Starting phenix.real_space_refine on Fri Apr 12 19:06:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hae_34586/04_2024/8hae_34586.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hae_34586/04_2024/8hae_34586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hae_34586/04_2024/8hae_34586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hae_34586/04_2024/8hae_34586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hae_34586/04_2024/8hae_34586.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hae_34586/04_2024/8hae_34586.pdb" } resolution = 4.55 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= 0.000 sd= 1.000 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 98 5.16 5 C 8498 2.51 5 N 2322 2.21 5 O 2508 1.98 5 H 13272 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 740": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 748": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 740": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 748": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26698 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 13349 Classifications: {'peptide': 845} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 39, 'TRANS': 805} Chain breaks: 1 Chain: "B" Number of atoms: 13349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 13349 Classifications: {'peptide': 845} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 39, 'TRANS': 805} Chain breaks: 1 Time building chain proxies: 11.43, per 1000 atoms: 0.43 Number of scatterers: 26698 At special positions: 0 Unit cell: (164.813, 133.052, 83.2648, 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 98 16.00 O 2508 8.00 N 2322 7.00 C 8498 6.00 H 13272 1.00 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: 22.04 Conformation dependent library (CDL) restraints added in 2.7 seconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 10 sheets defined 64.9% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 1 through 4 removed outlier: 3.945A pdb=" N ALA A 4 " --> pdb=" O MET A 1 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1 through 4' Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 26 through 40 Proline residue: A 36 - end of helix Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.844A pdb=" N ALA A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN A 74 " --> pdb=" O HIS A 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.590A pdb=" N MET A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.693A pdb=" N ASN A 141 " --> pdb=" O TRP A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.933A pdb=" N CYS A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.811A pdb=" N GLN A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 removed outlier: 3.505A pdb=" N PHE A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 206 " --> pdb=" O TYR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.541A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.622A pdb=" N CYS A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 removed outlier: 3.679A pdb=" N TYR A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.654A pdb=" N ILE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 282 removed outlier: 4.396A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.534A pdb=" N ILE A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 381 Proline residue: A 359 - end of helix removed outlier: 4.222A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 462 removed outlier: 3.771A pdb=" N VAL A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 492 removed outlier: 3.867A pdb=" N ILE A 477 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.752A pdb=" N GLU A 507 " --> pdb=" O HIS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 522 removed outlier: 4.373A pdb=" N ARG A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 removed outlier: 3.645A pdb=" N ASP A 526 " --> pdb=" O PRO A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 526' Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 561 through 571 removed outlier: 3.764A pdb=" N CYS A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 593 through 608 removed outlier: 3.742A pdb=" N ASN A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 635 removed outlier: 4.247A pdb=" N TYR A 632 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 634 " --> pdb=" O SER A 631 " (cutoff:3.500A) Proline residue: A 635 - end of helix Processing helix chain 'A' and resid 636 through 654 removed outlier: 3.643A pdb=" N ASN A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.809A pdb=" N TYR A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 Processing helix chain 'A' and resid 684 through 697 removed outlier: 3.945A pdb=" N ASN A 690 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN A 697 " --> pdb=" O TRP A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 removed outlier: 4.425A pdb=" N GLY A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.749A pdb=" N ILE A 730 " --> pdb=" O GLY A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 735 No H-bonds generated for 'chain 'A' and resid 733 through 735' Processing helix chain 'A' and resid 736 through 750 removed outlier: 4.322A pdb=" N VAL A 741 " --> pdb=" O LYS A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 765 removed outlier: 3.789A pdb=" N GLN A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 removed outlier: 4.171A pdb=" N LEU A 775 " --> pdb=" O LEU A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 782 removed outlier: 4.153A pdb=" N GLU A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 799 Processing helix chain 'A' and resid 810 through 821 Processing helix chain 'A' and resid 824 through 837 removed outlier: 4.544A pdb=" N LEU A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 887 through 901 removed outlier: 4.526A pdb=" N LEU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 4 removed outlier: 3.944A pdb=" N ALA B 4 " --> pdb=" O MET B 1 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1 through 4' Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 26 through 40 Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.844A pdb=" N ALA B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN B 74 " --> pdb=" O HIS B 70 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 110 through 118 removed outlier: 3.589A pdb=" N MET B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 removed outlier: 3.693A pdb=" N ASN B 141 " --> pdb=" O TRP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.933A pdb=" N CYS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 173 " --> pdb=" O HIS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.812A pdb=" N GLN B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 removed outlier: 3.506A pdb=" N PHE B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 206 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.541A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.623A pdb=" N CYS B 236 " --> pdb=" O PRO B 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 removed outlier: 3.680A pdb=" N TYR B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.653A pdb=" N ILE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 removed outlier: 4.396A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 308 Processing helix chain 'B' and resid 314 through 334 removed outlier: 3.534A pdb=" N ILE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 381 Proline residue: B 359 - end of helix removed outlier: 4.222A pdb=" N LEU B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 462 removed outlier: 3.770A pdb=" N VAL B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 460 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 492 removed outlier: 3.867A pdb=" N ILE B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU B 485 " --> pdb=" O CYS B 481 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 508 removed outlier: 3.753A pdb=" N GLU B 507 " --> pdb=" O HIS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 522 removed outlier: 4.371A pdb=" N ARG B 514 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 519 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 526 removed outlier: 3.645A pdb=" N ASP B 526 " --> pdb=" O PRO B 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 526' Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 561 through 571 removed outlier: 3.764A pdb=" N CYS B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 Processing helix chain 'B' and resid 593 through 608 removed outlier: 3.742A pdb=" N ASN B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 635 removed outlier: 4.247A pdb=" N TYR B 632 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 634 " --> pdb=" O SER B 631 " (cutoff:3.500A) Proline residue: B 635 - end of helix Processing helix chain 'B' and resid 636 through 654 removed outlier: 3.642A pdb=" N ASN B 653 " --> pdb=" O GLY B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 672 removed outlier: 3.809A pdb=" N TYR B 667 " --> pdb=" O THR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 683 Processing helix chain 'B' and resid 684 through 697 removed outlier: 3.945A pdb=" N ASN B 690 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 697 " --> pdb=" O TRP B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 removed outlier: 4.425A pdb=" N GLY B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 730 removed outlier: 3.751A pdb=" N ILE B 730 " --> pdb=" O GLY B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 735 No H-bonds generated for 'chain 'B' and resid 733 through 735' Processing helix chain 'B' and resid 736 through 750 removed outlier: 4.321A pdb=" N VAL B 741 " --> pdb=" O LYS B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 765 removed outlier: 3.790A pdb=" N GLN B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN B 758 " --> pdb=" O GLN B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 776 removed outlier: 4.171A pdb=" N LEU B 775 " --> pdb=" O LEU B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.153A pdb=" N GLU B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 792 through 799 Processing helix chain 'B' and resid 810 through 821 Processing helix chain 'B' and resid 824 through 837 removed outlier: 4.544A pdb=" N LEU B 830 " --> pdb=" O GLU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 849 Processing helix chain 'B' and resid 887 through 901 removed outlier: 4.526A pdb=" N LEU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 897 " --> pdb=" O ASP B 893 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 336 through 337 removed outlier: 4.723A pdb=" N GLY A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 554 through 557 Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AA4, first strand: chain 'A' and resid 709 through 713 Processing sheet with id=AA5, first strand: chain 'A' and resid 801 through 803 removed outlier: 6.768A pdb=" N GLU A 801 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA A 862 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR A 803 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 336 through 337 removed outlier: 4.722A pdb=" N GLY B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 554 through 557 Processing sheet with id=AA8, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AA9, first strand: chain 'B' and resid 709 through 713 Processing sheet with id=AB1, first strand: chain 'B' and resid 801 through 803 removed outlier: 6.768A pdb=" N GLU B 801 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA B 862 " --> pdb=" O GLU B 801 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR B 803 " --> pdb=" O ALA B 862 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1728 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: 9.91 Time building geometry restraints manager: 22.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 13228 1.03 - 1.22: 48 1.22 - 1.42: 5747 1.42 - 1.62: 7815 1.62 - 1.82: 152 Bond restraints: 26990 Sorted by residual: bond pdb=" CA VAL A 741 " pdb=" HA VAL A 741 " ideal model delta sigma weight residual 0.970 0.914 0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" CD LYS A 798 " pdb=" CE LYS A 798 " ideal model delta sigma weight residual 1.520 1.596 -0.076 3.00e-02 1.11e+03 6.40e+00 bond pdb=" CD LYS B 798 " pdb=" CE LYS B 798 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.22e+00 bond pdb=" CG2 THR B 707 " pdb="HG22 THR B 707 " ideal model delta sigma weight residual 0.970 1.016 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" CD ARG B 44 " pdb=" NE ARG B 44 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.40e-02 5.10e+03 4.66e+00 ... (remaining 26985 not shown) Histogram of bond angle deviations from ideal: 66.02 - 79.62: 70 79.62 - 93.23: 9 93.23 - 106.84: 1299 106.84 - 120.44: 39505 120.44 - 134.05: 7869 Bond angle restraints: 48752 Sorted by residual: angle pdb=" N VAL A 741 " pdb=" CA VAL A 741 " pdb=" HA VAL A 741 " ideal model delta sigma weight residual 110.00 66.62 43.38 3.00e+00 1.11e-01 2.09e+02 angle pdb=" C GLU A 25 " pdb=" CA GLU A 25 " pdb=" HA GLU A 25 " ideal model delta sigma weight residual 109.00 66.02 42.98 3.00e+00 1.11e-01 2.05e+02 angle pdb=" C LEU A 869 " pdb=" CA LEU A 869 " pdb=" HA LEU A 869 " ideal model delta sigma weight residual 109.00 68.22 40.78 3.00e+00 1.11e-01 1.85e+02 angle pdb=" C PHE A 708 " pdb=" CA PHE A 708 " pdb=" HA PHE A 708 " ideal model delta sigma weight residual 109.00 68.55 40.45 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C SER A 729 " pdb=" CA SER A 729 " pdb=" HA SER A 729 " ideal model delta sigma weight residual 109.00 68.57 40.43 3.00e+00 1.11e-01 1.82e+02 ... (remaining 48747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.05: 11352 14.05 - 28.11: 1008 28.11 - 42.16: 262 42.16 - 56.21: 91 56.21 - 70.27: 29 Dihedral angle restraints: 12742 sinusoidal: 6956 harmonic: 5786 Sorted by residual: dihedral pdb=" CA PHE B 515 " pdb=" C PHE B 515 " pdb=" N MET B 516 " pdb=" CA MET B 516 " ideal model delta harmonic sigma weight residual 180.00 131.34 48.66 0 5.00e+00 4.00e-02 9.47e+01 dihedral pdb=" CA PHE A 515 " pdb=" C PHE A 515 " pdb=" N MET A 516 " pdb=" CA MET A 516 " ideal model delta harmonic sigma weight residual 180.00 131.36 48.64 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA LYS A 496 " pdb=" C LYS A 496 " pdb=" N ILE A 497 " pdb=" CA ILE A 497 " ideal model delta harmonic sigma weight residual -180.00 -140.88 -39.12 0 5.00e+00 4.00e-02 6.12e+01 ... (remaining 12739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2038 0.156 - 0.312: 30 0.312 - 0.468: 6 0.468 - 0.624: 2 0.624 - 0.780: 6 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CG LEU B 855 " pdb=" CB LEU B 855 " pdb=" CD1 LEU B 855 " pdb=" CD2 LEU B 855 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CG LEU A 855 " pdb=" CB LEU A 855 " pdb=" CD1 LEU A 855 " pdb=" CD2 LEU A 855 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CG LEU B 891 " pdb=" CB LEU B 891 " pdb=" CD1 LEU B 891 " pdb=" CD2 LEU B 891 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.29e+01 ... (remaining 2079 not shown) Planarity restraints: 4032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 610 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO A 611 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 611 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 611 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 610 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO B 611 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 611 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 611 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 626 " -0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 627 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 627 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 627 " -0.033 5.00e-02 4.00e+02 ... (remaining 4029 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1502 2.19 - 2.79: 55890 2.79 - 3.39: 71650 3.39 - 4.00: 89507 4.00 - 4.60: 140392 Nonbonded interactions: 358941 Sorted by model distance: nonbonded pdb=" H2 MET B 1 " pdb=" HA MET B 1 " model vdw 1.582 1.816 nonbonded pdb=" H ALA A 862 " pdb=" HA ALA A 862 " model vdw 1.582 1.816 nonbonded pdb=" H SER A 729 " pdb=" HA SER A 729 " model vdw 1.588 1.816 nonbonded pdb=" H LEU A 15 " pdb=" HA LEU A 15 " model vdw 1.594 1.816 nonbonded pdb=" H LEU A 869 " pdb=" HA LEU A 869 " model vdw 1.595 1.816 ... (remaining 358936 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' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.420 Extract box with map and model: 6.600 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 84.730 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.009 0.076 13718 Z= 0.609 Angle : 1.043 11.207 18604 Z= 0.600 Chirality : 0.073 0.780 2082 Planarity : 0.006 0.065 2424 Dihedral : 10.838 70.267 5092 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.27 % Allowed : 2.13 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -3.55 (0.18), residues: 1682 helix: -2.74 (0.13), residues: 846 sheet: -0.44 (0.93), residues: 24 loop : -1.87 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 600 HIS 0.014 0.003 HIS A 279 PHE 0.029 0.004 PHE B 479 TYR 0.035 0.004 TYR B 806 ARG 0.020 0.002 ARG B 527 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 ILE cc_start: 0.9313 (mt) cc_final: 0.9110 (tt) REVERT: A 500 ASP cc_start: 0.8088 (t0) cc_final: 0.7874 (t70) REVERT: A 718 MET cc_start: 0.7107 (mpt) cc_final: 0.6844 (mpp) REVERT: A 788 MET cc_start: 0.8500 (ptm) cc_final: 0.8210 (mmt) outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.5232 time to fit residues: 75.6299 Evaluate side-chains 69 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 128 ASN B 141 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN ** B 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 ASN B 799 ASN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13718 Z= 0.214 Angle : 0.789 11.167 18604 Z= 0.425 Chirality : 0.115 1.609 2082 Planarity : 0.006 0.055 2424 Dihedral : 7.445 35.434 1820 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.13 % Allowed : 0.66 % Favored : 99.20 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.94 (0.19), residues: 1682 helix: -1.88 (0.15), residues: 938 sheet: -0.21 (0.89), residues: 24 loop : -1.94 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 817 HIS 0.009 0.001 HIS B 279 PHE 0.015 0.002 PHE B 666 TYR 0.024 0.002 TYR B 740 ARG 0.007 0.001 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 471 MET cc_start: 0.8013 (ttt) cc_final: 0.7375 (tpp) REVERT: B 500 ASP cc_start: 0.7802 (t0) cc_final: 0.7588 (t70) REVERT: B 762 GLN cc_start: 0.8410 (mt0) cc_final: 0.8103 (tm-30) outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.4356 time to fit residues: 55.4628 Evaluate side-chains 78 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 550 ASN ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 13718 Z= 0.532 Angle : 0.971 11.388 18604 Z= 0.528 Chirality : 0.120 1.676 2082 Planarity : 0.008 0.176 2424 Dihedral : 7.461 33.153 1820 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.53 % Favored : 88.23 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.90 (0.17), residues: 1682 helix: -2.53 (0.13), residues: 924 sheet: -0.17 (0.87), residues: 24 loop : -2.63 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 600 HIS 0.012 0.002 HIS A 252 PHE 0.028 0.003 PHE A 331 TYR 0.017 0.002 TYR A 806 ARG 0.022 0.001 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8196 (mt-10) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.4895 time to fit residues: 55.0153 Evaluate side-chains 66 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.0980 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 0.0570 chunk 162 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 145 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13718 Z= 0.177 Angle : 0.708 11.448 18604 Z= 0.377 Chirality : 0.118 1.662 2082 Planarity : 0.005 0.052 2424 Dihedral : 6.637 26.621 1820 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.13 % 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: -3.34 (0.18), residues: 1682 helix: -2.13 (0.14), residues: 940 sheet: -0.76 (0.80), residues: 24 loop : -2.24 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 600 HIS 0.009 0.001 HIS B 900 PHE 0.023 0.002 PHE A 479 TYR 0.019 0.001 TYR B 740 ARG 0.003 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3383 time to fit residues: 43.0015 Evaluate side-chains 78 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 82 optimal weight: 0.0670 chunk 145 optimal weight: 0.0060 chunk 40 optimal weight: 0.7980 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13718 Z= 0.162 Angle : 0.662 11.465 18604 Z= 0.352 Chirality : 0.116 1.688 2082 Planarity : 0.004 0.046 2424 Dihedral : 5.919 24.813 1820 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.13 % 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: -3.15 (0.18), residues: 1682 helix: -1.82 (0.14), residues: 960 sheet: -1.20 (0.64), residues: 24 loop : -2.38 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 364 HIS 0.004 0.001 HIS A 558 PHE 0.017 0.001 PHE B 666 TYR 0.020 0.001 TYR B 740 ARG 0.005 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8462 (p0) cc_final: 0.8239 (p0) REVERT: A 243 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8307 (mt-10) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.3235 time to fit residues: 41.9217 Evaluate side-chains 71 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 95 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 162 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13718 Z= 0.156 Angle : 0.655 11.350 18604 Z= 0.349 Chirality : 0.118 1.675 2082 Planarity : 0.004 0.046 2424 Dihedral : 5.638 23.842 1820 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.13 % 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: -2.79 (0.19), residues: 1682 helix: -1.55 (0.15), residues: 946 sheet: -1.19 (0.68), residues: 24 loop : -2.17 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 600 HIS 0.004 0.001 HIS B 207 PHE 0.018 0.001 PHE B 666 TYR 0.022 0.001 TYR A 740 ARG 0.005 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8468 (p0) cc_final: 0.8241 (p0) REVERT: A 243 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8334 (mp0) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3274 time to fit residues: 41.6290 Evaluate side-chains 75 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 90 optimal weight: 0.0470 chunk 161 optimal weight: 0.0470 chunk 101 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13718 Z= 0.152 Angle : 0.642 11.748 18604 Z= 0.341 Chirality : 0.119 1.674 2082 Planarity : 0.004 0.045 2424 Dihedral : 5.397 22.914 1820 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.13 % 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: -2.53 (0.19), residues: 1682 helix: -1.22 (0.15), residues: 942 sheet: -1.70 (0.71), residues: 24 loop : -2.22 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 364 HIS 0.004 0.001 HIS A 558 PHE 0.018 0.002 PHE A 666 TYR 0.012 0.001 TYR B 806 ARG 0.004 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8466 (p0) cc_final: 0.7842 (p0) REVERT: A 813 ILE cc_start: 0.5937 (mt) cc_final: 0.5694 (mt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.3237 time to fit residues: 40.1569 Evaluate side-chains 77 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 0.2980 chunk 110 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 0.0970 chunk 147 optimal weight: 6.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 279 HIS ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13718 Z= 0.144 Angle : 0.628 11.642 18604 Z= 0.333 Chirality : 0.119 1.692 2082 Planarity : 0.004 0.045 2424 Dihedral : 5.163 21.879 1820 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.13 % 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: -2.41 (0.19), residues: 1682 helix: -1.06 (0.15), residues: 956 sheet: -1.54 (0.73), residues: 24 loop : -2.29 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 530 HIS 0.008 0.001 HIS B 207 PHE 0.016 0.001 PHE B 666 TYR 0.010 0.001 TYR B 806 ARG 0.004 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8338 (p0) cc_final: 0.7936 (p0) REVERT: A 243 GLU cc_start: 0.8316 (mp0) cc_final: 0.7867 (mp0) REVERT: A 328 CYS cc_start: 0.8524 (m) cc_final: 0.8254 (t) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.3330 time to fit residues: 42.6675 Evaluate side-chains 77 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 0.0970 chunk 90 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13718 Z= 0.149 Angle : 0.628 11.756 18604 Z= 0.333 Chirality : 0.119 1.687 2082 Planarity : 0.004 0.044 2424 Dihedral : 5.007 21.469 1820 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.13 % 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: -2.26 (0.19), residues: 1682 helix: -0.88 (0.16), residues: 946 sheet: -1.44 (0.75), residues: 24 loop : -2.31 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 530 HIS 0.013 0.001 HIS A 207 PHE 0.017 0.001 PHE B 666 TYR 0.010 0.001 TYR A 806 ARG 0.004 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LEU cc_start: 0.8812 (tp) cc_final: 0.8592 (tp) REVERT: B 243 GLU cc_start: 0.8090 (mp0) cc_final: 0.7863 (mp0) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.3380 time to fit residues: 44.1196 Evaluate side-chains 77 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.0010 chunk 75 optimal weight: 0.6980 chunk 110 optimal weight: 0.0060 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 0.0010 chunk 102 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 0.1980 overall best weight: 0.1208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13718 Z= 0.142 Angle : 0.621 11.525 18604 Z= 0.326 Chirality : 0.119 1.711 2082 Planarity : 0.004 0.045 2424 Dihedral : 4.808 20.733 1820 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.13 % 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: -1.93 (0.19), residues: 1682 helix: -0.62 (0.16), residues: 932 sheet: -1.39 (0.74), residues: 24 loop : -2.12 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 530 HIS 0.006 0.001 HIS B 207 PHE 0.016 0.001 PHE A 666 TYR 0.010 0.001 TYR A 806 ARG 0.006 0.000 ARG B 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.7825 (tpm170) cc_final: 0.7057 (mmp80) REVERT: A 201 LEU cc_start: 0.8835 (tp) cc_final: 0.8628 (tp) REVERT: A 211 ASP cc_start: 0.8086 (p0) cc_final: 0.7879 (p0) REVERT: A 243 GLU cc_start: 0.8210 (mp0) cc_final: 0.7982 (mp0) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3252 time to fit residues: 44.2548 Evaluate side-chains 78 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.0050 chunk 122 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 16 optimal weight: 0.0980 chunk 24 optimal weight: 0.0770 chunk 117 optimal weight: 0.4980 chunk 7 optimal weight: 9.9990 overall best weight: 0.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.089562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.069940 restraints weight = 106467.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.072790 restraints weight = 57857.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.074658 restraints weight = 37820.694| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13718 Z= 0.137 Angle : 0.620 11.738 18604 Z= 0.325 Chirality : 0.121 1.726 2082 Planarity : 0.004 0.044 2424 Dihedral : 4.663 20.280 1820 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.13 % 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: -1.80 (0.19), residues: 1682 helix: -0.45 (0.16), residues: 932 sheet: -2.09 (0.72), residues: 24 loop : -2.14 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 364 HIS 0.004 0.001 HIS A 558 PHE 0.017 0.001 PHE A 666 TYR 0.010 0.001 TYR B 806 ARG 0.005 0.000 ARG A 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3662.12 seconds wall clock time: 66 minutes 59.49 seconds (4019.49 seconds total)