Starting phenix.real_space_refine on Mon Dec 11 05:37:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/12_2023/7e9h_31032_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/12_2023/7e9h_31032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/12_2023/7e9h_31032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/12_2023/7e9h_31032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/12_2023/7e9h_31032_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/12_2023/7e9h_31032_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 108 5.16 5 C 10657 2.51 5 N 2905 2.21 5 O 3175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 104": "NH1" <-> "NH2" Residue "R ARG 111": "NH1" <-> "NH2" Residue "R ARG 149": "NH1" <-> "NH2" Residue "R ARG 170": "NH1" <-> "NH2" Residue "R ARG 191": "NH1" <-> "NH2" Residue "R ARG 197": "NH1" <-> "NH2" Residue "R ARG 214": "NH1" <-> "NH2" Residue "R ARG 243": "NH1" <-> "NH2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 270": "NH1" <-> "NH2" Residue "R ARG 271": "NH1" <-> "NH2" Residue "R ARG 292": "NH1" <-> "NH2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "R ARG 342": "NH1" <-> "NH2" Residue "R ARG 346": "NH1" <-> "NH2" Residue "R ARG 351": "NH1" <-> "NH2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R ASP 368": "OD1" <-> "OD2" Residue "R ARG 391": "NH1" <-> "NH2" Residue "R ARG 393": "NH1" <-> "NH2" Residue "R ARG 425": "NH1" <-> "NH2" Residue "R ARG 437": "NH1" <-> "NH2" Residue "R ARG 451": "NH1" <-> "NH2" Residue "R ARG 502": "NH1" <-> "NH2" Residue "R ARG 565": "NH1" <-> "NH2" Residue "R GLU 624": "OE1" <-> "OE2" Residue "R ARG 656": "NH1" <-> "NH2" Residue "R PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ARG 104": "NH1" <-> "NH2" Residue "S ARG 111": "NH1" <-> "NH2" Residue "S ARG 170": "NH1" <-> "NH2" Residue "S ARG 191": "NH1" <-> "NH2" Residue "S ARG 214": "NH1" <-> "NH2" Residue "S GLU 236": "OE1" <-> "OE2" Residue "S ARG 243": "NH1" <-> "NH2" Residue "S ARG 258": "NH1" <-> "NH2" Residue "S ARG 270": "NH1" <-> "NH2" Residue "S ARG 271": "NH1" <-> "NH2" Residue "S ASP 289": "OD1" <-> "OD2" Residue "S ARG 292": "NH1" <-> "NH2" Residue "S ARG 338": "NH1" <-> "NH2" Residue "S ARG 342": "NH1" <-> "NH2" Residue "S ARG 346": "NH1" <-> "NH2" Residue "S ARG 351": "NH1" <-> "NH2" Residue "S ARG 391": "NH1" <-> "NH2" Residue "S ARG 393": "NH1" <-> "NH2" Residue "S ARG 425": "NH1" <-> "NH2" Residue "S ARG 437": "NH1" <-> "NH2" Residue "S ARG 451": "NH1" <-> "NH2" Residue "S ASP 497": "OD1" <-> "OD2" Residue "S ARG 529": "NH1" <-> "NH2" Residue "S ARG 554": "NH1" <-> "NH2" Residue "S ARG 565": "NH1" <-> "NH2" Residue "S ARG 570": "NH1" <-> "NH2" Residue "S ASP 750": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D ASP 137": "OD1" <-> "OD2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16847 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 5580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5580 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 37, 'TRANS': 728} Chain breaks: 4 Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 587 Unresolved non-hydrogen dihedrals: 400 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 7, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 6, 'GLU:plan': 10, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 271 Chain: "S" Number of atoms: 5547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5547 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 36, 'TRANS': 724} Chain breaks: 4 Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 397 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 10, 'GLU:plan': 14, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 278 Chain: "A" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1627 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2208 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 300} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 12, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 113 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 121 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1742 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 9.52, per 1000 atoms: 0.57 Number of scatterers: 16847 At special positions: 0 Unit cell: (225.72, 146.3, 151.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 2 15.00 O 3175 8.00 N 2905 7.00 C 10657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS R 67 " - pdb=" SG CYS R 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 249 " - pdb=" SG CYS R 538 " distance=2.03 Simple disulfide: pdb=" SG CYS R 428 " - pdb=" SG CYS R 435 " distance=2.03 Simple disulfide: pdb=" SG CYS R 520 " - pdb=" SG CYS R 539 " distance=2.03 Simple disulfide: pdb=" SG CYS R 524 " - pdb=" SG CYS R 542 " distance=2.03 Simple disulfide: pdb=" SG CYS R 545 " - pdb=" SG CYS R 557 " distance=2.03 Simple disulfide: pdb=" SG CYS R 560 " - pdb=" SG CYS R 573 " distance=2.03 Simple disulfide: pdb=" SG CYS R 652 " - pdb=" SG CYS R 746 " distance=2.03 Simple disulfide: pdb=" SG CYS S 249 " - pdb=" SG CYS S 538 " distance=2.03 Simple disulfide: pdb=" SG CYS S 372 " - pdb=" SG CYS S 388 " distance=2.03 Simple disulfide: pdb=" SG CYS S 428 " - pdb=" SG CYS S 435 " distance=2.03 Simple disulfide: pdb=" SG CYS S 520 " - pdb=" SG CYS S 539 " distance=2.03 Simple disulfide: pdb=" SG CYS S 524 " - pdb=" SG CYS S 542 " distance=2.03 Simple disulfide: pdb=" SG CYS S 545 " - pdb=" SG CYS S 557 " distance=2.03 Simple disulfide: pdb=" SG CYS S 560 " - pdb=" SG CYS S 573 " distance=2.03 Simple disulfide: pdb=" SG CYS S 652 " - pdb=" SG CYS S 746 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " 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: 6.75 Conformation dependent library (CDL) restraints added in 3.2 seconds 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 24 sheets defined 33.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'R' and resid 75 through 91 Processing helix chain 'R' and resid 112 through 126 Processing helix chain 'R' and resid 159 through 169 removed outlier: 3.679A pdb=" N MET R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE R 168 " --> pdb=" O MET R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 187 Processing helix chain 'R' and resid 202 through 215 Processing helix chain 'R' and resid 231 through 245 removed outlier: 3.788A pdb=" N ASP R 245 " --> pdb=" O LYS R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 274 Processing helix chain 'R' and resid 287 through 300 Processing helix chain 'R' and resid 342 through 349 Processing helix chain 'R' and resid 360 through 369 removed outlier: 4.096A pdb=" N GLU R 364 " --> pdb=" O ILE R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 427 removed outlier: 3.704A pdb=" N PHE R 408 " --> pdb=" O GLY R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 438 No H-bonds generated for 'chain 'R' and resid 436 through 438' Processing helix chain 'R' and resid 443 through 451 removed outlier: 3.665A pdb=" N ARG R 451 " --> pdb=" O LEU R 447 " (cutoff:3.500A) Processing helix chain 'R' and resid 458 through 460 No H-bonds generated for 'chain 'R' and resid 458 through 460' Processing helix chain 'R' and resid 589 through 611 Processing helix chain 'R' and resid 616 through 620 Processing helix chain 'R' and resid 623 through 643 removed outlier: 4.555A pdb=" N THR R 640 " --> pdb=" O CYS R 636 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE R 641 " --> pdb=" O TYR R 637 " (cutoff:3.500A) Processing helix chain 'R' and resid 649 through 686 removed outlier: 4.259A pdb=" N PHE R 681 " --> pdb=" O ILE R 677 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU R 682 " --> pdb=" O TYR R 678 " (cutoff:3.500A) Processing helix chain 'R' and resid 696 through 720 Processing helix chain 'R' and resid 749 through 774 removed outlier: 3.550A pdb=" N THR R 768 " --> pdb=" O MET R 764 " (cutoff:3.500A) Processing helix chain 'R' and resid 785 through 810 Proline residue: R 803 - end of helix Processing helix chain 'R' and resid 815 through 847 removed outlier: 4.367A pdb=" N THR R 819 " --> pdb=" O LEU R 815 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR R 820 " --> pdb=" O TYR R 816 " (cutoff:3.500A) Proline residue: R 840 - end of helix Processing helix chain 'S' and resid 77 through 91 Processing helix chain 'S' and resid 112 through 123 Processing helix chain 'S' and resid 159 through 171 Processing helix chain 'S' and resid 184 through 186 No H-bonds generated for 'chain 'S' and resid 184 through 186' Processing helix chain 'S' and resid 202 through 215 Processing helix chain 'S' and resid 228 through 244 removed outlier: 3.656A pdb=" N GLU S 232 " --> pdb=" O GLY S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 266 through 273 removed outlier: 3.626A pdb=" N LEU S 272 " --> pdb=" O ILE S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 298 Processing helix chain 'S' and resid 312 through 314 No H-bonds generated for 'chain 'S' and resid 312 through 314' Processing helix chain 'S' and resid 319 through 326 removed outlier: 4.093A pdb=" N LEU S 322 " --> pdb=" O ALA S 319 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS S 323 " --> pdb=" O PRO S 320 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 350 removed outlier: 3.943A pdb=" N SER S 350 " --> pdb=" O ARG S 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 361 through 369 Processing helix chain 'S' and resid 406 through 427 Processing helix chain 'S' and resid 436 through 438 No H-bonds generated for 'chain 'S' and resid 436 through 438' Processing helix chain 'S' and resid 443 through 452 removed outlier: 3.720A pdb=" N TYR S 449 " --> pdb=" O GLN S 445 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN S 452 " --> pdb=" O LYS S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 589 through 611 removed outlier: 3.797A pdb=" N VAL S 597 " --> pdb=" O PHE S 593 " (cutoff:3.500A) Processing helix chain 'S' and resid 616 through 618 No H-bonds generated for 'chain 'S' and resid 616 through 618' Processing helix chain 'S' and resid 624 through 643 removed outlier: 4.398A pdb=" N THR S 640 " --> pdb=" O CYS S 636 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE S 641 " --> pdb=" O TYR S 637 " (cutoff:3.500A) Processing helix chain 'S' and resid 649 through 681 removed outlier: 3.810A pdb=" N ILE S 680 " --> pdb=" O ARG S 676 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE S 681 " --> pdb=" O ILE S 677 " (cutoff:3.500A) Processing helix chain 'S' and resid 697 through 719 Processing helix chain 'S' and resid 750 through 773 Processing helix chain 'S' and resid 783 through 807 removed outlier: 3.890A pdb=" N ILE S 787 " --> pdb=" O GLU S 783 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE S 802 " --> pdb=" O TRP S 798 " (cutoff:3.500A) Proline residue: S 803 - end of helix Processing helix chain 'S' and resid 814 through 835 removed outlier: 3.542A pdb=" N SER S 833 " --> pdb=" O SER S 829 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU S 834 " --> pdb=" O ALA S 830 " (cutoff:3.500A) Processing helix chain 'S' and resid 839 through 847 Processing helix chain 'A' and resid 7 through 30 removed outlier: 3.730A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.688A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.926A pdb=" N ASP A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'R' and resid 43 through 45 removed outlier: 3.762A pdb=" N PHE R 55 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY R 152 " --> pdb=" O GLY R 52 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N LEU R 54 " --> pdb=" O GLY R 152 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE R 154 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'R' and resid 281 through 283 removed outlier: 6.696A pdb=" N SER R 222 " --> pdb=" O ILE R 282 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'R' and resid 331 through 334 removed outlier: 4.065A pdb=" N GLY R 493 " --> pdb=" O ILE R 477 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN R 479 " --> pdb=" O VAL R 491 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL R 491 " --> pdb=" O GLN R 479 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN R 481 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR R 489 " --> pdb=" O GLN R 481 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'R' and resid 530 through 532 removed outlier: 3.838A pdb=" N HIS R 541 " --> pdb=" O THR R 532 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'R' and resid 564 through 566 Processing sheet with id= F, first strand: chain 'S' and resid 43 through 45 removed outlier: 7.299A pdb=" N GLY S 53 " --> pdb=" O LEU S 106 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'S' and resid 152 through 154 No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'S' and resid 253 through 255 removed outlier: 9.212A pdb=" N VAL S 254 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR S 223 " --> pdb=" O VAL S 254 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA S 280 " --> pdb=" O SER S 222 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL S 224 " --> pdb=" O ALA S 280 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE S 282 " --> pdb=" O VAL S 224 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE S 307 " --> pdb=" O VAL S 281 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE S 283 " --> pdb=" O PHE S 307 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET S 309 " --> pdb=" O ILE S 283 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'S' and resid 331 through 336 removed outlier: 4.314A pdb=" N GLN S 481 " --> pdb=" O GLU S 488 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU S 488 " --> pdb=" O GLN S 481 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 530 through 533 Processing sheet with id= K, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.882A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 225 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 36 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 61 through 63 removed outlier: 3.902A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= N, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.786A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.545A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 250 through 254 removed outlier: 3.685A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 244 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.733A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.684A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.967A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.208A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL D 12 " --> pdb=" O THR D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 33 through 35 Processing sheet with id= V, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.781A pdb=" N TYR D 50 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR D 59 " --> pdb=" O TYR D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 155 through 159 removed outlier: 3.880A pdb=" N SER D 204 " --> pdb=" O THR D 215 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 226 through 229 removed outlier: 3.861A pdb=" N VAL D 226 " --> pdb=" O GLN D 179 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE D 189 " --> pdb=" O TRP D 176 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU D 187 " --> pdb=" O LEU D 178 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.47 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5563 1.34 - 1.46: 4102 1.46 - 1.58: 7382 1.58 - 1.70: 2 1.70 - 1.82: 145 Bond restraints: 17194 Sorted by residual: bond pdb=" O2P SEP S1001 " pdb=" P SEP S1001 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O1P SEP S1001 " pdb=" P SEP S1001 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O1P SEP R1001 " pdb=" P SEP R1001 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" O2P SEP R1001 " pdb=" P SEP R1001 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" O3P SEP R1001 " pdb=" P SEP R1001 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 17189 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.03: 474 107.03 - 113.77: 9566 113.77 - 120.51: 6624 120.51 - 127.26: 6605 127.26 - 134.00: 180 Bond angle restraints: 23449 Sorted by residual: angle pdb=" N VAL D 224 " pdb=" CA VAL D 224 " pdb=" C VAL D 224 " ideal model delta sigma weight residual 113.20 108.84 4.36 9.60e-01 1.09e+00 2.06e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.42 109.61 3.81 1.17e+00 7.31e-01 1.06e+01 angle pdb=" C CYS R 524 " pdb=" N GLN R 525 " pdb=" CA GLN R 525 " ideal model delta sigma weight residual 119.78 123.29 -3.51 1.24e+00 6.50e-01 8.03e+00 angle pdb=" CB SEP R1001 " pdb=" OG SEP R1001 " pdb=" P SEP R1001 " ideal model delta sigma weight residual 110.00 118.39 -8.39 3.00e+00 1.11e-01 7.82e+00 angle pdb=" CB SEP S1001 " pdb=" OG SEP S1001 " pdb=" P SEP S1001 " ideal model delta sigma weight residual 110.00 118.31 -8.31 3.00e+00 1.11e-01 7.67e+00 ... (remaining 23444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9529 17.91 - 35.82: 535 35.82 - 53.73: 79 53.73 - 71.64: 11 71.64 - 89.55: 14 Dihedral angle restraints: 10168 sinusoidal: 3512 harmonic: 6656 Sorted by residual: dihedral pdb=" CB CYS R 249 " pdb=" SG CYS R 249 " pdb=" SG CYS R 538 " pdb=" CB CYS R 538 " ideal model delta sinusoidal sigma weight residual 93.00 161.56 -68.56 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS S 520 " pdb=" SG CYS S 520 " pdb=" SG CYS S 539 " pdb=" CB CYS S 539 " ideal model delta sinusoidal sigma weight residual -86.00 -24.23 -61.77 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" CB CYS S 560 " pdb=" SG CYS S 560 " pdb=" SG CYS S 573 " pdb=" CB CYS S 573 " ideal model delta sinusoidal sigma weight residual 93.00 37.74 55.26 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 10165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1665 0.029 - 0.058: 740 0.058 - 0.087: 192 0.087 - 0.116: 123 0.116 - 0.145: 16 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CB ILE S 282 " pdb=" CA ILE S 282 " pdb=" CG1 ILE S 282 " pdb=" CG2 ILE S 282 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE S 256 " pdb=" N ILE S 256 " pdb=" C ILE S 256 " pdb=" CB ILE S 256 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CB ILE A 264 " pdb=" CA ILE A 264 " pdb=" CG1 ILE A 264 " pdb=" CG2 ILE A 264 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 2733 not shown) Planarity restraints: 3021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 104 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C ARG R 104 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG R 104 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE R 105 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 777 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO R 778 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO R 778 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 778 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 471 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO R 472 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO R 472 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 472 " -0.018 5.00e-02 4.00e+02 ... (remaining 3018 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1409 2.74 - 3.28: 17258 3.28 - 3.82: 28316 3.82 - 4.36: 31131 4.36 - 4.90: 53935 Nonbonded interactions: 132049 Sorted by model distance: nonbonded pdb=" O ASP R 648 " pdb=" N THR R 651 " model vdw 2.202 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.214 2.440 nonbonded pdb=" OG1 THR S 223 " pdb=" OG SER S 253 " model vdw 2.215 2.440 nonbonded pdb=" O CYS R 636 " pdb=" OG1 THR R 639 " model vdw 2.221 2.440 nonbonded pdb=" N GLY R 330 " pdb=" O TYR R 480 " model vdw 2.231 2.520 ... (remaining 132044 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 'R' and (resid 41 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 93 or (resid 94 and (name N or nam \ e CA or name C or name O or name CB )) or resid 95 through 126 or resid 148 or ( \ resid 149 and (name N or name CA or name C or name O or name CB )) or resid 150 \ through 172 or (resid 173 and (name N or name CA or name C or name O or name CB \ )) or resid 174 through 258 or (resid 259 and (name N or name CA or name C or na \ me O or name CB )) or resid 260 through 294 or (resid 295 through 297 and (name \ N or name CA or name C or name O or name CB )) or resid 298 through 300 or (resi \ d 301 and (name N or name CA or name C or name O or name CB )) or resid 302 thro \ ugh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) o \ r resid 323 or (resid 324 through 326 and (name N or name CA or name C or name O \ or name CB )) or resid 327 through 356 or (resid 357 and (name N or name CA or \ name C or name O or name CB )) or resid 358 through 372 or (resid 373 and (name \ N or name CA or name C or name O or name CB )) or resid 386 through 425 or (resi \ d 426 and (name N or name CA or name C or name O or name CB )) or resid 427 thro \ ugh 441 or (resid 442 and (name N or name CA or name C or name O or name CB )) o \ r resid 443 through 447 or (resid 448 and (name N or name CA or name C or name O \ or name CB )) or resid 449 through 466 or (resid 467 and (name N or name CA or \ name C or name O or name CB )) or resid 468 through 473 or (resid 474 and (name \ N or name CA or name C or name O or name CB )) or resid 475 through 487 or (resi \ d 488 and (name N or name CA or name C or name O or name CB )) or resid 489 or ( \ resid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 \ through 503 or resid 515 through 516 or (resid 517 and (name N or name CA or nam \ e C or name O or name CB )) or resid 518 through 588 or (resid 589 through 590 a \ nd (name N or name CA or name C or name O or name CB )) or resid 591 through 618 \ or (resid 619 through 620 and (name N or name CA or name C or name O or name CB \ )) or resid 621 through 623 or (resid 624 through 625 and (name N or name CA or \ name C or name O or name CB )) or resid 626 through 633 or (resid 634 through 6 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 636 or (res \ id 637 through 638 and (name N or name CA or name C or name O or name CB )) or r \ esid 639 through 640 or (resid 641 and (name N or name CA or name C or name O or \ name CB )) or resid 642 through 645 or (resid 646 and (name N or name CA or nam \ e C or name O or name CB )) or resid 647 through 648 or (resid 649 and (name N o \ r name CA or name C or name O or name CB )) or resid 650 through 655 or (resid 6 \ 56 through 658 and (name N or name CA or name C or name O or name CB )) or resid \ 659 through 681 or (resid 682 through 683 and (name N or name CA or name C or n \ ame O or name CB )) or resid 692 or (resid 693 through 694 and (name N or name C \ A or name C or name O or name CB )) or resid 695 through 703 or (resid 704 and ( \ name N or name CA or name C or name O or name CB )) or resid 705 through 706 or \ (resid 707 and (name N or name CA or name C or name O or name CB )) or resid 708 \ or (resid 709 and (name N or name CA or name C or name O or name CB )) or resid \ 710 or (resid 711 through 712 and (name N or name CA or name C or name O or nam \ e CB )) or resid 713 or (resid 714 and (name N or name CA or name C or name O or \ name CB )) or resid 715 through 726 or (resid 727 through 733 and (name N or na \ me CA or name C or name O or name CB )) or resid 734 or (resid 735 through 736 a \ nd (name N or name CA or name C or name O or name CB )) or resid 737 through 753 \ or (resid 754 and (name N or name CA or name C or name O or name CB )) or resid \ 755 or (resid 756 through 757 and (name N or name CA or name C or name O or nam \ e CB )) or resid 758 through 768 or (resid 769 through 773 and (name N or name C \ A or name C or name O or name CB )) or resid 774 or (resid 775 and (name N or na \ me CA or name C or name O or name CB )) or resid 776 through 780 or (resid 781 t \ hrough 785 and (name N or name CA or name C or name O or name CB )) or resid 786 \ through 817 or (resid 818 and (name N or name CA or name C or name O or name CB \ )) or resid 819 through 835 or (resid 836 and (name N or name CA or name C or n \ ame O or name CB )) or resid 837 through 848 or resid 1001)) selection = (chain 'S' and (resid 41 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 278 or (resid 279 through 280 and \ (name N or name CA or name C or name O or name CB )) or resid 281 through 290 or \ (resid 291 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 2 through 369 or (resid 370 and (name N or name CA or name C or name O or name C \ B )) or resid 371 through 373 or (resid 386 through 387 and (name N or name CA o \ r name C or name O or name CB )) or resid 388 through 400 or (resid 401 and (nam \ e N or name CA or name C or name O or name CB )) or resid 402 through 483 or res \ id 487 through 503 or resid 515 through 521 or (resid 522 and (name N or name CA \ or name C or name O or name CB )) or resid 523 through 528 or (resid 529 and (n \ ame N or name CA or name C or name O or name CB )) or resid 530 or (resid 531 th \ rough 534 and (name N or name CA or name C or name O or name CB )) or resid 535 \ through 539 or (resid 540 and (name N or name CA or name C or name O or name CB \ )) or resid 541 through 542 or (resid 543 and (name N or name CA or name C or na \ me O or name CB )) or resid 544 through 545 or (resid 546 and (name N or name CA \ or name C or name O or name CB )) or resid 547 or (resid 548 and (name N or nam \ e CA or name C or name O or name CB )) or resid 549 or (resid 550 through 556 an \ d (name N or name CA or name C or name O or name CB )) or resid 557 through 558 \ or (resid 559 and (name N or name CA or name C or name O or name CB )) or resid \ 560 through 561 or (resid 562 through 563 and (name N or name CA or name C or na \ me O or name CB )) or resid 564 through 567 or (resid 568 and (name N or name CA \ or name C or name O or name CB )) or resid 569 or (resid 570 through 571 and (n \ ame N or name CA or name C or name O or name CB )) or resid 572 through 577 or ( \ resid 578 through 583 and (name N or name CA or name C or name O or name CB )) o \ r resid 584 through 591 or (resid 592 through 593 and (name N or name CA or name \ C or name O or name CB )) or resid 594 through 596 or (resid 597 and (name N or \ name CA or name C or name O or name CB )) or resid 598 through 607 or (resid 60 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 609 through \ 611 or (resid 612 and (name N or name CA or name C or name O or name CB )) or re \ sid 613 through 643 or (resid 644 through 646 and (name N or name CA or name C o \ r name O or name CB )) or resid 647 through 656 or (resid 657 through 658 and (n \ ame N or name CA or name C or name O or name CB )) or resid 659 through 680 or ( \ resid 681 through 683 and (name N or name CA or name C or name O or name CB )) o \ r resid 692 through 715 or (resid 716 and (name N or name CA or name C or name O \ or name CB )) or resid 717 through 725 or (resid 726 through 733 and (name N or \ name CA or name C or name O or name CB )) or resid 734 through 737 or (resid 73 \ 8 through 741 and (name N or name CA or name C or name O or name CB )) or resid \ 742 through 748 or (resid 749 and (name N or name CA or name C or name O or name \ CB )) or resid 750 through 751 or (resid 752 through 754 and (name N or name CA \ or name C or name O or name CB )) or resid 755 through 769 or (resid 770 throug \ h 773 and (name N or name CA or name C or name O or name CB )) or resid 774 thro \ ugh 782 or (resid 783 through 785 and (name N or name CA or name C or name O or \ name CB )) or resid 786 through 790 or (resid 791 and (name N or name CA or name \ C or name O or name CB )) or resid 792 through 813 or (resid 814 and (name N or \ name CA or name C or name O or name CB )) or resid 815 through 837 or (resid 83 \ 8 through 839 and (name N or name CA or name C or name O or name CB )) or resid \ 840 or (resid 841 and (name N or name CA or name C or name O or name CB )) or re \ sid 842 through 848 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 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: 11.370 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 48.280 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 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 : 0.003 0.101 17194 Z= 0.173 Angle : 0.484 8.388 23449 Z= 0.262 Chirality : 0.039 0.145 2736 Planarity : 0.003 0.033 3021 Dihedral : 11.361 89.552 5829 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.15), residues: 2275 helix: -0.47 (0.16), residues: 812 sheet: -2.17 (0.24), residues: 349 loop : -2.94 (0.15), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 366 HIS 0.002 0.000 HIS S 418 PHE 0.012 0.001 PHE S 847 TYR 0.008 0.001 TYR S 843 ARG 0.002 0.000 ARG S 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 393 average time/residue: 0.3472 time to fit residues: 192.8844 Evaluate side-chains 273 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6976 time to fit residues: 3.6235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 9.9990 chunk 172 optimal weight: 0.0170 chunk 95 optimal weight: 0.0770 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 133 optimal weight: 0.3980 chunk 207 optimal weight: 20.0000 overall best weight: 0.8578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 77 HIS R 114 HIS ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 GLN R 445 GLN R 549 GLN R 699 GLN R 818 GLN S 77 HIS S 118 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 ASN S 355 ASN S 402 GLN ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 675 ASN S 683 GLN A 188 HIS A 244 HIS ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 295 ASN D 77 ASN D 142 GLN D 179 GLN ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17194 Z= 0.234 Angle : 0.578 14.572 23449 Z= 0.285 Chirality : 0.042 0.234 2736 Planarity : 0.004 0.044 3021 Dihedral : 3.891 60.890 2478 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.69 % Allowed : 14.53 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.16), residues: 2275 helix: 0.55 (0.18), residues: 808 sheet: -1.82 (0.25), residues: 355 loop : -2.50 (0.16), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 176 HIS 0.008 0.002 HIS A 188 PHE 0.018 0.002 PHE A 199 TYR 0.019 0.001 TYR D 103 ARG 0.007 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 292 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 301 average time/residue: 0.3050 time to fit residues: 137.3478 Evaluate side-chains 263 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 247 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1647 time to fit residues: 7.3334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.5980 chunk 64 optimal weight: 20.0000 chunk 172 optimal weight: 0.4980 chunk 140 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 207 optimal weight: 0.2980 chunk 224 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN D 142 GLN D 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17194 Z= 0.196 Angle : 0.544 12.765 23449 Z= 0.265 Chirality : 0.040 0.144 2736 Planarity : 0.003 0.045 3021 Dihedral : 3.792 61.392 2478 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.15 % Allowed : 18.44 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.17), residues: 2275 helix: 0.99 (0.19), residues: 806 sheet: -1.51 (0.25), residues: 364 loop : -2.28 (0.16), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS S 541 PHE 0.021 0.001 PHE S 465 TYR 0.013 0.001 TYR D 103 ARG 0.008 0.000 ARG R 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 272 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 277 average time/residue: 0.3030 time to fit residues: 126.4400 Evaluate side-chains 261 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 248 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1656 time to fit residues: 6.6976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 139 optimal weight: 0.0970 chunk 208 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 108 optimal weight: 0.6980 chunk 197 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN R 445 GLN R 699 GLN R 818 GLN S 118 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 445 GLN B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17194 Z= 0.310 Angle : 0.617 14.141 23449 Z= 0.305 Chirality : 0.043 0.158 2736 Planarity : 0.004 0.040 3021 Dihedral : 4.189 58.151 2478 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.53 % Allowed : 19.65 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.17), residues: 2275 helix: 0.90 (0.19), residues: 810 sheet: -1.33 (0.27), residues: 361 loop : -2.13 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 339 HIS 0.009 0.002 HIS S 507 PHE 0.019 0.002 PHE R 348 TYR 0.019 0.001 TYR S 548 ARG 0.015 0.001 ARG S 529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 267 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 29 residues processed: 292 average time/residue: 0.3144 time to fit residues: 137.3043 Evaluate side-chains 272 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1582 time to fit residues: 11.2736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 188 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 112 optimal weight: 0.0770 chunk 197 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN R 418 HIS R 500 HIS R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 277 ASN ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 613 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 17194 Z= 0.377 Angle : 0.650 10.812 23449 Z= 0.325 Chirality : 0.044 0.158 2736 Planarity : 0.004 0.060 3021 Dihedral : 4.561 59.554 2478 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.47 % Allowed : 22.24 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2275 helix: 0.79 (0.19), residues: 799 sheet: -1.49 (0.25), residues: 402 loop : -1.99 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 99 HIS 0.008 0.002 HIS R 418 PHE 0.028 0.002 PHE R 362 TYR 0.017 0.002 TYR S 204 ARG 0.009 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 268 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 293 average time/residue: 0.2973 time to fit residues: 131.1166 Evaluate side-chains 269 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1548 time to fit residues: 10.0651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.5980 chunk 198 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 277 ASN ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 500 HIS A 255 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17194 Z= 0.217 Angle : 0.593 8.941 23449 Z= 0.289 Chirality : 0.041 0.240 2736 Planarity : 0.004 0.048 3021 Dihedral : 4.271 59.144 2478 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.15 % Allowed : 23.81 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2275 helix: 0.99 (0.19), residues: 808 sheet: -1.29 (0.26), residues: 371 loop : -1.93 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 339 HIS 0.006 0.001 HIS S 305 PHE 0.024 0.001 PHE S 465 TYR 0.014 0.001 TYR B 59 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 264 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 271 average time/residue: 0.3108 time to fit residues: 124.3900 Evaluate side-chains 262 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 2.179 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1597 time to fit residues: 6.4732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 125 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 185 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 219 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN ** R 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17194 Z= 0.291 Angle : 0.622 9.896 23449 Z= 0.305 Chirality : 0.042 0.183 2736 Planarity : 0.004 0.044 3021 Dihedral : 4.377 58.420 2478 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.15 % Allowed : 25.02 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2275 helix: 0.95 (0.19), residues: 806 sheet: -1.46 (0.26), residues: 375 loop : -1.85 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 339 HIS 0.006 0.001 HIS A 244 PHE 0.020 0.002 PHE R 805 TYR 0.012 0.001 TYR S 475 ARG 0.007 0.001 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 260 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 269 average time/residue: 0.3212 time to fit residues: 128.4596 Evaluate side-chains 255 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 246 time to evaluate : 2.153 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1697 time to fit residues: 5.5895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 7.9990 chunk 87 optimal weight: 0.0970 chunk 131 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 108 optimal weight: 0.0170 chunk 20 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 overall best weight: 1.0218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN ** R 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS D 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17194 Z= 0.267 Angle : 0.632 12.959 23449 Z= 0.308 Chirality : 0.042 0.220 2736 Planarity : 0.004 0.043 3021 Dihedral : 4.371 58.700 2478 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.21 % Allowed : 26.04 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2275 helix: 0.96 (0.19), residues: 809 sheet: -1.37 (0.27), residues: 357 loop : -1.81 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.027 0.002 PHE A 259 TYR 0.011 0.001 TYR B 59 ARG 0.013 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 265 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 273 average time/residue: 0.3189 time to fit residues: 130.4434 Evaluate side-chains 262 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 247 time to evaluate : 2.097 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1711 time to fit residues: 7.4505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 204 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 185 optimal weight: 0.1980 chunk 193 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN ** R 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 323 HIS ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17194 Z= 0.268 Angle : 0.634 11.596 23449 Z= 0.309 Chirality : 0.042 0.202 2736 Planarity : 0.004 0.054 3021 Dihedral : 4.403 58.211 2478 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.96 % Allowed : 26.76 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.17), residues: 2275 helix: 0.93 (0.18), residues: 813 sheet: -1.38 (0.27), residues: 360 loop : -1.76 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 339 HIS 0.006 0.001 HIS A 244 PHE 0.046 0.002 PHE R 362 TYR 0.015 0.001 TYR R 792 ARG 0.012 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 258 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 269 average time/residue: 0.3115 time to fit residues: 125.6220 Evaluate side-chains 251 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 245 time to evaluate : 1.945 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2332 time to fit residues: 4.8719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 102 optimal weight: 0.0070 chunk 150 optimal weight: 10.0000 chunk 227 optimal weight: 0.0000 chunk 209 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 GLN R 818 GLN S 323 HIS ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17194 Z= 0.195 Angle : 0.624 12.539 23449 Z= 0.301 Chirality : 0.041 0.196 2736 Planarity : 0.004 0.051 3021 Dihedral : 4.305 61.231 2478 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.78 % Allowed : 27.43 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2275 helix: 1.12 (0.19), residues: 806 sheet: -1.33 (0.27), residues: 371 loop : -1.68 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 339 HIS 0.006 0.001 HIS S 305 PHE 0.024 0.001 PHE A 259 TYR 0.019 0.001 TYR R 637 ARG 0.012 0.001 ARG R 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 253 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 261 average time/residue: 0.3140 time to fit residues: 121.6752 Evaluate side-chains 251 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 243 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1746 time to fit residues: 5.2837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 186 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 159 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 818 GLN S 323 HIS ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.116496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096062 restraints weight = 59337.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.096518 restraints weight = 53971.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096922 restraints weight = 39702.638| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17194 Z= 0.204 Angle : 0.624 11.978 23449 Z= 0.301 Chirality : 0.042 0.199 2736 Planarity : 0.004 0.044 3021 Dihedral : 4.284 59.967 2478 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.42 % Allowed : 27.25 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2275 helix: 1.17 (0.19), residues: 806 sheet: -1.32 (0.27), residues: 372 loop : -1.62 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 339 HIS 0.006 0.001 HIS S 305 PHE 0.023 0.001 PHE R 362 TYR 0.017 0.001 TYR R 637 ARG 0.011 0.000 ARG R 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3773.12 seconds wall clock time: 69 minutes 14.49 seconds (4154.49 seconds total)