9199 (mp) cc_final: 0.8997 (mp) REVERT: B 351 MET cc_start: 0.9085 (mmt) cc_final: 0.8867 (mmm) REVERT: B 364 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7814 (tp30) REVERT: B 414 ASP cc_start: 0.8003 (m-30) cc_final: 0.7143 (t0) REVERT: B 439 TYR cc_start: 0.9009 (m-80) cc_final: 0.8748 (m-10) REVERT: B 440 MET cc_start: 0.8398 (tpp) cc_final: 0.7744 (tpp) REVERT: B 461 TYR cc_start: 0.6507 (t80) cc_final: 0.6247 (t80) REVERT: B 506 PHE cc_start: 0.9047 (t80) cc_final: 0.8574 (m-80) REVERT: B 561 ASN cc_start: 0.8883 (m-40) cc_final: 0.7929 (m110) REVERT: B 591 LEU cc_start: 0.8946 (tp) cc_final: 0.8491 (tt) REVERT: B 595 ILE cc_start: 0.9288 (mt) cc_final: 0.8995 (mt) REVERT: B 677 MET cc_start: 0.8421 (mmm) cc_final: 0.8143 (tpp) REVERT: B 688 SER cc_start: 0.8934 (t) cc_final: 0.8724 (t) REVERT: B 704 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8158 (tp30) REVERT: B 728 PHE cc_start: 0.7717 (m-80) cc_final: 0.7273 (m-80) REVERT: C 139 LEU cc_start: 0.9357 (mm) cc_final: 0.9108 (tp) REVERT: C 196 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8920 (tm-30) REVERT: C 220 ASN cc_start: 0.9141 (m110) cc_final: 0.8731 (m110) REVERT: C 282 MET cc_start: 0.8862 (tpp) cc_final: 0.8642 (tpp) REVERT: C 290 THR cc_start: 0.9398 (m) cc_final: 0.9131 (p) REVERT: C 322 ASP cc_start: 0.8903 (t0) cc_final: 0.8295 (t0) REVERT: C 323 MET cc_start: 0.9009 (ttm) cc_final: 0.8660 (tmm) REVERT: C 326 LEU cc_start: 0.9195 (mp) cc_final: 0.8994 (mp) REVERT: C 351 MET cc_start: 0.9073 (mmt) cc_final: 0.8848 (mmm) REVERT: C 364 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7830 (tp30) REVERT: C 414 ASP cc_start: 0.8002 (m-30) cc_final: 0.7164 (t0) REVERT: C 439 TYR cc_start: 0.9014 (m-80) cc_final: 0.8696 (m-10) REVERT: C 440 MET cc_start: 0.8417 (tpp) cc_final: 0.7758 (tpp) REVERT: C 461 TYR cc_start: 0.6541 (t80) cc_final: 0.6259 (t80) REVERT: C 506 PHE cc_start: 0.9055 (t80) cc_final: 0.8582 (m-80) REVERT: C 555 MET cc_start: 0.8818 (mtp) cc_final: 0.8370 (mtt) REVERT: C 561 ASN cc_start: 0.8887 (m-40) cc_final: 0.7962 (m110) REVERT: C 574 MET cc_start: 0.8946 (tpp) cc_final: 0.8720 (tpp) REVERT: C 591 LEU cc_start: 0.8917 (tp) cc_final: 0.8460 (tt) REVERT: C 595 ILE cc_start: 0.9298 (mt) cc_final: 0.8994 (mt) REVERT: C 677 MET cc_start: 0.8347 (mmm) cc_final: 0.8022 (tpp) REVERT: C 688 SER cc_start: 0.8929 (t) cc_final: 0.8358 (t) REVERT: C 704 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8163 (tp30) REVERT: C 728 PHE cc_start: 0.7696 (m-80) cc_final: 0.7255 (m-80) REVERT: D 139 LEU cc_start: 0.9353 (mm) cc_final: 0.9098 (tp) REVERT: D 196 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8920 (tm-30) REVERT: D 220 ASN cc_start: 0.9157 (m110) cc_final: 0.8731 (m110) REVERT: D 282 MET cc_start: 0.8863 (tpp) cc_final: 0.8641 (tpp) REVERT: D 290 THR cc_start: 0.9333 (m) cc_final: 0.9091 (p) REVERT: D 322 ASP cc_start: 0.8895 (t0) cc_final: 0.8280 (t0) REVERT: D 323 MET cc_start: 0.9019 (ttm) cc_final: 0.8684 (tmm) REVERT: D 326 LEU cc_start: 0.9198 (mp) cc_final: 0.8987 (mp) REVERT: D 351 MET cc_start: 0.9076 (mmt) cc_final: 0.8845 (mmm) REVERT: D 414 ASP cc_start: 0.7993 (m-30) cc_final: 0.7130 (t0) REVERT: D 439 TYR cc_start: 0.8995 (m-80) cc_final: 0.8717 (m-10) REVERT: D 440 MET cc_start: 0.8401 (tpp) cc_final: 0.7713 (tpp) REVERT: D 461 TYR cc_start: 0.6542 (t80) cc_final: 0.6301 (t80) REVERT: D 506 PHE cc_start: 0.9052 (t80) cc_final: 0.8596 (m-80) REVERT: D 561 ASN cc_start: 0.8908 (m-40) cc_final: 0.7961 (m110) REVERT: D 565 TYR cc_start: 0.9266 (m-80) cc_final: 0.8970 (m-80) REVERT: D 574 MET cc_start: 0.8953 (tpp) cc_final: 0.8727 (tpp) REVERT: D 591 LEU cc_start: 0.8910 (tp) cc_final: 0.8458 (tt) REVERT: D 595 ILE cc_start: 0.9296 (mt) cc_final: 0.8990 (mt) REVERT: D 677 MET cc_start: 0.8354 (mmm) cc_final: 0.8035 (tpp) REVERT: D 688 SER cc_start: 0.8928 (t) cc_final: 0.8354 (t) REVERT: D 704 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8081 (tp30) REVERT: D 717 MET cc_start: 0.7940 (tpp) cc_final: 0.7436 (tmm) REVERT: D 728 PHE cc_start: 0.7675 (m-80) cc_final: 0.7260 (m-80) outliers start: 0 outliers final: 0 residues processed: 740 average time/residue: 0.2910 time to fit residues: 338.0851 Evaluate side-chains 537 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 232 optimal weight: 0.1980 chunk 251 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 GLN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 735 ASN C 452 ASN ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 452 ASN ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 GLN ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21460 Z= 0.279 Angle : 0.754 10.678 29032 Z= 0.385 Chirality : 0.043 0.223 3308 Planarity : 0.004 0.054 3624 Dihedral : 6.086 32.812 2808 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.67 % Favored : 86.18 % Rotamer: Outliers : 0.17 % Allowed : 5.22 % Favored : 94.61 % 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: -2.70 (0.15), residues: 2568 helix: -0.49 (0.13), residues: 1476 sheet: -3.97 (0.39), residues: 68 loop : -3.68 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 742 HIS 0.008 0.001 HIS D 301 PHE 0.032 0.002 PHE C 633 TYR 0.015 0.001 TYR A 382 ARG 0.005 0.001 ARG D 375 *********************** 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 673 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 669 time to evaluate : 2.429 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 122 ARG cc_start: 0.8374 (tpt-90) cc_final: 0.7945 (mmm160) REVERT: A 139 LEU cc_start: 0.9395 (mm) cc_final: 0.9106 (tp) REVERT: A 159 MET cc_start: 0.8666 (mmm) cc_final: 0.8404 (tpt) REVERT: A 196 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8893 (tm-30) REVERT: A 220 ASN cc_start: 0.9010 (m110) cc_final: 0.8583 (m110) REVERT: A 290 THR cc_start: 0.9407 (m) cc_final: 0.9127 (p) REVERT: A 322 ASP cc_start: 0.8941 (t0) cc_final: 0.8534 (t0) REVERT: A 351 MET cc_start: 0.8971 (mmt) cc_final: 0.8768 (mmm) REVERT: A 440 MET cc_start: 0.8341 (tpp) cc_final: 0.7722 (tpp) REVERT: A 506 PHE cc_start: 0.9052 (t80) cc_final: 0.8501 (m-80) REVERT: A 555 MET cc_start: 0.9076 (mtp) cc_final: 0.8806 (mtp) REVERT: A 565 TYR cc_start: 0.9416 (m-80) cc_final: 0.9023 (m-80) REVERT: A 591 LEU cc_start: 0.9010 (tp) cc_final: 0.8483 (tt) REVERT: A 595 ILE cc_start: 0.9286 (mt) cc_final: 0.9037 (mt) REVERT: A 677 MET cc_start: 0.8419 (mmm) cc_final: 0.8132 (tpp) REVERT: A 699 THR cc_start: 0.9689 (p) cc_final: 0.9417 (t) REVERT: A 704 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8259 (tm-30) REVERT: A 707 LEU cc_start: 0.7068 (mm) cc_final: 0.6545 (mm) REVERT: A 728 PHE cc_start: 0.7558 (m-80) cc_final: 0.7141 (m-80) REVERT: B 139 LEU cc_start: 0.9397 (mm) cc_final: 0.9145 (tp) REVERT: B 196 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8914 (tm-30) REVERT: B 220 ASN cc_start: 0.9046 (m110) cc_final: 0.8631 (m110) REVERT: B 322 ASP cc_start: 0.9040 (t0) cc_final: 0.8379 (t70) REVERT: B 351 MET cc_start: 0.9008 (mmt) cc_final: 0.8795 (mmm) REVERT: B 440 MET cc_start: 0.8312 (tpp) cc_final: 0.7697 (tpp) REVERT: B 471 HIS cc_start: 0.7718 (p90) cc_final: 0.7435 (p90) REVERT: B 501 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 506 PHE cc_start: 0.9054 (t80) cc_final: 0.8499 (m-80) REVERT: B 555 MET cc_start: 0.9153 (mtt) cc_final: 0.8781 (mtt) REVERT: B 585 HIS cc_start: 0.8304 (t-90) cc_final: 0.8004 (t-90) REVERT: B 591 LEU cc_start: 0.8962 (tp) cc_final: 0.8492 (tt) REVERT: B 595 ILE cc_start: 0.9249 (mt) cc_final: 0.8968 (mt) REVERT: B 677 MET cc_start: 0.8343 (mmm) cc_final: 0.8030 (tpp) REVERT: B 699 THR cc_start: 0.9709 (p) cc_final: 0.9428 (t) REVERT: B 704 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8285 (tm-30) REVERT: B 707 LEU cc_start: 0.7090 (mm) cc_final: 0.6538 (mm) REVERT: B 728 PHE cc_start: 0.7513 (m-80) cc_final: 0.7098 (m-80) REVERT: B 742 TRP cc_start: 0.7640 (m-90) cc_final: 0.7119 (m-90) REVERT: C 139 LEU cc_start: 0.9402 (mm) cc_final: 0.9154 (tp) REVERT: C 196 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8912 (tm-30) REVERT: C 220 ASN cc_start: 0.9052 (m110) cc_final: 0.8634 (m110) REVERT: C 322 ASP cc_start: 0.9043 (t0) cc_final: 0.8579 (t70) REVERT: C 351 MET cc_start: 0.8974 (mmt) cc_final: 0.8770 (mmm) REVERT: C 440 MET cc_start: 0.8344 (tpp) cc_final: 0.7726 (tpp) REVERT: C 471 HIS cc_start: 0.7700 (p90) cc_final: 0.7487 (p90) REVERT: C 506 PHE cc_start: 0.9055 (t80) cc_final: 0.8520 (m-80) REVERT: C 555 MET cc_start: 0.8772 (mtp) cc_final: 0.8264 (mtt) REVERT: C 585 HIS cc_start: 0.8161 (t-90) cc_final: 0.7883 (t-90) REVERT: C 591 LEU cc_start: 0.8957 (tp) cc_final: 0.8588 (tt) REVERT: C 595 ILE cc_start: 0.9282 (mt) cc_final: 0.9042 (mt) REVERT: C 642 LEU cc_start: 0.9459 (pp) cc_final: 0.8869 (tt) REVERT: C 677 MET cc_start: 0.8350 (mmm) cc_final: 0.8060 (tpp) REVERT: C 699 THR cc_start: 0.9683 (p) cc_final: 0.9410 (t) REVERT: C 704 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8291 (tm-30) REVERT: C 728 PHE cc_start: 0.7515 (m-80) cc_final: 0.7103 (m-80) REVERT: C 742 TRP cc_start: 0.7693 (m-90) cc_final: 0.7220 (m-90) REVERT: D 139 LEU cc_start: 0.9408 (mm) cc_final: 0.9165 (tp) REVERT: D 196 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8897 (tm-30) REVERT: D 220 ASN cc_start: 0.9059 (m110) cc_final: 0.8631 (m110) REVERT: D 320 MET cc_start: 0.8957 (ttm) cc_final: 0.8738 (ttm) REVERT: D 322 ASP cc_start: 0.9030 (t0) cc_final: 0.8401 (t70) REVERT: D 414 ASP cc_start: 0.8164 (m-30) cc_final: 0.7157 (t0) REVERT: D 440 MET cc_start: 0.8364 (tpp) cc_final: 0.7742 (tpp) REVERT: D 506 PHE cc_start: 0.9069 (t80) cc_final: 0.8554 (m-80) REVERT: D 551 LEU cc_start: 0.9617 (tp) cc_final: 0.9302 (tp) REVERT: D 555 MET cc_start: 0.9138 (mtt) cc_final: 0.8739 (mtt) REVERT: D 565 TYR cc_start: 0.9412 (m-80) cc_final: 0.9017 (m-80) REVERT: D 572 MET cc_start: 0.8818 (ttp) cc_final: 0.8597 (tmm) REVERT: D 585 HIS cc_start: 0.8147 (t-90) cc_final: 0.7854 (t-90) REVERT: D 591 LEU cc_start: 0.8951 (tp) cc_final: 0.8566 (tt) REVERT: D 595 ILE cc_start: 0.9267 (mt) cc_final: 0.9030 (mt) REVERT: D 677 MET cc_start: 0.8367 (mmm) cc_final: 0.8085 (tpp) REVERT: D 699 THR cc_start: 0.9676 (p) cc_final: 0.9408 (t) REVERT: D 704 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8282 (tm-30) REVERT: D 728 PHE cc_start: 0.7512 (m-80) cc_final: 0.7121 (m-80) REVERT: D 742 TRP cc_start: 0.7704 (m-90) cc_final: 0.7193 (m-90) outliers start: 4 outliers final: 4 residues processed: 673 average time/residue: 0.2841 time to fit residues: 303.8671 Evaluate side-chains 509 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 505 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 156 optimal weight: 0.0970 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 585 HIS ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 452 ASN B 643 ASN ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN C 452 ASN C 643 ASN ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN D 273 ASN D 452 ASN D 643 ASN ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4832 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= 0.188 Angle : 0.702 9.905 29032 Z= 0.352 Chirality : 0.042 0.228 3308 Planarity : 0.004 0.047 3624 Dihedral : 5.711 29.885 2808 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.54 % Favored : 87.31 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.16), residues: 2568 helix: -0.03 (0.13), residues: 1488 sheet: -3.81 (0.41), residues: 68 loop : -3.53 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 493 HIS 0.005 0.001 HIS D 301 PHE 0.021 0.001 PHE B 489 TYR 0.017 0.001 TYR C 565 ARG 0.007 0.000 ARG D 122 *********************** 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 669 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 669 time to evaluate : 2.382 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: 0.9398 (mm) cc_final: 0.9092 (tp) REVERT: A 159 MET cc_start: 0.8611 (mmm) cc_final: 0.8313 (tpt) REVERT: A 196 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8874 (tm-30) REVERT: A 220 ASN cc_start: 0.8999 (m110) cc_final: 0.8555 (m110) REVERT: A 322 ASP cc_start: 0.8940 (t0) cc_final: 0.8320 (t0) REVERT: A 440 MET cc_start: 0.8242 (tpp) cc_final: 0.7677 (tpp) REVERT: A 471 HIS cc_start: 0.7622 (p90) cc_final: 0.7400 (p90) REVERT: A 501 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7911 (mm-30) REVERT: A 506 PHE cc_start: 0.9023 (t80) cc_final: 0.8451 (m-80) REVERT: A 555 MET cc_start: 0.9100 (mtp) cc_final: 0.8585 (mtt) REVERT: A 561 ASN cc_start: 0.8811 (m-40) cc_final: 0.8559 (m110) REVERT: A 565 TYR cc_start: 0.9370 (m-80) cc_final: 0.9005 (m-80) REVERT: A 572 MET cc_start: 0.8564 (tmm) cc_final: 0.8221 (tmm) REVERT: A 591 LEU cc_start: 0.8968 (tp) cc_final: 0.8408 (tt) REVERT: A 595 ILE cc_start: 0.9278 (mt) cc_final: 0.8978 (mt) REVERT: A 677 MET cc_start: 0.8169 (mmm) cc_final: 0.7857 (tpp) REVERT: A 699 THR cc_start: 0.9705 (p) cc_final: 0.9442 (t) REVERT: B 139 LEU cc_start: 0.9418 (mm) cc_final: 0.9065 (tp) REVERT: B 159 MET cc_start: 0.8594 (mmm) cc_final: 0.8318 (tpt) REVERT: B 220 ASN cc_start: 0.9050 (m110) cc_final: 0.8608 (m110) REVERT: B 290 THR cc_start: 0.9363 (m) cc_final: 0.9124 (p) REVERT: B 322 ASP cc_start: 0.8953 (t0) cc_final: 0.8446 (t0) REVERT: B 351 MET cc_start: 0.9095 (mmt) cc_final: 0.8861 (mmm) REVERT: B 440 MET cc_start: 0.8196 (tpp) cc_final: 0.7696 (tpp) REVERT: B 501 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7932 (mm-30) REVERT: B 506 PHE cc_start: 0.9035 (t80) cc_final: 0.8485 (m-80) REVERT: B 551 LEU cc_start: 0.9576 (tp) cc_final: 0.9286 (tp) REVERT: B 555 MET cc_start: 0.9131 (mtt) cc_final: 0.8724 (mtt) REVERT: B 561 ASN cc_start: 0.8805 (m-40) cc_final: 0.8526 (m110) REVERT: B 585 HIS cc_start: 0.8316 (t-90) cc_final: 0.8108 (t-90) REVERT: B 591 LEU cc_start: 0.8988 (tp) cc_final: 0.8423 (tt) REVERT: B 595 ILE cc_start: 0.9222 (mt) cc_final: 0.8911 (mt) REVERT: B 642 LEU cc_start: 0.9378 (pp) cc_final: 0.8741 (tt) REVERT: B 677 MET cc_start: 0.8238 (mmm) cc_final: 0.7969 (tpp) REVERT: B 699 THR cc_start: 0.9693 (p) cc_final: 0.9429 (t) REVERT: C 139 LEU cc_start: 0.9425 (mm) cc_final: 0.9069 (tp) REVERT: C 159 MET cc_start: 0.8585 (mmm) cc_final: 0.8296 (tpt) REVERT: C 220 ASN cc_start: 0.9041 (m110) cc_final: 0.8603 (m110) REVERT: C 290 THR cc_start: 0.9374 (m) cc_final: 0.9123 (p) REVERT: C 322 ASP cc_start: 0.8959 (t0) cc_final: 0.8356 (t70) REVERT: C 351 MET cc_start: 0.9047 (mmt) cc_final: 0.8827 (mmm) REVERT: C 440 MET cc_start: 0.8221 (tpp) cc_final: 0.7758 (tpp) REVERT: C 501 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7927 (mm-30) REVERT: C 506 PHE cc_start: 0.9043 (t80) cc_final: 0.8496 (m-80) REVERT: C 572 MET cc_start: 0.8560 (tmm) cc_final: 0.8230 (tmm) REVERT: C 585 HIS cc_start: 0.8265 (t-90) cc_final: 0.7979 (t-90) REVERT: C 591 LEU cc_start: 0.8963 (tp) cc_final: 0.8434 (tt) REVERT: C 595 ILE cc_start: 0.9226 (mt) cc_final: 0.8925 (mt) REVERT: C 677 MET cc_start: 0.8195 (mmm) cc_final: 0.7915 (tpp) REVERT: C 699 THR cc_start: 0.9714 (p) cc_final: 0.9462 (t) REVERT: C 707 LEU cc_start: 0.7077 (mm) cc_final: 0.6754 (mm) REVERT: D 139 LEU cc_start: 0.9437 (mm) cc_final: 0.9087 (tp) REVERT: D 159 MET cc_start: 0.8575 (mmm) cc_final: 0.8285 (tpt) REVERT: D 220 ASN cc_start: 0.9046 (m110) cc_final: 0.8590 (m110) REVERT: D 290 THR cc_start: 0.9354 (m) cc_final: 0.9146 (p) REVERT: D 320 MET cc_start: 0.8774 (ttm) cc_final: 0.8516 (ttp) REVERT: D 322 ASP cc_start: 0.8934 (t0) cc_final: 0.8416 (t0) REVERT: D 323 MET cc_start: 0.8983 (tmm) cc_final: 0.8742 (tmm) REVERT: D 440 MET cc_start: 0.8255 (tpp) cc_final: 0.7698 (tpp) REVERT: D 471 HIS cc_start: 0.7595 (p90) cc_final: 0.7312 (p90) REVERT: D 501 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7899 (mm-30) REVERT: D 506 PHE cc_start: 0.9022 (t80) cc_final: 0.8471 (m-80) REVERT: D 551 LEU cc_start: 0.9575 (tp) cc_final: 0.9268 (tp) REVERT: D 555 MET cc_start: 0.9124 (mtt) cc_final: 0.8727 (mtt) REVERT: D 565 TYR cc_start: 0.9364 (m-80) cc_final: 0.8998 (m-80) REVERT: D 585 HIS cc_start: 0.8252 (t-90) cc_final: 0.8019 (t-90) REVERT: D 591 LEU cc_start: 0.8978 (tp) cc_final: 0.8424 (tt) REVERT: D 595 ILE cc_start: 0.9219 (mt) cc_final: 0.8895 (mt) REVERT: D 642 LEU cc_start: 0.9377 (pp) cc_final: 0.8808 (tt) REVERT: D 677 MET cc_start: 0.8300 (mmm) cc_final: 0.8046 (tpp) REVERT: D 699 THR cc_start: 0.9687 (p) cc_final: 0.9435 (t) REVERT: D 745 HIS cc_start: 0.8055 (m-70) cc_final: 0.7519 (m90) outliers start: 0 outliers final: 0 residues processed: 669 average time/residue: 0.2726 time to fit residues: 294.1630 Evaluate side-chains 505 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 10.0000 chunk 140 optimal weight: 0.0870 chunk 3 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 62 optimal weight: 0.0570 overall best weight: 3.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 273 ASN ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN ** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 GLN ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN C 671 ASN ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 273 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 GLN ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21460 Z= 0.273 Angle : 0.743 9.401 29032 Z= 0.375 Chirality : 0.044 0.235 3308 Planarity : 0.004 0.049 3624 Dihedral : 5.709 27.088 2808 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.14 % Favored : 85.71 % Rotamer: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.82 (0.16), residues: 2568 helix: 0.27 (0.13), residues: 1488 sheet: -3.86 (0.41), residues: 68 loop : -3.39 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 481 HIS 0.006 0.001 HIS C 301 PHE 0.013 0.001 PHE B 715 TYR 0.015 0.001 TYR A 359 ARG 0.005 0.000 ARG B 375 *********************** 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 631 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 630 time to evaluate : 2.390 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: 0.9303 (mm) cc_final: 0.8950 (tp) REVERT: A 159 MET cc_start: 0.8666 (mmm) cc_final: 0.8307 (tpt) REVERT: A 220 ASN cc_start: 0.9094 (m110) cc_final: 0.8668 (m110) REVERT: A 290 THR cc_start: 0.9365 (m) cc_final: 0.9139 (p) REVERT: A 322 ASP cc_start: 0.8841 (t0) cc_final: 0.8055 (t0) REVERT: A 440 MET cc_start: 0.8346 (tpp) cc_final: 0.7709 (tpp) REVERT: A 501 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7851 (mm-30) REVERT: A 506 PHE cc_start: 0.9080 (t80) cc_final: 0.8485 (m-80) REVERT: A 547 TYR cc_start: 0.6659 (m-10) cc_final: 0.6446 (m-80) REVERT: A 555 MET cc_start: 0.9057 (mtp) cc_final: 0.8590 (mtt) REVERT: A 565 TYR cc_start: 0.9412 (m-80) cc_final: 0.9005 (m-80) REVERT: A 572 MET cc_start: 0.8629 (tmm) cc_final: 0.8222 (tmm) REVERT: A 585 HIS cc_start: 0.8138 (t-90) cc_final: 0.7857 (t-90) REVERT: A 591 LEU cc_start: 0.9002 (tp) cc_final: 0.8444 (tt) REVERT: A 595 ILE cc_start: 0.9264 (mt) cc_final: 0.8926 (mt) REVERT: A 677 MET cc_start: 0.8311 (mmm) cc_final: 0.8075 (tpp) REVERT: A 699 THR cc_start: 0.9702 (p) cc_final: 0.9424 (t) REVERT: A 735 ASN cc_start: 0.8423 (m-40) cc_final: 0.8096 (m-40) REVERT: A 745 HIS cc_start: 0.8148 (m-70) cc_final: 0.7689 (m90) REVERT: B 139 LEU cc_start: 0.9391 (mm) cc_final: 0.9092 (tp) REVERT: B 220 ASN cc_start: 0.9152 (m110) cc_final: 0.8728 (m110) REVERT: B 290 THR cc_start: 0.9384 (m) cc_final: 0.9114 (p) REVERT: B 322 ASP cc_start: 0.8895 (t0) cc_final: 0.8152 (t0) REVERT: B 351 MET cc_start: 0.9058 (mmt) cc_final: 0.8856 (mmm) REVERT: B 440 MET cc_start: 0.8322 (tpp) cc_final: 0.7682 (tpp) REVERT: B 501 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7896 (mm-30) REVERT: B 506 PHE cc_start: 0.9122 (t80) cc_final: 0.8516 (m-80) REVERT: B 547 TYR cc_start: 0.6772 (m-10) cc_final: 0.6536 (m-80) REVERT: B 555 MET cc_start: 0.9110 (mtt) cc_final: 0.8733 (mtt) REVERT: B 561 ASN cc_start: 0.8871 (m-40) cc_final: 0.8569 (m110) REVERT: B 588 LEU cc_start: 0.9017 (mm) cc_final: 0.8767 (tt) REVERT: B 591 LEU cc_start: 0.9015 (tp) cc_final: 0.8410 (tt) REVERT: B 595 ILE cc_start: 0.9223 (mt) cc_final: 0.8929 (mt) REVERT: B 642 LEU cc_start: 0.9393 (pp) cc_final: 0.8816 (tt) REVERT: B 677 MET cc_start: 0.8323 (mmm) cc_final: 0.8061 (tpp) REVERT: B 699 THR cc_start: 0.9693 (p) cc_final: 0.9408 (t) REVERT: B 732 LEU cc_start: 0.8947 (mt) cc_final: 0.8600 (mt) REVERT: B 742 TRP cc_start: 0.7492 (m-90) cc_final: 0.7045 (m-90) REVERT: B 745 HIS cc_start: 0.8181 (m-70) cc_final: 0.7711 (m-70) REVERT: C 139 LEU cc_start: 0.9394 (mm) cc_final: 0.9103 (tp) REVERT: C 220 ASN cc_start: 0.9147 (m110) cc_final: 0.8719 (m110) REVERT: C 290 THR cc_start: 0.9388 (m) cc_final: 0.9115 (p) REVERT: C 322 ASP cc_start: 0.8876 (t0) cc_final: 0.8124 (t0) REVERT: C 351 MET cc_start: 0.9057 (mmt) cc_final: 0.8847 (mmm) REVERT: C 440 MET cc_start: 0.8312 (tpp) cc_final: 0.7777 (tpp) REVERT: C 501 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7879 (mm-30) REVERT: C 506 PHE cc_start: 0.9116 (t80) cc_final: 0.8500 (m-80) REVERT: C 547 TYR cc_start: 0.6743 (m-10) cc_final: 0.6525 (m-80) REVERT: C 561 ASN cc_start: 0.8812 (m-40) cc_final: 0.8579 (m110) REVERT: C 572 MET cc_start: 0.8611 (tmm) cc_final: 0.8176 (tmm) REVERT: C 588 LEU cc_start: 0.9013 (mm) cc_final: 0.8757 (tt) REVERT: C 591 LEU cc_start: 0.9011 (tp) cc_final: 0.8406 (tt) REVERT: C 595 ILE cc_start: 0.9224 (mt) cc_final: 0.8913 (mt) REVERT: C 642 LEU cc_start: 0.9361 (pp) cc_final: 0.8843 (tt) REVERT: C 677 MET cc_start: 0.8279 (mmm) cc_final: 0.8077 (tpp) REVERT: C 699 THR cc_start: 0.9710 (p) cc_final: 0.9431 (t) REVERT: C 732 LEU cc_start: 0.8947 (mt) cc_final: 0.8574 (mt) REVERT: C 742 TRP cc_start: 0.7414 (m-90) cc_final: 0.6991 (m-90) REVERT: C 745 HIS cc_start: 0.8170 (m-70) cc_final: 0.7716 (m-70) REVERT: D 139 LEU cc_start: 0.9402 (mm) cc_final: 0.9109 (tp) REVERT: D 220 ASN cc_start: 0.9168 (m110) cc_final: 0.8730 (m110) REVERT: D 290 THR cc_start: 0.9383 (m) cc_final: 0.9123 (p) REVERT: D 322 ASP cc_start: 0.8932 (t0) cc_final: 0.8297 (t70) REVERT: D 440 MET cc_start: 0.8332 (tpp) cc_final: 0.7714 (tpp) REVERT: D 501 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7867 (mm-30) REVERT: D 506 PHE cc_start: 0.9115 (t80) cc_final: 0.8503 (m-80) REVERT: D 551 LEU cc_start: 0.9571 (tp) cc_final: 0.9262 (tp) REVERT: D 555 MET cc_start: 0.9102 (mtt) cc_final: 0.8715 (mtt) REVERT: D 565 TYR cc_start: 0.9405 (m-80) cc_final: 0.8988 (m-80) REVERT: D 572 MET cc_start: 0.8667 (tmm) cc_final: 0.8363 (tmm) REVERT: D 588 LEU cc_start: 0.9018 (mm) cc_final: 0.8782 (tt) REVERT: D 591 LEU cc_start: 0.9005 (tp) cc_final: 0.8574 (tt) REVERT: D 595 ILE cc_start: 0.9220 (mt) cc_final: 0.8980 (mt) REVERT: D 642 LEU cc_start: 0.9383 (pp) cc_final: 0.8814 (tt) REVERT: D 699 THR cc_start: 0.9690 (p) cc_final: 0.9416 (t) REVERT: D 715 PHE cc_start: 0.7804 (t80) cc_final: 0.7458 (t80) REVERT: D 732 LEU cc_start: 0.9007 (mt) cc_final: 0.8687 (mt) REVERT: D 742 TRP cc_start: 0.7375 (m-90) cc_final: 0.6916 (m-90) REVERT: D 745 HIS cc_start: 0.8152 (m-70) cc_final: 0.7696 (m-70) outliers start: 1 outliers final: 0 residues processed: 631 average time/residue: 0.2777 time to fit residues: 284.3833 Evaluate side-chains 487 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 487 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.0000 chunk 222 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 145 optimal weight: 0.0030 chunk 61 optimal weight: 5.9990 chunk 247 optimal weight: 0.9980 chunk 205 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN A 580 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN A 695 GLN B 452 ASN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN B 735 ASN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 695 GLN C 735 ASN D 452 ASN ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN ** D 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21460 Z= 0.165 Angle : 0.687 9.085 29032 Z= 0.339 Chirality : 0.041 0.219 3308 Planarity : 0.003 0.048 3624 Dihedral : 5.363 25.267 2808 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.34 % Favored : 87.50 % 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: -1.59 (0.17), residues: 2568 helix: 0.36 (0.13), residues: 1504 sheet: -3.14 (0.46), residues: 60 loop : -3.25 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 493 HIS 0.004 0.001 HIS B 745 PHE 0.024 0.001 PHE B 489 TYR 0.014 0.001 TYR A 359 ARG 0.004 0.000 ARG C 567 *********************** 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 691 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 691 time to evaluate : 2.338 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: 0.9248 (mm) cc_final: 0.8849 (tp) REVERT: A 159 MET cc_start: 0.8632 (mmm) cc_final: 0.8281 (tpt) REVERT: A 208 TYR cc_start: 0.8655 (m-80) cc_final: 0.8290 (m-10) REVERT: A 220 ASN cc_start: 0.9114 (m110) cc_final: 0.8682 (m110) REVERT: A 290 THR cc_start: 0.9343 (m) cc_final: 0.9141 (p) REVERT: A 308 GLU cc_start: 0.6738 (pm20) cc_final: 0.5805 (pm20) REVERT: A 322 ASP cc_start: 0.8408 (t0) cc_final: 0.7704 (t0) REVERT: A 440 MET cc_start: 0.8143 (tpp) cc_final: 0.7817 (tpp) REVERT: A 501 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7798 (mm-30) REVERT: A 506 PHE cc_start: 0.9009 (t80) cc_final: 0.8464 (m-80) REVERT: A 555 MET cc_start: 0.9035 (mtp) cc_final: 0.8572 (mtt) REVERT: A 561 ASN cc_start: 0.8660 (m-40) cc_final: 0.8376 (m110) REVERT: A 565 TYR cc_start: 0.9272 (m-80) cc_final: 0.8706 (m-80) REVERT: A 585 HIS cc_start: 0.8311 (t-90) cc_final: 0.7990 (t-90) REVERT: A 591 LEU cc_start: 0.8965 (tp) cc_final: 0.8412 (tt) REVERT: A 595 ILE cc_start: 0.9235 (mt) cc_final: 0.8855 (mt) REVERT: A 686 LYS cc_start: 0.9535 (mmmm) cc_final: 0.9256 (mtpt) REVERT: A 699 THR cc_start: 0.9582 (p) cc_final: 0.9329 (t) REVERT: A 732 LEU cc_start: 0.8782 (mt) cc_final: 0.8498 (mt) REVERT: A 745 HIS cc_start: 0.7914 (m-70) cc_final: 0.7518 (m90) REVERT: A 751 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8614 (mm-30) REVERT: B 139 LEU cc_start: 0.9395 (mm) cc_final: 0.9055 (tp) REVERT: B 208 TYR cc_start: 0.8663 (m-80) cc_final: 0.8303 (m-10) REVERT: B 220 ASN cc_start: 0.9138 (m110) cc_final: 0.8731 (m110) REVERT: B 290 THR cc_start: 0.9376 (m) cc_final: 0.9134 (p) REVERT: B 322 ASP cc_start: 0.8462 (t0) cc_final: 0.7716 (t0) REVERT: B 440 MET cc_start: 0.8092 (tpp) cc_final: 0.7822 (tpp) REVERT: B 501 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7885 (mm-30) REVERT: B 506 PHE cc_start: 0.9046 (t80) cc_final: 0.8406 (m-80) REVERT: B 551 LEU cc_start: 0.9550 (tp) cc_final: 0.9280 (tp) REVERT: B 555 MET cc_start: 0.9100 (mtt) cc_final: 0.8752 (mtt) REVERT: B 574 MET cc_start: 0.8971 (tpp) cc_final: 0.8307 (mmm) REVERT: B 585 HIS cc_start: 0.8392 (t-90) cc_final: 0.8186 (t-90) REVERT: B 591 LEU cc_start: 0.8983 (tp) cc_final: 0.8404 (tt) REVERT: B 595 ILE cc_start: 0.9226 (mt) cc_final: 0.8795 (mt) REVERT: B 677 MET cc_start: 0.8165 (mmm) cc_final: 0.7758 (tpp) REVERT: B 689 GLU cc_start: 0.9218 (tt0) cc_final: 0.8712 (tp30) REVERT: B 699 THR cc_start: 0.9575 (p) cc_final: 0.9336 (t) REVERT: B 745 HIS cc_start: 0.7925 (m-70) cc_final: 0.7398 (m-70) REVERT: C 139 LEU cc_start: 0.9368 (mm) cc_final: 0.9028 (tp) REVERT: C 191 LEU cc_start: 0.9640 (mt) cc_final: 0.9425 (mt) REVERT: C 208 TYR cc_start: 0.8662 (m-80) cc_final: 0.8299 (m-10) REVERT: C 220 ASN cc_start: 0.9141 (m110) cc_final: 0.8723 (m110) REVERT: C 290 THR cc_start: 0.9394 (m) cc_final: 0.9151 (p) REVERT: C 322 ASP cc_start: 0.8461 (t0) cc_final: 0.7824 (t0) REVERT: C 440 MET cc_start: 0.8080 (tpp) cc_final: 0.7814 (tpp) REVERT: C 501 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7862 (mm-30) REVERT: C 506 PHE cc_start: 0.9049 (t80) cc_final: 0.8420 (m-80) REVERT: C 551 LEU cc_start: 0.9433 (tp) cc_final: 0.8924 (tp) REVERT: C 555 MET cc_start: 0.8934 (mtp) cc_final: 0.8667 (mmm) REVERT: C 585 HIS cc_start: 0.8389 (t-90) cc_final: 0.8101 (t-90) REVERT: C 591 LEU cc_start: 0.8975 (tp) cc_final: 0.8481 (tt) REVERT: C 595 ILE cc_start: 0.9235 (mt) cc_final: 0.8895 (mt) REVERT: C 677 MET cc_start: 0.8278 (mmm) cc_final: 0.8073 (tpp) REVERT: C 699 THR cc_start: 0.9603 (p) cc_final: 0.9347 (t) REVERT: C 745 HIS cc_start: 0.7917 (m-70) cc_final: 0.7405 (m-70) REVERT: D 139 LEU cc_start: 0.9378 (mm) cc_final: 0.9039 (tp) REVERT: D 177 LEU cc_start: 0.9517 (mm) cc_final: 0.9288 (mm) REVERT: D 191 LEU cc_start: 0.9642 (mt) cc_final: 0.9423 (mt) REVERT: D 208 TYR cc_start: 0.8640 (m-80) cc_final: 0.8312 (m-10) REVERT: D 220 ASN cc_start: 0.9134 (m110) cc_final: 0.8698 (m110) REVERT: D 290 THR cc_start: 0.9393 (m) cc_final: 0.9165 (p) REVERT: D 322 ASP cc_start: 0.8464 (t0) cc_final: 0.7770 (t0) REVERT: D 440 MET cc_start: 0.8153 (tpp) cc_final: 0.7847 (tpp) REVERT: D 501 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7830 (mm-30) REVERT: D 506 PHE cc_start: 0.9040 (t80) cc_final: 0.8433 (m-80) REVERT: D 551 LEU cc_start: 0.9547 (tp) cc_final: 0.9244 (tp) REVERT: D 555 MET cc_start: 0.9093 (mtt) cc_final: 0.8722 (mtt) REVERT: D 565 TYR cc_start: 0.9298 (m-80) cc_final: 0.8729 (m-80) REVERT: D 585 HIS cc_start: 0.8258 (t-90) cc_final: 0.7981 (t-90) REVERT: D 591 LEU cc_start: 0.8973 (tp) cc_final: 0.8405 (tt) REVERT: D 595 ILE cc_start: 0.9226 (mt) cc_final: 0.8785 (mt) REVERT: D 699 THR cc_start: 0.9579 (p) cc_final: 0.9312 (t) REVERT: D 715 PHE cc_start: 0.7639 (t80) cc_final: 0.7159 (t80) REVERT: D 745 HIS cc_start: 0.7916 (m-70) cc_final: 0.7387 (m-70) outliers start: 0 outliers final: 0 residues processed: 691 average time/residue: 0.2866 time to fit residues: 319.4046 Evaluate side-chains 533 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 141 optimal weight: 0.1980 chunk 180 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 246 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 113 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 735 ASN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 580 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 695 GLN D 735 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21460 Z= 0.165 Angle : 0.702 8.924 29032 Z= 0.337 Chirality : 0.042 0.235 3308 Planarity : 0.003 0.046 3624 Dihedral : 5.155 23.227 2808 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.58 % Favored : 87.27 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -1.48 (0.17), residues: 2568 helix: 0.47 (0.13), residues: 1492 sheet: -3.67 (0.42), residues: 76 loop : -3.12 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 742 HIS 0.004 0.001 HIS D 745 PHE 0.016 0.001 PHE D 203 TYR 0.020 0.001 TYR A 382 ARG 0.002 0.000 ARG D 327 *********************** 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 675 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 675 time to evaluate : 2.314 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: 0.9250 (mm) cc_final: 0.8849 (tp) REVERT: A 220 ASN cc_start: 0.9122 (m110) cc_final: 0.8689 (m110) REVERT: A 290 THR cc_start: 0.9293 (m) cc_final: 0.9067 (p) REVERT: A 322 ASP cc_start: 0.8646 (t0) cc_final: 0.8308 (t0) REVERT: A 326 LEU cc_start: 0.9141 (mp) cc_final: 0.8741 (pp) REVERT: A 440 MET cc_start: 0.8161 (tpp) cc_final: 0.7872 (tpp) REVERT: A 501 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7733 (mm-30) REVERT: A 505 ILE cc_start: 0.9609 (pt) cc_final: 0.9333 (tt) REVERT: A 506 PHE cc_start: 0.9007 (t80) cc_final: 0.8448 (m-80) REVERT: A 555 MET cc_start: 0.8964 (mtp) cc_final: 0.8542 (mtt) REVERT: A 565 TYR cc_start: 0.9241 (m-80) cc_final: 0.8595 (m-80) REVERT: A 572 MET cc_start: 0.8628 (tmm) cc_final: 0.8350 (tmm) REVERT: A 585 HIS cc_start: 0.8353 (t-90) cc_final: 0.8105 (t-90) REVERT: A 591 LEU cc_start: 0.8964 (tp) cc_final: 0.8481 (tt) REVERT: A 595 ILE cc_start: 0.9183 (mt) cc_final: 0.8852 (mt) REVERT: A 686 LYS cc_start: 0.9580 (mmmm) cc_final: 0.9239 (mtpt) REVERT: A 743 LYS cc_start: 0.7964 (pttt) cc_final: 0.7664 (pttm) REVERT: A 745 HIS cc_start: 0.7909 (m-70) cc_final: 0.7452 (m-70) REVERT: B 139 LEU cc_start: 0.9382 (mm) cc_final: 0.8988 (tp) REVERT: B 191 LEU cc_start: 0.9686 (mt) cc_final: 0.9389 (mm) REVERT: B 220 ASN cc_start: 0.9153 (m110) cc_final: 0.8711 (m110) REVERT: B 290 THR cc_start: 0.9392 (m) cc_final: 0.9151 (p) REVERT: B 322 ASP cc_start: 0.8504 (t0) cc_final: 0.8006 (t0) REVERT: B 326 LEU cc_start: 0.9096 (mp) cc_final: 0.8784 (pp) REVERT: B 327 ARG cc_start: 0.8481 (tpt170) cc_final: 0.8217 (tpt170) REVERT: B 501 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7648 (tp30) REVERT: B 506 PHE cc_start: 0.9044 (t80) cc_final: 0.8432 (m-80) REVERT: B 551 LEU cc_start: 0.9531 (tp) cc_final: 0.9262 (tp) REVERT: B 555 MET cc_start: 0.9029 (mtt) cc_final: 0.8664 (mtt) REVERT: B 561 ASN cc_start: 0.8703 (m-40) cc_final: 0.8475 (m110) REVERT: B 574 MET cc_start: 0.9038 (tpp) cc_final: 0.7444 (mmm) REVERT: B 585 HIS cc_start: 0.8367 (t-90) cc_final: 0.8155 (t-90) REVERT: B 591 LEU cc_start: 0.8970 (tp) cc_final: 0.8392 (tt) REVERT: B 595 ILE cc_start: 0.9126 (mt) cc_final: 0.8673 (mt) REVERT: B 677 MET cc_start: 0.7859 (mmm) cc_final: 0.7542 (tpp) REVERT: B 686 LYS cc_start: 0.9563 (mmmm) cc_final: 0.9239 (mtpt) REVERT: B 689 GLU cc_start: 0.9210 (tt0) cc_final: 0.8836 (tp30) REVERT: B 745 HIS cc_start: 0.7929 (m-70) cc_final: 0.7437 (m-70) REVERT: C 139 LEU cc_start: 0.9372 (mm) cc_final: 0.8990 (tp) REVERT: C 220 ASN cc_start: 0.9146 (m110) cc_final: 0.8702 (m110) REVERT: C 290 THR cc_start: 0.9370 (m) cc_final: 0.9101 (p) REVERT: C 322 ASP cc_start: 0.8388 (t0) cc_final: 0.7862 (t0) REVERT: C 501 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7640 (tp30) REVERT: C 506 PHE cc_start: 0.9031 (t80) cc_final: 0.8404 (m-80) REVERT: C 551 LEU cc_start: 0.9416 (tp) cc_final: 0.8932 (tp) REVERT: C 555 MET cc_start: 0.8884 (mtp) cc_final: 0.8561 (mmm) REVERT: C 572 MET cc_start: 0.8591 (tmm) cc_final: 0.8309 (tmm) REVERT: C 585 HIS cc_start: 0.8364 (t-90) cc_final: 0.8090 (t-90) REVERT: C 591 LEU cc_start: 0.8981 (tp) cc_final: 0.8425 (tt) REVERT: C 595 ILE cc_start: 0.9157 (mt) cc_final: 0.8694 (mt) REVERT: C 677 MET cc_start: 0.8242 (mmm) cc_final: 0.7758 (tpp) REVERT: C 699 THR cc_start: 0.9588 (p) cc_final: 0.9332 (t) REVERT: C 745 HIS cc_start: 0.7889 (m-70) cc_final: 0.7394 (m-70) REVERT: D 139 LEU cc_start: 0.9377 (mm) cc_final: 0.9008 (tp) REVERT: D 208 TYR cc_start: 0.8596 (m-80) cc_final: 0.8277 (m-10) REVERT: D 220 ASN cc_start: 0.9129 (m110) cc_final: 0.8704 (m110) REVERT: D 290 THR cc_start: 0.9366 (m) cc_final: 0.9119 (p) REVERT: D 322 ASP cc_start: 0.8560 (t0) cc_final: 0.7892 (t0) REVERT: D 440 MET cc_start: 0.8141 (tpp) cc_final: 0.7868 (tpp) REVERT: D 501 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7557 (tp30) REVERT: D 506 PHE cc_start: 0.9037 (t80) cc_final: 0.8418 (m-80) REVERT: D 551 LEU cc_start: 0.9552 (tp) cc_final: 0.9237 (tp) REVERT: D 555 MET cc_start: 0.9079 (mtt) cc_final: 0.8657 (mtt) REVERT: D 565 TYR cc_start: 0.9264 (m-80) cc_final: 0.8579 (m-80) REVERT: D 585 HIS cc_start: 0.8305 (t-90) cc_final: 0.8060 (t-90) REVERT: D 591 LEU cc_start: 0.8972 (tp) cc_final: 0.8452 (tt) REVERT: D 595 ILE cc_start: 0.9138 (mt) cc_final: 0.8772 (mt) REVERT: D 745 HIS cc_start: 0.7879 (m-70) cc_final: 0.7379 (m-70) outliers start: 0 outliers final: 0 residues processed: 675 average time/residue: 0.2759 time to fit residues: 299.3973 Evaluate side-chains 532 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 156 optimal weight: 0.0060 chunk 168 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 452 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 735 ASN C 452 ASN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 452 ASN ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21460 Z= 0.256 Angle : 0.736 8.240 29032 Z= 0.363 Chirality : 0.044 0.237 3308 Planarity : 0.004 0.054 3624 Dihedral : 5.297 21.558 2808 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.28 % Favored : 86.57 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -1.37 (0.17), residues: 2568 helix: 0.52 (0.13), residues: 1504 sheet: -3.44 (0.46), residues: 68 loop : -3.08 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 742 HIS 0.004 0.001 HIS A 256 PHE 0.015 0.001 PHE B 526 TYR 0.018 0.001 TYR D 359 ARG 0.004 0.000 ARG B 567 *********************** 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 635 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 635 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9295 (mm) cc_final: 0.8903 (tp) REVERT: A 220 ASN cc_start: 0.9160 (m110) cc_final: 0.8751 (m110) REVERT: A 290 THR cc_start: 0.9343 (m) cc_final: 0.9124 (p) REVERT: A 322 ASP cc_start: 0.8772 (t0) cc_final: 0.8153 (t0) REVERT: A 440 MET cc_start: 0.8346 (tpp) cc_final: 0.7971 (tpp) REVERT: A 501 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7606 (mm-30) REVERT: A 506 PHE cc_start: 0.9062 (t80) cc_final: 0.8497 (m-80) REVERT: A 565 TYR cc_start: 0.9343 (m-80) cc_final: 0.8632 (m-80) REVERT: A 572 MET cc_start: 0.8651 (tmm) cc_final: 0.8318 (tmm) REVERT: A 585 HIS cc_start: 0.8430 (t-90) cc_final: 0.8214 (t-90) REVERT: A 591 LEU cc_start: 0.8994 (tp) cc_final: 0.8494 (tt) REVERT: A 595 ILE cc_start: 0.9263 (mt) cc_final: 0.8943 (mt) REVERT: A 682 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7022 (mm-30) REVERT: A 745 HIS cc_start: 0.7970 (m-70) cc_final: 0.7551 (m-70) REVERT: B 139 LEU cc_start: 0.9408 (mm) cc_final: 0.9102 (tp) REVERT: B 159 MET cc_start: 0.8211 (mmm) cc_final: 0.7796 (mmm) REVERT: B 185 GLU cc_start: 0.9096 (mp0) cc_final: 0.8515 (pm20) REVERT: B 220 ASN cc_start: 0.9194 (m110) cc_final: 0.8803 (m110) REVERT: B 290 THR cc_start: 0.9326 (m) cc_final: 0.9101 (p) REVERT: B 309 ASP cc_start: 0.8137 (m-30) cc_final: 0.7914 (p0) REVERT: B 327 ARG cc_start: 0.8566 (tpt170) cc_final: 0.8362 (tpt170) REVERT: B 351 MET cc_start: 0.9055 (mmt) cc_final: 0.8722 (mmm) REVERT: B 440 MET cc_start: 0.8261 (tpp) cc_final: 0.7943 (tpp) REVERT: B 501 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 551 LEU cc_start: 0.9557 (tp) cc_final: 0.9309 (tp) REVERT: B 555 MET cc_start: 0.9052 (mtt) cc_final: 0.8650 (mtt) REVERT: B 565 TYR cc_start: 0.9250 (m-80) cc_final: 0.8518 (m-80) REVERT: B 578 MET cc_start: 0.8850 (mmt) cc_final: 0.8554 (tpp) REVERT: B 591 LEU cc_start: 0.9010 (tp) cc_final: 0.8510 (tt) REVERT: B 595 ILE cc_start: 0.9247 (mt) cc_final: 0.8924 (mt) REVERT: B 745 HIS cc_start: 0.8003 (m-70) cc_final: 0.7610 (m-70) REVERT: C 139 LEU cc_start: 0.9390 (mm) cc_final: 0.9091 (tp) REVERT: C 159 MET cc_start: 0.8309 (mmm) cc_final: 0.8025 (mmm) REVERT: C 185 GLU cc_start: 0.9150 (mp0) cc_final: 0.8551 (pm20) REVERT: C 220 ASN cc_start: 0.9187 (m110) cc_final: 0.8785 (m110) REVERT: C 290 THR cc_start: 0.9344 (m) cc_final: 0.9133 (p) REVERT: C 351 MET cc_start: 0.9037 (mmt) cc_final: 0.8731 (mmm) REVERT: C 440 MET cc_start: 0.8233 (tpp) cc_final: 0.7954 (tpp) REVERT: C 501 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7734 (mm-30) REVERT: C 555 MET cc_start: 0.8936 (mtp) cc_final: 0.8512 (mmm) REVERT: C 561 ASN cc_start: 0.8733 (m-40) cc_final: 0.8307 (m110) REVERT: C 565 TYR cc_start: 0.9248 (m-80) cc_final: 0.8483 (m-80) REVERT: C 572 MET cc_start: 0.8643 (tmm) cc_final: 0.8312 (tmm) REVERT: C 585 HIS cc_start: 0.8476 (t-90) cc_final: 0.8203 (t-90) REVERT: C 591 LEU cc_start: 0.9015 (tp) cc_final: 0.8531 (tt) REVERT: C 595 ILE cc_start: 0.9239 (mt) cc_final: 0.8904 (mt) REVERT: C 652 ILE cc_start: 0.8556 (pt) cc_final: 0.8254 (mm) REVERT: C 745 HIS cc_start: 0.7979 (m-70) cc_final: 0.7500 (m-70) REVERT: D 139 LEU cc_start: 0.9388 (mm) cc_final: 0.9082 (tp) REVERT: D 159 MET cc_start: 0.8216 (mmm) cc_final: 0.7802 (mmm) REVERT: D 185 GLU cc_start: 0.9102 (mp0) cc_final: 0.8507 (pm20) REVERT: D 220 ASN cc_start: 0.9164 (m110) cc_final: 0.8765 (m110) REVERT: D 290 THR cc_start: 0.9337 (m) cc_final: 0.9111 (p) REVERT: D 440 MET cc_start: 0.8338 (tpp) cc_final: 0.7966 (tpp) REVERT: D 501 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7160 (mm-30) REVERT: D 551 LEU cc_start: 0.9572 (tp) cc_final: 0.9311 (tp) REVERT: D 555 MET cc_start: 0.9107 (mtt) cc_final: 0.8710 (mtt) REVERT: D 565 TYR cc_start: 0.9354 (m-80) cc_final: 0.8587 (m-80) REVERT: D 585 HIS cc_start: 0.8385 (t-90) cc_final: 0.8147 (t-90) REVERT: D 591 LEU cc_start: 0.9017 (tp) cc_final: 0.8488 (tt) REVERT: D 595 ILE cc_start: 0.9221 (mt) cc_final: 0.8859 (mt) REVERT: D 743 LYS cc_start: 0.8176 (pttt) cc_final: 0.7967 (pttm) REVERT: D 745 HIS cc_start: 0.7978 (m-70) cc_final: 0.7538 (m-70) outliers start: 0 outliers final: 0 residues processed: 635 average time/residue: 0.2811 time to fit residues: 282.7402 Evaluate side-chains 479 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 180 optimal weight: 0.1980 chunk 70 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 ASN B 452 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 735 ASN ** C 561 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21460 Z= 0.186 Angle : 0.726 8.338 29032 Z= 0.352 Chirality : 0.042 0.228 3308 Planarity : 0.004 0.047 3624 Dihedral : 5.212 22.532 2808 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.50 % Favored : 87.34 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.25 (0.17), residues: 2568 helix: 0.66 (0.14), residues: 1488 sheet: -3.44 (0.46), residues: 76 loop : -3.01 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 742 HIS 0.004 0.001 HIS B 745 PHE 0.023 0.001 PHE A 489 TYR 0.017 0.001 TYR B 382 ARG 0.003 0.000 ARG D 567 *********************** 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 654 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 654 time to evaluate : 2.571 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: 0.9269 (mm) cc_final: 0.8924 (tp) REVERT: A 220 ASN cc_start: 0.9110 (m110) cc_final: 0.8686 (m110) REVERT: A 271 CYS cc_start: 0.9491 (m) cc_final: 0.9272 (m) REVERT: A 290 THR cc_start: 0.9320 (m) cc_final: 0.9104 (p) REVERT: A 322 ASP cc_start: 0.8438 (t0) cc_final: 0.8042 (t0) REVERT: A 440 MET cc_start: 0.8257 (tpp) cc_final: 0.7869 (tpp) REVERT: A 501 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 506 PHE cc_start: 0.9022 (t80) cc_final: 0.8447 (m-80) REVERT: A 555 MET cc_start: 0.8942 (mtp) cc_final: 0.8698 (mmm) REVERT: A 565 TYR cc_start: 0.9319 (m-80) cc_final: 0.8573 (m-80) REVERT: A 572 MET cc_start: 0.8659 (tmm) cc_final: 0.8308 (tmm) REVERT: A 585 HIS cc_start: 0.8457 (t-90) cc_final: 0.8215 (t-90) REVERT: A 591 LEU cc_start: 0.9034 (tp) cc_final: 0.8417 (tt) REVERT: A 595 ILE cc_start: 0.9247 (mt) cc_final: 0.8923 (mt) REVERT: A 743 LYS cc_start: 0.8154 (pttt) cc_final: 0.7873 (pttm) REVERT: A 745 HIS cc_start: 0.7824 (m-70) cc_final: 0.7431 (m-70) REVERT: B 139 LEU cc_start: 0.9351 (mm) cc_final: 0.8977 (tp) REVERT: B 220 ASN cc_start: 0.9156 (m110) cc_final: 0.8734 (m110) REVERT: B 271 CYS cc_start: 0.9554 (m) cc_final: 0.9327 (m) REVERT: B 290 THR cc_start: 0.9292 (m) cc_final: 0.9081 (p) REVERT: B 440 MET cc_start: 0.8166 (tpp) cc_final: 0.7932 (tpp) REVERT: B 501 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7696 (mm-30) REVERT: B 551 LEU cc_start: 0.9549 (tp) cc_final: 0.9307 (tp) REVERT: B 555 MET cc_start: 0.9076 (mtt) cc_final: 0.8693 (mtt) REVERT: B 565 TYR cc_start: 0.9161 (m-80) cc_final: 0.8449 (m-80) REVERT: B 585 HIS cc_start: 0.8416 (t-90) cc_final: 0.8205 (t-90) REVERT: B 591 LEU cc_start: 0.9070 (tp) cc_final: 0.8443 (tt) REVERT: B 595 ILE cc_start: 0.9238 (mt) cc_final: 0.8881 (mt) REVERT: B 689 GLU cc_start: 0.9235 (tt0) cc_final: 0.8560 (tp30) REVERT: B 695 GLN cc_start: 0.8733 (tt0) cc_final: 0.8154 (tp-100) REVERT: B 743 LYS cc_start: 0.8210 (pttt) cc_final: 0.7923 (pttm) REVERT: B 745 HIS cc_start: 0.7811 (m-70) cc_final: 0.7419 (m-70) REVERT: C 139 LEU cc_start: 0.9385 (mm) cc_final: 0.8998 (tp) REVERT: C 159 MET cc_start: 0.8395 (mmm) cc_final: 0.8000 (mmm) REVERT: C 185 GLU cc_start: 0.9080 (mp0) cc_final: 0.8497 (pm20) REVERT: C 220 ASN cc_start: 0.9149 (m110) cc_final: 0.8715 (m110) REVERT: C 308 GLU cc_start: 0.7137 (pm20) cc_final: 0.6157 (pm20) REVERT: C 440 MET cc_start: 0.8113 (tpp) cc_final: 0.7900 (tpp) REVERT: C 501 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7690 (mm-30) REVERT: C 506 PHE cc_start: 0.8591 (t80) cc_final: 0.7983 (m-80) REVERT: C 555 MET cc_start: 0.8892 (mtp) cc_final: 0.8420 (mtt) REVERT: C 561 ASN cc_start: 0.8672 (m-40) cc_final: 0.8124 (m110) REVERT: C 565 TYR cc_start: 0.9142 (m-80) cc_final: 0.8376 (m-80) REVERT: C 572 MET cc_start: 0.8668 (tmm) cc_final: 0.8317 (tmm) REVERT: C 585 HIS cc_start: 0.8453 (t-90) cc_final: 0.8211 (t-90) REVERT: C 591 LEU cc_start: 0.9079 (tp) cc_final: 0.8473 (tt) REVERT: C 595 ILE cc_start: 0.9240 (mt) cc_final: 0.8897 (mt) REVERT: C 652 ILE cc_start: 0.8578 (pt) cc_final: 0.8316 (mm) REVERT: C 743 LYS cc_start: 0.8178 (pttt) cc_final: 0.7870 (pttm) REVERT: C 745 HIS cc_start: 0.7815 (m-70) cc_final: 0.7414 (m-70) REVERT: D 139 LEU cc_start: 0.9382 (mm) cc_final: 0.8987 (tp) REVERT: D 185 GLU cc_start: 0.9070 (mp0) cc_final: 0.8499 (pm20) REVERT: D 220 ASN cc_start: 0.9090 (m110) cc_final: 0.8699 (m110) REVERT: D 290 THR cc_start: 0.9305 (m) cc_final: 0.9096 (p) REVERT: D 396 ASP cc_start: 0.8441 (t0) cc_final: 0.8215 (t0) REVERT: D 440 MET cc_start: 0.8242 (tpp) cc_final: 0.7844 (tpp) REVERT: D 501 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7725 (mm-30) REVERT: D 506 PHE cc_start: 0.8607 (t80) cc_final: 0.8027 (m-80) REVERT: D 551 LEU cc_start: 0.9556 (tp) cc_final: 0.9299 (tp) REVERT: D 555 MET cc_start: 0.9090 (mtt) cc_final: 0.8701 (mtt) REVERT: D 565 TYR cc_start: 0.9284 (m-80) cc_final: 0.8576 (m-80) REVERT: D 585 HIS cc_start: 0.8383 (t-90) cc_final: 0.8140 (t-90) REVERT: D 591 LEU cc_start: 0.9050 (tp) cc_final: 0.8414 (tt) REVERT: D 595 ILE cc_start: 0.9240 (mt) cc_final: 0.8892 (mt) REVERT: D 616 LYS cc_start: 0.9047 (mptt) cc_final: 0.8498 (mptt) REVERT: D 682 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7192 (mm-30) REVERT: D 743 LYS cc_start: 0.8182 (pttt) cc_final: 0.7897 (pttm) REVERT: D 745 HIS cc_start: 0.7804 (m-70) cc_final: 0.7416 (m-70) outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.2922 time to fit residues: 305.1013 Evaluate side-chains 495 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 255 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 203 optimal weight: 0.9980 chunk 21 optimal weight: 0.0070 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 ASN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 683 ASN D 735 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21460 Z= 0.180 Angle : 0.721 9.989 29032 Z= 0.347 Chirality : 0.042 0.222 3308 Planarity : 0.004 0.042 3624 Dihedral : 5.086 22.885 2808 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.46 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.17 (0.17), residues: 2568 helix: 0.70 (0.14), residues: 1488 sheet: -3.09 (0.50), residues: 76 loop : -2.98 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 742 HIS 0.004 0.001 HIS D 745 PHE 0.018 0.001 PHE D 203 TYR 0.017 0.001 TYR D 359 ARG 0.002 0.000 ARG D 733 ********************** 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 653 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 653 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9271 (mm) cc_final: 0.8914 (tp) REVERT: A 220 ASN cc_start: 0.9088 (m110) cc_final: 0.8686 (m110) REVERT: A 290 THR cc_start: 0.9312 (m) cc_final: 0.9082 (p) REVERT: A 308 GLU cc_start: 0.7009 (pm20) cc_final: 0.6638 (pm20) REVERT: A 331 TRP cc_start: 0.8845 (m100) cc_final: 0.8608 (m-90) REVERT: A 440 MET cc_start: 0.8227 (tpp) cc_final: 0.7938 (tpp) REVERT: A 501 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7752 (mm-30) REVERT: A 506 PHE cc_start: 0.9016 (t80) cc_final: 0.8444 (m-80) REVERT: A 555 MET cc_start: 0.8896 (mtp) cc_final: 0.8402 (mtp) REVERT: A 565 TYR cc_start: 0.9245 (m-80) cc_final: 0.8573 (m-80) REVERT: A 572 MET cc_start: 0.8630 (tmm) cc_final: 0.8276 (tmm) REVERT: A 585 HIS cc_start: 0.8387 (t-90) cc_final: 0.8174 (t-90) REVERT: A 591 LEU cc_start: 0.9044 (tp) cc_final: 0.8384 (tt) REVERT: A 595 ILE cc_start: 0.9246 (mt) cc_final: 0.8834 (mt) REVERT: A 616 LYS cc_start: 0.9047 (mptt) cc_final: 0.8554 (mptt) REVERT: A 743 LYS cc_start: 0.8158 (pttt) cc_final: 0.7885 (pttm) REVERT: A 745 HIS cc_start: 0.7814 (m-70) cc_final: 0.7450 (m-70) REVERT: B 139 LEU cc_start: 0.9352 (mm) cc_final: 0.8979 (tp) REVERT: B 220 ASN cc_start: 0.9145 (m110) cc_final: 0.8742 (m110) REVERT: B 271 CYS cc_start: 0.9572 (m) cc_final: 0.9339 (m) REVERT: B 290 THR cc_start: 0.9268 (m) cc_final: 0.9031 (p) REVERT: B 331 TRP cc_start: 0.8922 (m100) cc_final: 0.8644 (m-90) REVERT: B 353 LYS cc_start: 0.9616 (mmtt) cc_final: 0.9290 (mmtp) REVERT: B 501 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 506 PHE cc_start: 0.8606 (t80) cc_final: 0.8101 (m-80) REVERT: B 551 LEU cc_start: 0.9538 (tp) cc_final: 0.9280 (tp) REVERT: B 555 MET cc_start: 0.9013 (mtt) cc_final: 0.8661 (mtt) REVERT: B 565 TYR cc_start: 0.9099 (m-80) cc_final: 0.8316 (m-80) REVERT: B 578 MET cc_start: 0.8912 (mmt) cc_final: 0.8441 (tpp) REVERT: B 585 HIS cc_start: 0.8437 (t-90) cc_final: 0.8199 (t-90) REVERT: B 591 LEU cc_start: 0.9055 (tp) cc_final: 0.8402 (tt) REVERT: B 595 ILE cc_start: 0.9238 (mt) cc_final: 0.8796 (mt) REVERT: B 686 LYS cc_start: 0.9520 (mmmm) cc_final: 0.9156 (mtpt) REVERT: B 743 LYS cc_start: 0.8207 (pttt) cc_final: 0.7917 (pttm) REVERT: B 745 HIS cc_start: 0.7761 (m-70) cc_final: 0.7437 (m-70) REVERT: C 135 LEU cc_start: 0.9514 (tp) cc_final: 0.9296 (pp) REVERT: C 139 LEU cc_start: 0.9358 (mm) cc_final: 0.8881 (tp) REVERT: C 185 GLU cc_start: 0.9068 (mp0) cc_final: 0.8494 (pm20) REVERT: C 220 ASN cc_start: 0.9125 (m110) cc_final: 0.8716 (m110) REVERT: C 271 CYS cc_start: 0.9460 (m) cc_final: 0.9207 (m) REVERT: C 501 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7676 (mm-30) REVERT: C 506 PHE cc_start: 0.8575 (t80) cc_final: 0.8054 (m-80) REVERT: C 555 MET cc_start: 0.8835 (mtp) cc_final: 0.8340 (mtp) REVERT: C 561 ASN cc_start: 0.8674 (m-40) cc_final: 0.8220 (m110) REVERT: C 565 TYR cc_start: 0.9099 (m-80) cc_final: 0.8473 (m-80) REVERT: C 572 MET cc_start: 0.8729 (tmm) cc_final: 0.8373 (tmm) REVERT: C 585 HIS cc_start: 0.8484 (t-90) cc_final: 0.8210 (t-90) REVERT: C 591 LEU cc_start: 0.9047 (tp) cc_final: 0.8440 (tt) REVERT: C 595 ILE cc_start: 0.9236 (mt) cc_final: 0.8888 (mt) REVERT: C 616 LYS cc_start: 0.9068 (mptt) cc_final: 0.8525 (mptt) REVERT: C 652 ILE cc_start: 0.8542 (pt) cc_final: 0.8284 (mm) REVERT: D 139 LEU cc_start: 0.9358 (mm) cc_final: 0.8999 (tp) REVERT: D 185 GLU cc_start: 0.9056 (mp0) cc_final: 0.8495 (pm20) REVERT: D 220 ASN cc_start: 0.9074 (m110) cc_final: 0.8666 (m110) REVERT: D 290 THR cc_start: 0.9263 (m) cc_final: 0.9028 (p) REVERT: D 440 MET cc_start: 0.8205 (tpp) cc_final: 0.7948 (tpp) REVERT: D 501 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7708 (mm-30) REVERT: D 506 PHE cc_start: 0.8604 (t80) cc_final: 0.8111 (m-80) REVERT: D 551 LEU cc_start: 0.9564 (tp) cc_final: 0.9294 (tp) REVERT: D 555 MET cc_start: 0.9030 (mtt) cc_final: 0.8668 (mtt) REVERT: D 565 TYR cc_start: 0.9267 (m-80) cc_final: 0.8521 (m-80) REVERT: D 574 MET cc_start: 0.8881 (tpp) cc_final: 0.7141 (tpt) REVERT: D 585 HIS cc_start: 0.8439 (t-90) cc_final: 0.8224 (t-90) REVERT: D 591 LEU cc_start: 0.9046 (tp) cc_final: 0.8431 (tt) REVERT: D 595 ILE cc_start: 0.9204 (mt) cc_final: 0.8850 (mt) REVERT: D 616 LYS cc_start: 0.9027 (mptt) cc_final: 0.8511 (mptt) REVERT: D 689 GLU cc_start: 0.9190 (tt0) cc_final: 0.8720 (tp30) REVERT: D 715 PHE cc_start: 0.7250 (t80) cc_final: 0.5912 (t80) outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 0.2860 time to fit residues: 294.2778 Evaluate side-chains 530 residues out of total 2300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 187 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 HIS A 735 ASN B 452 ASN ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN B 735 ASN ** C 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN C 745 HIS D 735 ASN D 745 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.079085 restraints weight = 60167.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.081537 restraints weight = 37401.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.083395 restraints weight = 26614.976| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21460 Z= 0.210 Angle : 0.727 8.341 29032 Z= 0.353 Chirality : 0.043 0.221 3308 Planarity : 0.004 0.042 3624 Dihedral : 5.099 22.479 2808 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.89 % Favored : 86.95 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2568 helix: 0.72 (0.14), residues: 1496 sheet: -3.01 (0.51), residues: 76 loop : -2.94 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 742 HIS 0.004 0.001 HIS D 745 PHE 0.023 0.001 PHE A 489 TYR 0.017 0.001 TYR D 359 ARG 0.006 0.000 ARG B 363 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5329.94 seconds wall clock time: 96 minutes 8.94 seconds (5768.94 seconds total)