Starting phenix.real_space_refine (version: dev) on Tue Apr 5 09:18:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/04_2022/7dgd_30671_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/04_2022/7dgd_30671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/04_2022/7dgd_30671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/04_2022/7dgd_30671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/04_2022/7dgd_30671_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/04_2022/7dgd_30671_neut.pdb" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.022 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 566": "OD1" <-> "OD2" Residue "B GLU 592": "OE1" <-> "OE2" Residue "B TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 12381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6194 Classifications: {'peptide': 786} Link IDs: {'PTRANS': 34, 'TRANS': 751} Chain breaks: 1 Chain: "B" Number of atoms: 6187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6187 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 751, 'PCIS': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 7.05, per 1000 atoms: 0.57 Number of scatterers: 12381 At special positions: 0 Unit cell: (119.85, 95.88, 186.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 2251 8.00 N 2074 7.00 C 7958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 291 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 544 " distance=2.04 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 578 " distance=2.04 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 394 " distance=2.04 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 544 " distance=2.05 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 562 " distance=2.05 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 657 " - pdb=" SG CYS B 746 " distance=2.03 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: 4.48 Conformation dependent library (CDL) restraints added in 1.9 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 15 sheets defined 46.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.886A pdb=" N GLU A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 4.469A pdb=" N LEU A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 132 removed outlier: 4.010A pdb=" N GLU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.563A pdb=" N LEU A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.719A pdb=" N LEU A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP A 194 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.954A pdb=" N GLN A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 removed outlier: 4.037A pdb=" N GLU A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.690A pdb=" N ALA A 321 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 removed outlier: 4.102A pdb=" N ASP A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 357 No H-bonds generated for 'chain 'A' and resid 356 through 357' Processing helix chain 'A' and resid 358 through 362 removed outlier: 4.004A pdb=" N ASN A 362 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 410 through 422 removed outlier: 4.054A pdb=" N ILE A 414 " --> pdb=" O MET A 410 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.911A pdb=" N HIS A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 456 removed outlier: 4.065A pdb=" N ASP A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 576 removed outlier: 4.001A pdb=" N THR A 576 " --> pdb=" O ALA A 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 593 through 615 removed outlier: 3.616A pdb=" N ILE A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 Processing helix chain 'A' and resid 627 through 649 removed outlier: 4.305A pdb=" N CYS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Proline residue: A 645 - end of helix removed outlier: 3.799A pdb=" N ILE A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 689 removed outlier: 3.563A pdb=" N SER A 668 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 removed outlier: 4.299A pdb=" N LEU A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 728 removed outlier: 4.310A pdb=" N GLN A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 718 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 770 removed outlier: 3.662A pdb=" N VAL A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Proline residue: A 756 - end of helix Processing helix chain 'A' and resid 772 through 776 removed outlier: 3.910A pdb=" N ARG A 775 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 808 removed outlier: 3.790A pdb=" N TYR A 786 " --> pdb=" O ASN A 782 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL A 802 " --> pdb=" O TRP A 798 " (cutoff:3.500A) Proline residue: A 803 - end of helix Processing helix chain 'A' and resid 810 through 837 removed outlier: 4.024A pdb=" N THR A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) Proline residue: A 833 - end of helix Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.597A pdb=" N VAL B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 125 through 132 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.765A pdb=" N GLN B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 252 Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.626A pdb=" N LEU B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 307 removed outlier: 3.711A pdb=" N VAL B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.790A pdb=" N ASP B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 377 Processing helix chain 'B' and resid 409 through 431 removed outlier: 4.019A pdb=" N ILE B 414 " --> pdb=" O MET B 410 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 415 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS B 429 " --> pdb=" O GLN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 509 through 512 Processing helix chain 'B' and resid 572 through 576 removed outlier: 4.061A pdb=" N THR B 576 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 613 removed outlier: 4.038A pdb=" N ALA B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 649 removed outlier: 4.064A pdb=" N CYS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 635 " --> pdb=" O CYS B 631 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY B 641 " --> pdb=" O GLY B 637 " (cutoff:3.500A) Proline residue: B 645 - end of helix removed outlier: 3.801A pdb=" N ILE B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 689 removed outlier: 4.409A pdb=" N SER B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER B 668 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 675 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE B 682 " --> pdb=" O LYS B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 726 removed outlier: 3.585A pdb=" N ILE B 708 " --> pdb=" O TRP B 704 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL B 721 " --> pdb=" O GLN B 717 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 725 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 755 Processing helix chain 'B' and resid 756 through 770 removed outlier: 4.109A pdb=" N LEU B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 800 removed outlier: 3.915A pdb=" N ILE B 796 " --> pdb=" O TYR B 792 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE B 797 " --> pdb=" O THR B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 808 removed outlier: 4.118A pdb=" N ILE B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 829 removed outlier: 4.081A pdb=" N VAL B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 827 " --> pdb=" O VAL B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 839 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.631A pdb=" N VAL A 45 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU A 104 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 47 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE A 46 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY A 158 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 184 removed outlier: 3.538A pdb=" N LEU A 202 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 231 removed outlier: 6.974A pdb=" N VAL A 230 " --> pdb=" O PHE A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 342 removed outlier: 3.866A pdb=" N GLY A 337 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A 482 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR A 479 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR A 499 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 481 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 533 through 535 Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA7, first strand: chain 'A' and resid 569 through 571 removed outlier: 4.371A pdb=" N TRP A 570 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 579 " --> pdb=" O TRP A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.424A pdb=" N VAL B 45 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLU B 104 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 47 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE B 46 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ILE B 160 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY B 48 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ILE B 183 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 159 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN B 182 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 258 removed outlier: 6.145A pdb=" N VAL B 227 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS B 257 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL B 288 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N SER B 228 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 290 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 230 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 341 through 342 removed outlier: 3.513A pdb=" N LYS B 341 " --> pdb=" O ASP B 480 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 458 through 460 removed outlier: 3.642A pdb=" N PHE B 459 " --> pdb=" O VAL B 467 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 467 " --> pdb=" O PHE B 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 484 through 486 Processing sheet with id=AB4, first strand: chain 'B' and resid 533 through 535 Processing sheet with id=AB5, first strand: chain 'B' and resid 554 through 558 removed outlier: 3.868A pdb=" N GLN B 557 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 732 through 733 removed outlier: 3.584A pdb=" N ILE B 733 " --> pdb=" O ILE B 745 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 745 " --> pdb=" O ILE B 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 469 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 5.02 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: 2753 1.34 - 1.47: 3594 1.47 - 1.59: 6173 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 12658 Sorted by residual: bond pdb=" CD GLU B 80 " pdb=" OE1 GLU B 80 " ideal model delta sigma weight residual 1.249 1.364 -0.115 1.90e-02 2.77e+03 3.65e+01 bond pdb=" CG ASP B 208 " pdb=" OD2 ASP B 208 " ideal model delta sigma weight residual 1.249 1.361 -0.112 1.90e-02 2.77e+03 3.49e+01 bond pdb=" CA VAL A 802 " pdb=" CB VAL A 802 " ideal model delta sigma weight residual 1.537 1.557 -0.021 5.00e-03 4.00e+04 1.69e+01 bond pdb=" CA PRO B 729 " pdb=" C PRO B 729 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.31e+01 bond pdb=" CA VAL A 62 " pdb=" C VAL A 62 " ideal model delta sigma weight residual 1.524 1.562 -0.037 1.05e-02 9.07e+03 1.26e+01 ... (remaining 12653 not shown) Histogram of bond angle deviations from ideal: 94.65 - 102.71: 67 102.71 - 110.78: 2858 110.78 - 118.84: 7862 118.84 - 126.91: 6162 126.91 - 134.97: 222 Bond angle restraints: 17171 Sorted by residual: angle pdb=" N VAL B 309 " pdb=" CA VAL B 309 " pdb=" C VAL B 309 " ideal model delta sigma weight residual 110.42 117.61 -7.19 9.60e-01 1.09e+00 5.60e+01 angle pdb=" CA ASP B 92 " pdb=" CB ASP B 92 " pdb=" CG ASP B 92 " ideal model delta sigma weight residual 112.60 119.69 -7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" C VAL A 308 " pdb=" N VAL A 309 " pdb=" CA VAL A 309 " ideal model delta sigma weight residual 120.56 128.80 -8.24 1.26e+00 6.30e-01 4.28e+01 angle pdb=" CA ASP B 318 " pdb=" CB ASP B 318 " pdb=" CG ASP B 318 " ideal model delta sigma weight residual 112.60 119.06 -6.46 1.00e+00 1.00e+00 4.17e+01 angle pdb=" CA ASN B 387 " pdb=" CB ASN B 387 " pdb=" CG ASN B 387 " ideal model delta sigma weight residual 112.60 118.91 -6.31 1.00e+00 1.00e+00 3.98e+01 ... (remaining 17166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 6783 17.20 - 34.40: 644 34.40 - 51.60: 147 51.60 - 68.79: 41 68.79 - 85.99: 17 Dihedral angle restraints: 7632 sinusoidal: 3053 harmonic: 4579 Sorted by residual: dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 544 " pdb=" CB CYS A 544 " ideal model delta sinusoidal sigma weight residual 93.00 167.38 -74.38 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CA SER A 589 " pdb=" C SER A 589 " pdb=" N ASN A 590 " pdb=" CA ASN A 590 " ideal model delta harmonic sigma weight residual 180.00 142.29 37.71 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA THR A 499 " pdb=" C THR A 499 " pdb=" N TRP A 500 " pdb=" CA TRP A 500 " ideal model delta harmonic sigma weight residual 180.00 145.81 34.19 0 5.00e+00 4.00e-02 4.68e+01 ... (remaining 7629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1246 0.104 - 0.208: 533 0.208 - 0.312: 144 0.312 - 0.415: 26 0.415 - 0.519: 5 Chirality restraints: 1954 Sorted by residual: chirality pdb=" CB THR B 607 " pdb=" CA THR B 607 " pdb=" OG1 THR B 607 " pdb=" CG2 THR B 607 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" CA GLU A 72 " pdb=" N GLU A 72 " pdb=" C GLU A 72 " pdb=" CB GLU A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CB THR B 611 " pdb=" CA THR B 611 " pdb=" OG1 THR B 611 " pdb=" CG2 THR B 611 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 1951 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 353 " 0.188 2.00e-02 2.50e+03 1.04e-01 2.17e+02 pdb=" CG TYR A 353 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 353 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 TYR A 353 " -0.082 2.00e-02 2.50e+03 pdb=" CE1 TYR A 353 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 353 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR A 353 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 353 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 672 " 0.158 2.00e-02 2.50e+03 8.39e-02 1.41e+02 pdb=" CG TYR A 672 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 672 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR A 672 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR A 672 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR A 672 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR A 672 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 672 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 770 " 0.113 2.00e-02 2.50e+03 5.91e-02 6.98e+01 pdb=" CG TYR A 770 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 770 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR A 770 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR A 770 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 770 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 770 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 770 " 0.065 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 2 2.52 - 3.12: 7579 3.12 - 3.71: 19449 3.71 - 4.31: 25982 4.31 - 4.90: 42319 Nonbonded interactions: 95331 Sorted by model distance: nonbonded pdb=" O LEU B 281 " pdb=" CG ARG B 285 " model vdw 1.930 3.440 nonbonded pdb=" O LEU B 281 " pdb=" CD ARG B 285 " model vdw 2.083 3.440 nonbonded pdb=" O ARG B 521 " pdb=" N VAL B 523 " model vdw 2.569 2.520 nonbonded pdb=" OG SER B 517 " pdb=" N GLY B 518 " model vdw 2.570 2.520 nonbonded pdb=" N TRP A 570 " pdb=" O TRP A 570 " model vdw 2.587 2.496 ... (remaining 95326 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 35 through 225 or (resid 226 and (name N or name CA or nam \ e C or name O or name CB )) or resid 227 through 839)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 7958 2.51 5 N 2074 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.300 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 33.010 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5286 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 : 0.015 0.115 12658 Z= 0.985 Angle : 2.083 10.905 17171 Z= 1.401 Chirality : 0.121 0.519 1954 Planarity : 0.013 0.104 2163 Dihedral : 15.162 85.992 4637 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.21 % Favored : 89.90 % Rotamer Outliers : 3.87 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.20 % 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: -4.26 (0.17), residues: 1564 helix: -2.39 (0.16), residues: 662 sheet: -2.84 (0.45), residues: 99 loop : -3.28 (0.18), residues: 803 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 1.466 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 outliers start: 53 outliers final: 13 residues processed: 216 average time/residue: 0.2410 time to fit residues: 75.0858 Evaluate side-chains 113 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.504 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1376 time to fit residues: 5.0920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 173 ASN A 182 GLN A 250 GLN A 365 ASN A 387 ASN A 485 GLN A 776 ASN B 77 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 173 ASN B 223 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS B 343 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 809 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5586 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 12658 Z= 0.251 Angle : 0.799 10.014 17171 Z= 0.413 Chirality : 0.047 0.283 1954 Planarity : 0.006 0.125 2163 Dihedral : 6.152 32.233 1713 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.25 % Favored : 91.69 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.93 (0.19), residues: 1564 helix: -0.98 (0.18), residues: 682 sheet: -2.77 (0.38), residues: 124 loop : -2.75 (0.20), residues: 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 110 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 18 residues processed: 144 average time/residue: 0.2117 time to fit residues: 46.7573 Evaluate side-chains 100 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1143 time to fit residues: 5.7131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 117 optimal weight: 0.0470 chunk 96 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN B 383 HIS ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 12658 Z= 0.298 Angle : 0.787 9.210 17171 Z= 0.406 Chirality : 0.046 0.223 1954 Planarity : 0.005 0.079 2163 Dihedral : 6.166 29.724 1713 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.40 % Favored : 90.54 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -2.55 (0.19), residues: 1564 helix: -0.58 (0.19), residues: 683 sheet: -2.52 (0.37), residues: 133 loop : -2.65 (0.20), residues: 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 95 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 18 residues processed: 130 average time/residue: 0.2077 time to fit residues: 41.9908 Evaluate side-chains 98 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1216 time to fit residues: 6.3355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 12658 Z= 0.333 Angle : 0.787 8.963 17171 Z= 0.406 Chirality : 0.047 0.198 1954 Planarity : 0.005 0.057 2163 Dihedral : 6.261 26.916 1713 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.10 % Favored : 89.83 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -2.35 (0.20), residues: 1564 helix: -0.42 (0.19), residues: 673 sheet: -2.11 (0.39), residues: 128 loop : -2.57 (0.21), residues: 763 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 96 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 16 residues processed: 132 average time/residue: 0.2374 time to fit residues: 47.7013 Evaluate side-chains 91 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1222 time to fit residues: 5.6129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 12658 Z= 0.379 Angle : 0.818 9.927 17171 Z= 0.420 Chirality : 0.048 0.213 1954 Planarity : 0.005 0.045 2163 Dihedral : 6.415 27.150 1713 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.76 % Favored : 88.17 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -2.36 (0.20), residues: 1564 helix: -0.50 (0.19), residues: 687 sheet: -1.89 (0.41), residues: 128 loop : -2.59 (0.21), residues: 749 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 86 time to evaluate : 1.669 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 125 average time/residue: 0.2042 time to fit residues: 40.7846 Evaluate side-chains 95 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1236 time to fit residues: 6.4682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 125 optimal weight: 0.0470 chunk 69 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 12658 Z= 0.255 Angle : 0.751 9.158 17171 Z= 0.381 Chirality : 0.045 0.220 1954 Planarity : 0.005 0.043 2163 Dihedral : 5.940 26.333 1713 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.27 % Favored : 90.66 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -2.13 (0.20), residues: 1564 helix: -0.22 (0.20), residues: 678 sheet: -1.92 (0.41), residues: 136 loop : -2.49 (0.21), residues: 750 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 1.440 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 110 average time/residue: 0.2210 time to fit residues: 37.6808 Evaluate side-chains 93 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1133 time to fit residues: 4.6520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 50.0000 chunk 93 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 12658 Z= 0.204 Angle : 0.716 9.873 17171 Z= 0.363 Chirality : 0.044 0.224 1954 Planarity : 0.004 0.042 2163 Dihedral : 5.484 26.652 1713 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.38 % Favored : 91.56 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -1.88 (0.21), residues: 1564 helix: -0.13 (0.20), residues: 684 sheet: -1.71 (0.42), residues: 136 loop : -2.26 (0.22), residues: 744 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 105 average time/residue: 0.2384 time to fit residues: 38.9749 Evaluate side-chains 88 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 1.448 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1278 time to fit residues: 3.7804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 50.0000 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 0.1980 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 74 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 12658 Z= 0.196 Angle : 0.705 13.280 17171 Z= 0.353 Chirality : 0.043 0.203 1954 Planarity : 0.004 0.042 2163 Dihedral : 5.211 26.229 1713 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.99 % Favored : 91.94 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -1.73 (0.21), residues: 1564 helix: -0.01 (0.20), residues: 686 sheet: -1.50 (0.42), residues: 136 loop : -2.21 (0.22), residues: 742 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.590 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 97 average time/residue: 0.2265 time to fit residues: 34.0647 Evaluate side-chains 79 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 1.376 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1242 time to fit residues: 2.5263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 144 optimal weight: 30.0000 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 139 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 12658 Z= 0.242 Angle : 0.754 17.663 17171 Z= 0.378 Chirality : 0.044 0.221 1954 Planarity : 0.005 0.132 2163 Dihedral : 5.376 26.210 1713 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.08 % Favored : 90.86 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -1.76 (0.21), residues: 1564 helix: -0.03 (0.20), residues: 691 sheet: -1.53 (0.42), residues: 136 loop : -2.24 (0.22), residues: 737 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.518 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 84 average time/residue: 0.2197 time to fit residues: 30.4474 Evaluate side-chains 83 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1415 time to fit residues: 3.2705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 40.0000 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 12658 Z= 0.310 Angle : 0.802 17.924 17171 Z= 0.403 Chirality : 0.046 0.195 1954 Planarity : 0.005 0.118 2163 Dihedral : 5.761 26.183 1713 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.42 % Favored : 89.51 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -1.88 (0.21), residues: 1564 helix: -0.13 (0.20), residues: 684 sheet: -1.55 (0.43), residues: 133 loop : -2.30 (0.22), residues: 747 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.313 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 87 average time/residue: 0.2173 time to fit residues: 29.9378 Evaluate side-chains 82 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1216 time to fit residues: 2.7411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 123 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 15 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.145434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.108086 restraints weight = 29660.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.106155 restraints weight = 20273.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.107743 restraints weight = 17548.996| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 12658 Z= 0.209 Angle : 0.752 17.674 17171 Z= 0.378 Chirality : 0.044 0.189 1954 Planarity : 0.005 0.108 2163 Dihedral : 5.267 26.074 1713 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.99 % Favored : 91.94 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.21), residues: 1564 helix: 0.03 (0.20), residues: 689 sheet: -1.29 (0.44), residues: 136 loop : -2.21 (0.22), residues: 739 =============================================================================== Job complete usr+sys time: 2099.15 seconds wall clock time: 39 minutes 33.99 seconds (2373.99 seconds total)