Starting phenix.real_space_refine (version: dev) on Thu Apr 7 03:44:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/04_2022/6d03_7783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/04_2022/6d03_7783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/04_2022/6d03_7783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/04_2022/6d03_7783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/04_2022/6d03_7783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d03_7783/04_2022/6d03_7783_updated.pdb" } resolution = 3.68 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= 0.002 sd= 0.017 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 ARG 121": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C ARG 568": "NH1" <-> "NH2" Residue "C ARG 581": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "D ARG 7": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 324": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D ARG 522": "NH1" <-> "NH2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 581": "NH1" <-> "NH2" Residue "D ARG 632": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 242": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 468": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 24844 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'CIS': 1, 'TRANS': 614} Chain: "B" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'CIS': 2, 'TRANS': 644, 'PCIS': 3} Chain: "D" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'CIS': 2, 'TRANS': 644, 'PCIS': 3} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 6, 'CIS': 3, 'TRANS': 455, 'PCIS': 1} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' CA': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' CA': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'CO3': 2, ' FE': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Unusual residues: {'CO3': 2, ' FE': 2, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 13.77, per 1000 atoms: 0.55 Number of scatterers: 24844 At special positions: 0 Unit cell: (144.45, 149.85, 163.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 132 16.00 O 4749 8.00 N 4200 7.00 C 15757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 363 " distance=2.02 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 363 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 596 " distance=2.02 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 674 " distance=2.02 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 637 " distance=2.02 Simple disulfide: pdb=" SG CYS C 450 " - pdb=" SG CYS C 523 " distance=2.02 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 665 " distance=2.03 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 506 " distance=2.02 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 48 " distance=2.02 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 174 " distance=2.02 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 171 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 241 " distance=2.01 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 596 " distance=2.03 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 377 " distance=2.01 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 368 " distance=2.03 Simple disulfide: pdb=" SG CYS D 402 " - pdb=" SG CYS D 674 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 637 " distance=2.03 Simple disulfide: pdb=" SG CYS D 450 " - pdb=" SG CYS D 523 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 665 " distance=2.02 Simple disulfide: pdb=" SG CYS D 484 " - pdb=" SG CYS D 498 " distance=2.02 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 506 " distance=2.02 Simple disulfide: pdb=" SG CYS D 563 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 620 " distance=2.02 Simple disulfide: pdb=" SG CYS E 240 " - pdb=" SG CYS E 284 " distance=2.05 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " 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=1, symmetry=0 Links applied BETA1-4 " NAG A 803 " - " NAG A 804 " " NAG A 805 " - " NAG A 806 " " NAG B 803 " - " NAG B 804 " " NAG B 805 " - " NAG B 806 " " NAG D 705 " - " NAG D 706 " NAG-ASN " NAG A 802 " - " ASN A 251 " " NAG A 803 " - " ASN A 317 " " NAG A 805 " - " ASN A 727 " " NAG B 802 " - " ASN B 251 " " NAG B 803 " - " ASN B 317 " " NAG B 805 " - " ASN B 727 " " NAG C 705 " - " ASN C 413 " " NAG C 707 " - " ASN C 611 " " NAG D 705 " - " ASN D 413 " " NAG D 707 " - " ASN D 611 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.22 Conformation dependent library (CDL) restraints added in 3.7 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 22 sheets defined 39.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.885A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.883A pdb=" N LEU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 438 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 500 through 511 removed outlier: 4.815A pdb=" N THR A 504 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 583 through 601 Processing helix chain 'A' and resid 611 through 635 removed outlier: 3.680A pdb=" N TYR A 614 " --> pdb=" O TYR A 611 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 616 " --> pdb=" O ARG A 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 619 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 622 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 623 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A 626 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN A 627 " --> pdb=" O ASP A 624 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A 629 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 630 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A 633 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 661 Processing helix chain 'A' and resid 669 through 678 removed outlier: 3.656A pdb=" N LYS A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 709 through 717 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 728 through 749 Processing helix chain 'B' and resid 124 through 135 removed outlier: 3.741A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 148 removed outlier: 3.539A pdb=" N ASN B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.808A pdb=" N ARG B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.576A pdb=" N LYS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 438 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.942A pdb=" N TRP B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 511 removed outlier: 5.028A pdb=" N THR B 504 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 545 No H-bonds generated for 'chain 'B' and resid 542 through 545' Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 583 through 602 Processing helix chain 'B' and resid 613 through 635 removed outlier: 3.563A pdb=" N LEU B 619 " --> pdb=" O SER B 616 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 622 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 623 " --> pdb=" O SER B 620 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 626 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN B 627 " --> pdb=" O ASP B 624 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA B 630 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 632 " --> pdb=" O ARG B 629 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS B 633 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 661 Processing helix chain 'B' and resid 669 through 681 removed outlier: 3.912A pdb=" N LYS B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 674 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 681 " --> pdb=" O ARG B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 709 through 721 removed outlier: 4.396A pdb=" N LEU B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN B 721 " --> pdb=" O LYS B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 749 Processing helix chain 'C' and resid 13 through 29 removed outlier: 4.778A pdb=" N LYS C 18 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL C 29 " --> pdb=" O HIS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 64 through 67 No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 125 through 134 removed outlier: 5.323A pdb=" N ILE C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) Proline residue: C 131 - end of helix Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 146 through 151 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 209 through 213 Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 260 through 274 removed outlier: 3.583A pdb=" N GLN C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU C 272 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 374 through 383 removed outlier: 3.680A pdb=" N ALA C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 461 through 471 removed outlier: 4.047A pdb=" N ASN C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 496 No H-bonds generated for 'chain 'C' and resid 493 through 496' Processing helix chain 'C' and resid 516 through 526 Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 549 through 552 No H-bonds generated for 'chain 'C' and resid 549 through 552' Processing helix chain 'C' and resid 594 through 608 removed outlier: 3.804A pdb=" N HIS C 606 " --> pdb=" O ARG C 602 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 608 " --> pdb=" O GLN C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 651 Processing helix chain 'C' and resid 653 through 660 Processing helix chain 'C' and resid 669 through 675 Processing helix chain 'D' and resid 13 through 28 Processing helix chain 'D' and resid 45 through 53 Processing helix chain 'D' and resid 64 through 67 No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.777A pdb=" N LEU D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 131 through 135' Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'D' and resid 188 through 196 removed outlier: 3.599A pdb=" N PHE D 192 " --> pdb=" O TYR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 213 Processing helix chain 'D' and resid 217 through 222 removed outlier: 3.715A pdb=" N GLN D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.746A pdb=" N ARG D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 361 Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'D' and resid 393 through 401 removed outlier: 3.793A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 removed outlier: 3.625A pdb=" N LEU D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 470 " --> pdb=" O LEU D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 526 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 594 through 607 removed outlier: 3.513A pdb=" N GLN D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 Processing helix chain 'D' and resid 653 through 665 removed outlier: 4.220A pdb=" N LEU D 662 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 663 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LYS D 664 " --> pdb=" O GLY D 660 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N CYS D 665 " --> pdb=" O ASN D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 676 removed outlier: 3.571A pdb=" N THR D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 209 removed outlier: 3.923A pdb=" N ARG E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 239 removed outlier: 4.942A pdb=" N HIS E 222 " --> pdb=" O GLU E 219 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS E 223 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 225 " --> pdb=" O HIS E 222 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL E 226 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN E 227 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 230 " --> pdb=" O ASN E 227 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN E 231 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU E 232 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER E 234 " --> pdb=" O ASN E 231 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 237 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 255 removed outlier: 3.506A pdb=" N THR E 246 " --> pdb=" O ARG E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 Processing helix chain 'E' and resid 267 through 309 removed outlier: 3.840A pdb=" N ARG E 272 " --> pdb=" O ASP E 268 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS E 291 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ASN E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS E 309 " --> pdb=" O ASP E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 334 removed outlier: 3.643A pdb=" N LYS E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 363 removed outlier: 3.719A pdb=" N ARG E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS E 363 " --> pdb=" O ARG E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 406 Processing helix chain 'E' and resid 416 through 460 removed outlier: 4.519A pdb=" N ASP E 438 " --> pdb=" O LYS E 434 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER E 439 " --> pdb=" O PHE E 435 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 476 removed outlier: 4.057A pdb=" N GLU E 466 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLU E 467 " --> pdb=" O HIS E 464 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 470 " --> pdb=" O GLU E 467 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE E 473 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP E 474 " --> pdb=" O LYS E 471 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER E 475 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 509 removed outlier: 3.964A pdb=" N ASN E 484 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 565 removed outlier: 4.298A pdb=" N ASN E 527 " --> pdb=" O LYS E 523 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU E 556 " --> pdb=" O TYR E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 588 Processing helix chain 'E' and resid 592 through 631 removed outlier: 4.027A pdb=" N LEU E 616 " --> pdb=" O LYS E 612 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 180 through 193 removed outlier: 3.871A pdb=" N LYS A 180 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N GLU A 398 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 10.619A pdb=" N ILE A 449 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 13.326A pdb=" N ASP A 400 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 15.064A pdb=" N ALA A 451 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 15.397A pdb=" N TYR A 402 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 16.469A pdb=" N TRP A 453 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 15.244A pdb=" N VAL A 404 " --> pdb=" O TRP A 453 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 227 through 230 removed outlier: 3.870A pdb=" N VAL A 200 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 214 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 202 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU A 212 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.806A pdb=" N ILE A 254 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 282 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ILE A 281 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN A 335 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 495 through 498 Processing sheet with id= E, first strand: chain 'B' and resid 180 through 193 removed outlier: 3.641A pdb=" N LYS B 180 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP B 453 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL B 404 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR B 481 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY B 406 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASN B 483 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N GLN B 408 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 226 through 230 removed outlier: 5.865A pdb=" N ILE B 202 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU B 212 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 232 through 234 removed outlier: 6.680A pdb=" N ILE B 254 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 495 through 498 Processing sheet with id= I, first strand: chain 'C' and resid 5 through 10 removed outlier: 6.494A pdb=" N SER C 36 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TRP C 8 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 38 " --> pdb=" O TRP C 8 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA C 10 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL C 40 " --> pdb=" O ALA C 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 60 through 62 removed outlier: 3.677A pdb=" N VAL C 60 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 81 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 253 " --> pdb=" O PRO C 79 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY C 301 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 244 through 246 removed outlier: 3.827A pdb=" N ALA C 244 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 224 through 226 removed outlier: 3.565A pdb=" N LYS C 233 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 342 through 347 Processing sheet with id= N, first strand: chain 'C' and resid 389 through 391 removed outlier: 3.712A pdb=" N LEU C 408 " --> pdb=" O VAL C 587 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 589 " --> pdb=" O PRO C 406 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 580 through 582 removed outlier: 3.907A pdb=" N ALA C 580 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.745A pdb=" N SER D 36 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TRP D 8 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA D 38 " --> pdb=" O TRP D 8 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA D 10 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 40 " --> pdb=" O ALA D 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.692A pdb=" N VAL D 60 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL D 81 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA D 253 " --> pdb=" O PRO D 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 244 through 247 removed outlier: 3.856A pdb=" N ALA D 244 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 100 through 102 Processing sheet with id= T, first strand: chain 'D' and resid 342 through 345 Processing sheet with id= U, first strand: chain 'D' and resid 388 through 391 removed outlier: 3.604A pdb=" N LEU D 408 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR D 589 " --> pdb=" O PRO D 406 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS D 637 " --> pdb=" O ASN D 411 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 580 through 582 removed outlier: 3.903A pdb=" N ALA D 580 " --> pdb=" O ALA D 428 " (cutoff:3.500A) 882 hydrogen bonds defined for protein. 2424 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: 8.17 Time building geometry restraints manager: 10.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8008 1.34 - 1.47: 6440 1.47 - 1.60: 10762 1.60 - 1.73: 1 1.73 - 1.87: 176 Bond restraints: 25387 Sorted by residual: bond pdb=" CA GLU B 582 " pdb=" CB GLU B 582 " ideal model delta sigma weight residual 1.527 1.607 -0.080 2.48e-02 1.63e+03 1.04e+01 bond pdb=" C1 NAG D 706 " pdb=" O5 NAG D 706 " ideal model delta sigma weight residual 1.426 1.510 -0.084 3.20e-02 9.77e+02 6.96e+00 bond pdb=" CG1 ILE E 175 " pdb=" CD1 ILE E 175 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.25e+00 bond pdb=" N GLU A 759 " pdb=" CA GLU A 759 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.23e-02 6.61e+03 6.14e+00 bond pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.33e+00 ... (remaining 25382 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.71: 400 104.71 - 112.70: 13160 112.70 - 120.70: 12814 120.70 - 128.69: 7742 128.69 - 136.69: 211 Bond angle restraints: 34327 Sorted by residual: angle pdb=" C ALA E 569 " pdb=" N ASN E 570 " pdb=" CA ASN E 570 " ideal model delta sigma weight residual 122.07 135.44 -13.37 1.43e+00 4.89e-01 8.74e+01 angle pdb=" C ASN A 758 " pdb=" N GLU A 759 " pdb=" CA GLU A 759 " ideal model delta sigma weight residual 120.82 130.15 -9.33 1.50e+00 4.44e-01 3.87e+01 angle pdb=" C LEU C 629 " pdb=" N LEU C 630 " pdb=" CA LEU C 630 " ideal model delta sigma weight residual 121.54 132.55 -11.01 1.91e+00 2.74e-01 3.32e+01 angle pdb=" C ILE B 277 " pdb=" N GLY B 278 " pdb=" CA GLY B 278 " ideal model delta sigma weight residual 122.18 118.54 3.64 6.90e-01 2.10e+00 2.79e+01 angle pdb=" N SER D 348 " pdb=" CA SER D 348 " pdb=" C SER D 348 " ideal model delta sigma weight residual 110.91 116.72 -5.81 1.17e+00 7.31e-01 2.47e+01 ... (remaining 34322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.95: 14804 26.95 - 53.89: 490 53.89 - 80.84: 31 80.84 - 107.79: 15 107.79 - 134.73: 1 Dihedral angle restraints: 15341 sinusoidal: 6279 harmonic: 9062 Sorted by residual: dihedral pdb=" CA ALA E 569 " pdb=" C ALA E 569 " pdb=" N ASN E 570 " pdb=" CA ASN E 570 " ideal model delta harmonic sigma weight residual 180.00 45.27 134.73 0 5.00e+00 4.00e-02 7.26e+02 dihedral pdb=" CB CYS C 161 " pdb=" SG CYS C 161 " pdb=" SG CYS C 179 " pdb=" CB CYS C 179 " ideal model delta sinusoidal sigma weight residual -86.00 -175.56 89.56 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS C 345 " pdb=" SG CYS C 345 " pdb=" SG CYS C 377 " pdb=" CB CYS C 377 " ideal model delta sinusoidal sigma weight residual 93.00 -177.62 -89.38 1 1.00e+01 1.00e-02 9.50e+01 ... (remaining 15338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 3734 0.184 - 0.369: 34 0.369 - 0.553: 2 0.553 - 0.737: 0 0.737 - 0.921: 1 Chirality restraints: 3771 Sorted by residual: chirality pdb=" C1 NAG B 803 " pdb=" ND2 ASN B 317 " pdb=" C2 NAG B 803 " pdb=" O5 NAG B 803 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CG LEU E 447 " pdb=" CB LEU E 447 " pdb=" CD1 LEU E 447 " pdb=" CD2 LEU E 447 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C1 NAG D 706 " pdb=" O4 NAG D 705 " pdb=" C2 NAG D 706 " pdb=" O5 NAG D 706 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.14e+00 ... (remaining 3768 not shown) Planarity restraints: 4436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 691 " -0.058 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO B 692 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 692 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 692 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 521 " -0.021 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE E 521 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE E 521 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE E 521 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE E 521 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 521 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE E 521 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 334 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO C 335 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " 0.041 5.00e-02 4.00e+02 ... (remaining 4433 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 159 2.55 - 3.14: 18509 3.14 - 3.72: 37361 3.72 - 4.31: 51572 4.31 - 4.90: 85260 Nonbonded interactions: 192861 Sorted by model distance: nonbonded pdb="FE FE C 703 " pdb=" O1 CO3 C 704 " model vdw 1.960 2.260 nonbonded pdb=" OD1 ASP D 63 " pdb="FE FE D 703 " model vdw 2.005 2.260 nonbonded pdb="FE FE D 703 " pdb=" O3 CO3 D 704 " model vdw 2.012 2.260 nonbonded pdb=" OH TYR C 95 " pdb="FE FE C 703 " model vdw 2.015 2.260 nonbonded pdb=" OH TYR D 188 " pdb="FE FE D 703 " model vdw 2.040 2.260 ... (remaining 192856 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 S 132 5.16 5 C 15757 2.51 5 N 4200 2.21 5 O 4749 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.680 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.180 Process input model: 63.050 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 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 0.098 25387 Z= 0.605 Angle : 1.185 14.621 34327 Z= 0.661 Chirality : 0.063 0.921 3771 Planarity : 0.008 0.089 4426 Dihedral : 12.212 134.734 9381 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.33 % Favored : 94.61 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.23 % Twisted Proline : 0.83 % Twisted General : 0.10 % 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: -3.65 (0.12), residues: 3096 helix: -2.78 (0.10), residues: 1242 sheet: -1.75 (0.26), residues: 346 loop : -2.17 (0.13), residues: 1508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 343 time to evaluate : 3.071 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 outliers start: 30 outliers final: 6 residues processed: 367 average time/residue: 0.3778 time to fit residues: 212.9206 Evaluate side-chains 167 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 3.268 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2169 time to fit residues: 6.6661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 279 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 171 ASN A 206 ASN A 348 ASN A 379 ASN A 493 ASN A 515 HIS A 603 HIS A 626 ASN A 715 ASN B 171 ASN B 302 HIS B 483 ASN B 608 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 715 ASN C 25 HIS C 55 ASN C 213 ASN C 536 GLN C 540 GLN C 546 ASN C 603 GLN C 618 ASN D 25 HIS D 55 ASN D 172 GLN D 268 ASN D 383 ASN D 411 ASN D 417 ASN D 469 ASN D 541 ASN D 618 ASN E 174 ASN E 185 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN E 252 ASN E 289 ASN E 314 GLN ** E 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN E 444 ASN E 483 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 25387 Z= 0.200 Angle : 0.663 18.312 34327 Z= 0.345 Chirality : 0.045 0.576 3771 Planarity : 0.005 0.064 4426 Dihedral : 7.991 111.054 3454 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.84 % Favored : 96.06 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.12 (0.13), residues: 3096 helix: -1.00 (0.13), residues: 1273 sheet: -1.24 (0.27), residues: 348 loop : -1.75 (0.14), residues: 1475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 198 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 28 residues processed: 249 average time/residue: 0.3757 time to fit residues: 150.0130 Evaluate side-chains 179 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 151 time to evaluate : 2.995 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2543 time to fit residues: 17.4176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 chunk 302 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS B 348 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN D 383 ASN D 584 ASN E 185 ASN ** E 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 GLN E 428 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 25387 Z= 0.185 Angle : 0.603 19.135 34327 Z= 0.309 Chirality : 0.043 0.530 3771 Planarity : 0.004 0.067 4426 Dihedral : 7.560 110.861 3454 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.29 (0.14), residues: 3096 helix: -0.09 (0.14), residues: 1265 sheet: -1.00 (0.27), residues: 348 loop : -1.46 (0.15), residues: 1483 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 14 residues processed: 213 average time/residue: 0.3480 time to fit residues: 121.2284 Evaluate side-chains 147 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 2.770 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2277 time to fit residues: 9.7080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 chunk 297 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 266 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN D 383 ASN E 185 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 25387 Z= 0.207 Angle : 0.602 18.806 34327 Z= 0.308 Chirality : 0.043 0.512 3771 Planarity : 0.004 0.048 4426 Dihedral : 7.380 111.131 3454 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.87 (0.15), residues: 3096 helix: 0.45 (0.14), residues: 1253 sheet: -0.96 (0.27), residues: 360 loop : -1.36 (0.15), residues: 1483 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 13 residues processed: 183 average time/residue: 0.3385 time to fit residues: 102.1187 Evaluate side-chains 145 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 3.129 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.2798 time to fit residues: 10.3406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 205 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 267 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 540 GLN D 110 ASN D 383 ASN E 185 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 HIS E 628 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.135 25387 Z= 0.242 Angle : 0.606 19.363 34327 Z= 0.309 Chirality : 0.043 0.495 3771 Planarity : 0.004 0.043 4426 Dihedral : 7.254 111.245 3454 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % 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: -0.62 (0.15), residues: 3096 helix: 0.70 (0.15), residues: 1260 sheet: -0.87 (0.27), residues: 360 loop : -1.26 (0.15), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 15 residues processed: 179 average time/residue: 0.3502 time to fit residues: 104.6018 Evaluate side-chains 141 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 2.792 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2136 time to fit residues: 9.9256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 0.0070 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.085 25387 Z= 0.252 Angle : 0.617 19.247 34327 Z= 0.314 Chirality : 0.043 0.488 3771 Planarity : 0.004 0.045 4426 Dihedral : 7.230 111.368 3454 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.44 (0.15), residues: 3096 helix: 0.91 (0.15), residues: 1250 sheet: -0.88 (0.27), residues: 360 loop : -1.18 (0.16), residues: 1486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 169 average time/residue: 0.3561 time to fit residues: 99.2986 Evaluate side-chains 141 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 2.992 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.2302 time to fit residues: 10.9622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 166 optimal weight: 0.2980 chunk 296 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 640 GLN ** C 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.255 25387 Z= 0.348 Angle : 0.671 25.202 34327 Z= 0.346 Chirality : 0.045 0.505 3771 Planarity : 0.004 0.042 4426 Dihedral : 7.262 111.643 3454 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.50 (0.15), residues: 3096 helix: 0.87 (0.15), residues: 1247 sheet: -0.98 (0.27), residues: 360 loop : -1.19 (0.16), residues: 1489 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 155 average time/residue: 0.3750 time to fit residues: 94.5866 Evaluate side-chains 132 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 2.990 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2191 time to fit residues: 6.9634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 57 optimal weight: 0.0570 chunk 188 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 233 optimal weight: 0.5980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 464 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 25387 Z= 0.169 Angle : 0.589 19.055 34327 Z= 0.296 Chirality : 0.042 0.462 3771 Planarity : 0.003 0.047 4426 Dihedral : 7.140 111.441 3454 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.84 % Favored : 96.12 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.17 (0.15), residues: 3096 helix: 1.19 (0.15), residues: 1253 sheet: -0.83 (0.27), residues: 360 loop : -1.05 (0.16), residues: 1483 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 159 average time/residue: 0.3626 time to fit residues: 96.0763 Evaluate side-chains 139 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 2.997 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2424 time to fit residues: 5.8439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 9.9990 chunk 284 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 217 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 249 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.532 25387 Z= 0.421 Angle : 0.776 73.897 34327 Z= 0.367 Chirality : 0.045 0.491 3771 Planarity : 0.004 0.112 4426 Dihedral : 7.137 111.546 3454 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.27 (0.15), residues: 3096 helix: 1.12 (0.15), residues: 1248 sheet: -0.88 (0.27), residues: 360 loop : -1.11 (0.16), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 141 average time/residue: 0.3826 time to fit residues: 88.5563 Evaluate side-chains 136 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 3.006 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2215 time to fit residues: 5.9113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 7.9990 chunk 292 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 138 optimal weight: 0.0050 chunk 203 optimal weight: 4.9990 chunk 306 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.532 25387 Z= 0.421 Angle : 0.776 73.897 34327 Z= 0.367 Chirality : 0.045 0.491 3771 Planarity : 0.004 0.112 4426 Dihedral : 7.137 111.546 3454 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.27 (0.15), residues: 3096 helix: 1.12 (0.15), residues: 1248 sheet: -0.88 (0.27), residues: 360 loop : -1.11 (0.16), residues: 1488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.3742 time to fit residues: 82.4713 Evaluate side-chains 133 residues out of total 2686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 2.904 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2142 time to fit residues: 4.4691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 0.9980 chunk 260 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 251 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107212 restraints weight = 39226.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106853 restraints weight = 35106.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107815 restraints weight = 32861.578| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.532 25387 Z= 0.421 Angle : 0.776 73.897 34327 Z= 0.367 Chirality : 0.045 0.491 3771 Planarity : 0.004 0.112 4426 Dihedral : 7.137 111.546 3454 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.79 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.27 (0.15), residues: 3096 helix: 1.12 (0.15), residues: 1248 sheet: -0.88 (0.27), residues: 360 loop : -1.11 (0.16), residues: 1488 =============================================================================== Job complete usr+sys time: 3516.42 seconds wall clock time: 66 minutes 40.41 seconds (4000.41 seconds total)