Starting phenix.real_space_refine (version: dev) on Wed Apr 6 00:25:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/04_2022/7e9h_31032_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/04_2022/7e9h_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_31032/04_2022/7e9h_31032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/04_2022/7e9h_31032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/04_2022/7e9h_31032_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9h_31032/04_2022/7e9h_31032_updated.pdb" } resolution = 4.0 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= 0.000 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: 9.66, 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: 6.88 Conformation dependent library (CDL) restraints added in 2.6 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: 2.21 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: 5.67 Time building geometry restraints manager: 7.45 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 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. 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: 0.010 Normalize map: mean=0, sd=1: 4.410 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: 11.730 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.130 Process input model: 46.080 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 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 : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.06 % 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 *********************** 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 : 1.950 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: 0.3289 time to fit residues: 185.5481 Evaluate side-chains 272 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 1.985 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6617 time to fit residues: 3.4990 ------------------------------------------------------------------------------- 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 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 17194 Z= 0.251 Angle : 0.584 14.291 23449 Z= 0.290 Chirality : 0.042 0.222 2736 Planarity : 0.005 0.092 3021 Dihedral : 3.852 63.299 2478 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.75 % 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: -1.90 (0.16), residues: 2275 helix: 0.52 (0.18), residues: 809 sheet: -1.82 (0.25), residues: 355 loop : -2.51 (0.16), residues: 1111 *********************** 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 317 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 288 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 299 average time/residue: 0.2892 time to fit residues: 129.8435 Evaluate side-chains 264 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 246 time to evaluate : 1.925 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1908 time to fit residues: 8.5863 ------------------------------------------------------------------------------- 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: 0.0980 chunk 64 optimal weight: 0.5980 chunk 172 optimal weight: 0.6980 chunk 140 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 224 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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** S 541 HIS 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: 0.6400 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 17194 Z= 0.189 Angle : 0.559 12.399 23449 Z= 0.272 Chirality : 0.040 0.142 2736 Planarity : 0.004 0.091 3021 Dihedral : 3.788 62.417 2478 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.08 % 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: -1.45 (0.17), residues: 2275 helix: 0.95 (0.19), residues: 807 sheet: -1.42 (0.26), residues: 348 loop : -2.34 (0.16), residues: 1120 *********************** 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: 18 poor density : 273 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 280 average time/residue: 0.2831 time to fit residues: 120.3648 Evaluate side-chains 257 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1566 time to fit residues: 5.7638 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 197 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 445 GLN R 699 GLN R 818 GLN ** S 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 445 GLN ** S 500 HIS ** 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** D 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.112 17194 Z= 0.595 Angle : 0.796 16.148 23449 Z= 0.409 Chirality : 0.050 0.213 2736 Planarity : 0.006 0.098 3021 Dihedral : 5.039 61.347 2478 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 3.68 % 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: -1.74 (0.17), residues: 2275 helix: 0.30 (0.18), residues: 813 sheet: -1.46 (0.26), residues: 373 loop : -2.22 (0.17), residues: 1089 *********************** 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 332 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 271 time to evaluate : 2.173 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 42 residues processed: 307 average time/residue: 0.2978 time to fit residues: 137.6053 Evaluate side-chains 285 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 243 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.1495 time to fit residues: 14.5054 ------------------------------------------------------------------------------- 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: 0.1980 chunk 125 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 0 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 55 optimal weight: 0.4980 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 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 GLN R 500 HIS 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 500 HIS B 44 GLN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 17194 Z= 0.228 Angle : 0.623 16.665 23449 Z= 0.311 Chirality : 0.041 0.155 2736 Planarity : 0.004 0.105 3021 Dihedral : 4.360 62.549 2478 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 1.63 % 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: -1.23 (0.17), residues: 2275 helix: 0.88 (0.19), residues: 805 sheet: -1.20 (0.27), residues: 362 loop : -2.02 (0.17), residues: 1108 *********************** 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 302 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 275 time to evaluate : 1.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 293 average time/residue: 0.3116 time to fit residues: 134.4255 Evaluate side-chains 259 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 249 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1491 time to fit residues: 5.1639 ------------------------------------------------------------------------------- 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: 0.9990 chunk 198 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.156 17194 Z= 0.389 Angle : 0.697 20.188 23449 Z= 0.355 Chirality : 0.044 0.159 2736 Planarity : 0.005 0.110 3021 Dihedral : 4.597 58.055 2478 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2275 helix: 0.84 (0.19), residues: 795 sheet: -1.33 (0.27), residues: 376 loop : -1.99 (0.17), residues: 1104 *********************** 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 293 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 257 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 274 average time/residue: 0.2996 time to fit residues: 122.8808 Evaluate side-chains 261 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1550 time to fit residues: 8.2014 ------------------------------------------------------------------------------- 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: 20.0000 chunk 24 optimal weight: 0.0980 chunk 125 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 407 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.355 17194 Z= 0.409 Angle : 0.709 29.002 23449 Z= 0.367 Chirality : 0.043 0.183 2736 Planarity : 0.006 0.119 3021 Dihedral : 4.493 57.254 2478 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 1.63 % 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: -1.20 (0.17), residues: 2275 helix: 0.96 (0.19), residues: 795 sheet: -1.48 (0.26), residues: 381 loop : -1.91 (0.17), residues: 1099 *********************** 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 282 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 255 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 270 average time/residue: 0.3044 time to fit residues: 123.7061 Evaluate side-chains 257 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 244 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2083 time to fit residues: 7.5162 ------------------------------------------------------------------------------- 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: 10.0000 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** 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: 0.6695 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.151 17194 Z= 0.339 Angle : 0.703 17.682 23449 Z= 0.355 Chirality : 0.043 0.204 2736 Planarity : 0.005 0.108 3021 Dihedral : 4.527 57.030 2478 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 1.21 % 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: -1.19 (0.17), residues: 2275 helix: 0.89 (0.18), residues: 807 sheet: -1.57 (0.26), residues: 374 loop : -1.82 (0.18), residues: 1094 *********************** 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 279 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 259 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 270 average time/residue: 0.3020 time to fit residues: 123.5220 Evaluate side-chains 249 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 237 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1924 time to fit residues: 6.6433 ------------------------------------------------------------------------------- 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: 4.9990 chunk 210 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 0.1980 chunk 160 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 323 HIS ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN D 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.984 17194 Z= 0.722 Angle : 0.904 74.858 23449 Z= 0.438 Chirality : 0.043 0.220 2736 Planarity : 0.007 0.159 3021 Dihedral : 4.488 57.120 2478 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.05 % 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: -1.16 (0.17), residues: 2275 helix: 0.91 (0.18), residues: 806 sheet: -1.51 (0.26), residues: 383 loop : -1.81 (0.18), residues: 1086 *********************** 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 270 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 259 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 263 average time/residue: 0.3062 time to fit residues: 120.6802 Evaluate side-chains 253 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 2.011 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1779 time to fit residues: 4.3101 ------------------------------------------------------------------------------- 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: 5.9990 chunk 132 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 227 optimal weight: 20.0000 chunk 209 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 323 HIS ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.611 17194 Z= 0.602 Angle : 0.960 73.889 23449 Z= 0.471 Chirality : 0.045 0.266 2736 Planarity : 0.007 0.168 3021 Dihedral : 4.508 56.903 2478 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.05 % 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: -1.18 (0.17), residues: 2275 helix: 0.87 (0.18), residues: 806 sheet: -1.46 (0.27), residues: 368 loop : -1.82 (0.18), residues: 1101 ********************** 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 256 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 246 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 249 average time/residue: 0.3066 time to fit residues: 115.3038 Evaluate side-chains 254 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 245 time to evaluate : 1.916 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1595 time to fit residues: 5.3671 ------------------------------------------------------------------------------- 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: 7.9990 chunk 55 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 181 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 323 HIS ** S 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.108011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089374 restraints weight = 62131.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.089059 restraints weight = 56348.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.090144 restraints weight = 43880.206| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.492 17194 Z= 0.453 Angle : 0.860 41.206 23449 Z= 0.448 Chirality : 0.042 0.323 2736 Planarity : 0.007 0.172 3021 Dihedral : 4.419 59.224 2478 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 0.18 % 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: -1.08 (0.18), residues: 2275 helix: 0.94 (0.18), residues: 814 sheet: -1.43 (0.27), residues: 378 loop : -1.76 (0.18), residues: 1083 =============================================================================== Job complete usr+sys time: 3433.91 seconds wall clock time: 63 minutes 24.75 seconds (3804.75 seconds total)