Starting phenix.real_space_refine on Wed Mar 20 18:22:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btp_30181/03_2024/7btp_30181.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btp_30181/03_2024/7btp_30181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btp_30181/03_2024/7btp_30181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btp_30181/03_2024/7btp_30181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btp_30181/03_2024/7btp_30181.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btp_30181/03_2024/7btp_30181.pdb" } resolution = 4.01 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 ------------------------------------------------------------------------------- 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7905 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 12997 2.51 5 N 3388 2.21 5 O 3939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 989": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "F ARG 84": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20371 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3099 Classifications: {'peptide': 384} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 359} Chain: "A" Number of atoms: 8042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 8042 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 12, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 957} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3739 Classifications: {'peptide': 473} Link IDs: {'CIS': 18, 'PTRANS': 13, 'TRANS': 441} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3739 Classifications: {'peptide': 473} Link IDs: {'CIS': 18, 'PTRANS': 13, 'TRANS': 441} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 876 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "F" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 876 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Time building chain proxies: 11.02, per 1000 atoms: 0.54 Number of scatterers: 20371 At special positions: 0 Unit cell: (137.7, 149.85, 121.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 3939 8.00 N 3388 7.00 C 12997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.10 Conformation dependent library (CDL) restraints added in 3.8 seconds 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4850 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 15 sheets defined 48.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'E' and resid 111 through 119 removed outlier: 4.136A pdb=" N ASN E 119 " --> pdb=" O TYR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 157 through 193 removed outlier: 4.390A pdb=" N ILE E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU E 193 " --> pdb=" O TYR E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 226 Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.890A pdb=" N VAL E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 318 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 354 through 369 Processing helix chain 'E' and resid 374 through 394 Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 56 through 73 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 273 through 291 removed outlier: 3.547A pdb=" N ALA A 279 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 326 removed outlier: 4.340A pdb=" N THR A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.571A pdb=" N TYR A 350 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.554A pdb=" N TYR A 399 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 426 removed outlier: 3.628A pdb=" N GLN A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.548A pdb=" N ALA A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.546A pdb=" N THR A 491 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 492 " --> pdb=" O LEU A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 492' Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 509 through 528 removed outlier: 5.727A pdb=" N ARG A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 569 removed outlier: 3.972A pdb=" N ALA A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.975A pdb=" N MET A 604 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 624 removed outlier: 3.693A pdb=" N LYS A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 removed outlier: 4.000A pdb=" N GLN A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.601A pdb=" N GLN A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 718 removed outlier: 3.832A pdb=" N LEU A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 3.613A pdb=" N LEU A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 752 through 761 removed outlier: 3.557A pdb=" N GLU A 760 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 793 removed outlier: 4.119A pdb=" N GLU A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 804 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 811 through 823 Processing helix chain 'A' and resid 825 through 835 Processing helix chain 'A' and resid 839 through 857 Processing helix chain 'A' and resid 880 through 885 Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'A' and resid 910 through 918 removed outlier: 3.541A pdb=" N LYS A 915 " --> pdb=" O ILE A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 921 No H-bonds generated for 'chain 'A' and resid 919 through 921' Processing helix chain 'A' and resid 926 through 936 removed outlier: 4.083A pdb=" N LEU A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 Processing helix chain 'A' and resid 945 through 971 removed outlier: 3.886A pdb=" N ILE A 949 " --> pdb=" O ASP A 945 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 950 " --> pdb=" O LYS A 946 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP A 951 " --> pdb=" O ALA A 947 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 990 Processing helix chain 'A' and resid 999 through 1003 Processing helix chain 'A' and resid 1014 through 1031 removed outlier: 3.866A pdb=" N GLN A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.556A pdb=" N VAL B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 55 removed outlier: 3.651A pdb=" N PHE B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN B 34 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 removed outlier: 3.505A pdb=" N SER B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.991A pdb=" N SER B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.610A pdb=" N SER B 125 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 164 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 186 removed outlier: 3.547A pdb=" N GLU B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 231 through 239 removed outlier: 4.228A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 270 removed outlier: 3.612A pdb=" N ASN B 261 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS B 270 " --> pdb=" O ASN B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 335 through 344 removed outlier: 3.786A pdb=" N PHE B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 341 " --> pdb=" O PHE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 378 removed outlier: 3.686A pdb=" N GLU B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN B 378 " --> pdb=" O TYR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 445 removed outlier: 4.145A pdb=" N SER B 445 " --> pdb=" O GLN B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 484 through 508 removed outlier: 3.866A pdb=" N LEU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN B 489 " --> pdb=" O ILE B 485 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 removed outlier: 3.556A pdb=" N VAL C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 55 removed outlier: 3.651A pdb=" N PHE C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN C 34 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 removed outlier: 3.506A pdb=" N SER C 89 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 114 through 121 removed outlier: 3.991A pdb=" N SER C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.611A pdb=" N SER C 125 " --> pdb=" O GLY C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 164 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 178 through 186 removed outlier: 3.548A pdb=" N GLU C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 231 through 239 removed outlier: 4.228A pdb=" N ALA C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 270 removed outlier: 3.612A pdb=" N ASN C 261 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.787A pdb=" N PHE C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 340 " --> pdb=" O ASP C 336 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 378 removed outlier: 3.687A pdb=" N GLU C 368 " --> pdb=" O ARG C 364 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN C 378 " --> pdb=" O TYR C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 445 removed outlier: 4.145A pdb=" N SER C 445 " --> pdb=" O GLN C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 464 Processing helix chain 'C' and resid 484 through 508 removed outlier: 3.866A pdb=" N LEU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASN C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE C 499 " --> pdb=" O THR C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 26 removed outlier: 3.845A pdb=" N VAL D 10 " --> pdb=" O THR D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 4.048A pdb=" N ASP D 42 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN D 43 " --> pdb=" O MET D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 76 through 101 Processing helix chain 'F' and resid 6 through 26 removed outlier: 3.845A pdb=" N VAL F 10 " --> pdb=" O THR F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 45 removed outlier: 4.047A pdb=" N ASP F 42 " --> pdb=" O HIS F 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN F 43 " --> pdb=" O MET F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 76 through 101 Processing sheet with id=AA1, first strand: chain 'E' and resid 17 through 20 Processing sheet with id=AA2, first strand: chain 'E' and resid 26 through 28 removed outlier: 3.650A pdb=" N LYS E 99 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 202 through 205 removed outlier: 3.843A pdb=" N GLU E 202 " --> pdb=" O VAL E 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 249 through 251 removed outlier: 4.621A pdb=" N ASP E 249 " --> pdb=" O TRP E 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 284 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.328A pdb=" N GLU A 50 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLN A 138 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 152 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 154 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 108 through 113 removed outlier: 3.937A pdb=" N ARG A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 261 through 264 removed outlier: 4.141A pdb=" N THR A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 382 removed outlier: 6.537A pdb=" N LYS A 332 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE A 406 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 334 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR A 304 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER A 460 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP A 306 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 474 through 479 removed outlier: 7.079A pdb=" N LYS A 474 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE A 702 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS A 476 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR A 704 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP A 478 " --> pdb=" O THR A 704 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 669 " --> pdb=" O ASN A 701 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL A 703 " --> pdb=" O ASN A 669 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU A 671 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 539 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 670 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ALA A 540 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N VAL A 655 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 542 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA A 577 " --> pdb=" O ILE A 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 740 through 741 Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB4, first strand: chain 'B' and resid 296 through 300 removed outlier: 6.392A pdb=" N PHE B 296 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS B 350 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 298 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG B 352 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL B 300 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 354 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER B 405 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL B 381 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 413 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 384 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AB6, first strand: chain 'C' and resid 296 through 300 removed outlier: 6.391A pdb=" N PHE C 296 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS C 350 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 298 " --> pdb=" O LYS C 350 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG C 352 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL C 300 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C 354 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER C 405 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL C 381 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 413 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 384 " --> pdb=" O VAL C 413 " (cutoff:3.500A) 825 hydrogen bonds defined for protein. 2352 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: 6.19 Time building geometry restraints manager: 8.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6565 1.34 - 1.46: 4291 1.46 - 1.58: 9839 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 20780 Sorted by residual: bond pdb=" C LEU E 121 " pdb=" N PRO E 122 " ideal model delta sigma weight residual 1.332 1.351 -0.019 8.20e-03 1.49e+04 5.27e+00 bond pdb=" CA ARG B 142 " pdb=" C ARG B 142 " ideal model delta sigma weight residual 1.528 1.553 -0.025 1.18e-02 7.18e+03 4.50e+00 bond pdb=" CA ARG C 142 " pdb=" C ARG C 142 " ideal model delta sigma weight residual 1.528 1.552 -0.024 1.18e-02 7.18e+03 4.10e+00 bond pdb=" C THR C 409 " pdb=" N ASP C 410 " ideal model delta sigma weight residual 1.329 1.356 -0.027 1.40e-02 5.10e+03 3.78e+00 bond pdb=" C THR B 409 " pdb=" N ASP B 410 " ideal model delta sigma weight residual 1.329 1.356 -0.027 1.40e-02 5.10e+03 3.70e+00 ... (remaining 20775 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.75: 238 104.75 - 112.08: 9573 112.08 - 119.40: 7579 119.40 - 126.73: 10489 126.73 - 134.05: 227 Bond angle restraints: 28106 Sorted by residual: angle pdb=" C THR B 395 " pdb=" N THR B 396 " pdb=" CA THR B 396 " ideal model delta sigma weight residual 121.70 132.35 -10.65 1.80e+00 3.09e-01 3.50e+01 angle pdb=" C THR C 395 " pdb=" N THR C 396 " pdb=" CA THR C 396 " ideal model delta sigma weight residual 121.70 132.34 -10.64 1.80e+00 3.09e-01 3.50e+01 angle pdb=" C THR C 409 " pdb=" N ASP C 410 " pdb=" CA ASP C 410 " ideal model delta sigma weight residual 121.70 132.11 -10.41 1.80e+00 3.09e-01 3.34e+01 angle pdb=" C THR B 409 " pdb=" N ASP B 410 " pdb=" CA ASP B 410 " ideal model delta sigma weight residual 121.70 132.07 -10.37 1.80e+00 3.09e-01 3.32e+01 angle pdb=" C THR A 26 " pdb=" N GLY A 27 " pdb=" CA GLY A 27 " ideal model delta sigma weight residual 121.70 131.59 -9.89 1.80e+00 3.09e-01 3.02e+01 ... (remaining 28101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 11520 15.75 - 31.51: 777 31.51 - 47.26: 168 47.26 - 63.01: 6 63.01 - 78.76: 18 Dihedral angle restraints: 12489 sinusoidal: 5010 harmonic: 7479 Sorted by residual: dihedral pdb=" CA ARG A 678 " pdb=" C ARG A 678 " pdb=" N TYR A 679 " pdb=" CA TYR A 679 " ideal model delta harmonic sigma weight residual 180.00 -133.31 -46.69 0 5.00e+00 4.00e-02 8.72e+01 dihedral pdb=" CA VAL B 474 " pdb=" C VAL B 474 " pdb=" N GLU B 475 " pdb=" CA GLU B 475 " ideal model delta harmonic sigma weight residual 180.00 133.68 46.32 0 5.00e+00 4.00e-02 8.58e+01 dihedral pdb=" CA VAL C 474 " pdb=" C VAL C 474 " pdb=" N GLU C 475 " pdb=" CA GLU C 475 " ideal model delta harmonic sigma weight residual 180.00 133.75 46.25 0 5.00e+00 4.00e-02 8.56e+01 ... (remaining 12486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2399 0.069 - 0.138: 629 0.138 - 0.206: 66 0.206 - 0.275: 15 0.275 - 0.344: 5 Chirality restraints: 3114 Sorted by residual: chirality pdb=" CB ILE A 378 " pdb=" CA ILE A 378 " pdb=" CG1 ILE A 378 " pdb=" CG2 ILE A 378 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE B 79 " pdb=" CA ILE B 79 " pdb=" CG1 ILE B 79 " pdb=" CG2 ILE B 79 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB ILE C 79 " pdb=" CA ILE C 79 " pdb=" CG1 ILE C 79 " pdb=" CG2 ILE C 79 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3111 not shown) Planarity restraints: 3646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 72 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO E 73 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO E 73 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO E 73 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1007 " -0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO A1008 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A1008 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1008 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 765 " -0.051 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO A 766 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 766 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 766 " -0.040 5.00e-02 4.00e+02 ... (remaining 3643 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3179 2.76 - 3.29: 19815 3.29 - 3.83: 33595 3.83 - 4.36: 38405 4.36 - 4.90: 62850 Nonbonded interactions: 157844 Sorted by model distance: nonbonded pdb=" OH TYR F 7 " pdb=" OD2 ASP F 92 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR D 7 " pdb=" OD2 ASP D 92 " model vdw 2.222 2.440 nonbonded pdb=" O ALA E 255 " pdb=" OG SER E 259 " model vdw 2.265 2.440 nonbonded pdb=" O PRO A1008 " pdb=" OH TYR C 84 " model vdw 2.266 2.440 nonbonded pdb=" O LEU A 342 " pdb=" OG1 THR A 346 " model vdw 2.272 2.440 ... (remaining 157839 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 4.760 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 54.270 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.007 0.076 20780 Z= 0.447 Angle : 1.118 15.047 28106 Z= 0.608 Chirality : 0.061 0.344 3114 Planarity : 0.007 0.101 3646 Dihedral : 11.602 78.762 7639 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.63 % Favored : 88.33 % Rotamer: Outliers : 0.59 % Allowed : 5.33 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 1.41 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.13), residues: 2502 helix: -2.31 (0.12), residues: 1077 sheet: -2.73 (0.28), residues: 238 loop : -3.68 (0.14), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP E 117 HIS 0.011 0.003 HIS E 313 PHE 0.026 0.003 PHE A 599 TYR 0.039 0.003 TYR C 260 ARG 0.011 0.001 ARG A 841 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 373 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 217 THR cc_start: 0.5013 (m) cc_final: 0.4501 (m) REVERT: A 212 PHE cc_start: 0.7129 (m-80) cc_final: 0.6857 (m-80) REVERT: A 252 THR cc_start: 0.9145 (m) cc_final: 0.8723 (t) REVERT: A 315 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8705 (tt) REVERT: A 589 ASN cc_start: 0.6635 (p0) cc_final: 0.5413 (p0) REVERT: A 701 ASN cc_start: 0.8362 (m-40) cc_final: 0.8104 (m110) REVERT: B 235 LEU cc_start: 0.7910 (tt) cc_final: 0.7329 (tp) REVERT: B 262 LEU cc_start: 0.9214 (pp) cc_final: 0.8886 (pp) REVERT: B 436 ILE cc_start: 0.8434 (pp) cc_final: 0.8193 (pt) REVERT: B 440 MET cc_start: 0.7997 (tpt) cc_final: 0.7754 (tpt) REVERT: C 201 THR cc_start: 0.7087 (m) cc_final: 0.6700 (p) REVERT: C 223 ILE cc_start: 0.9213 (tt) cc_final: 0.9009 (mt) REVERT: D 15 TYR cc_start: 0.8056 (t80) cc_final: 0.7640 (t80) REVERT: D 48 TYR cc_start: 0.6981 (m-80) cc_final: 0.6687 (m-80) REVERT: D 79 ARG cc_start: 0.8770 (mmt90) cc_final: 0.8510 (mmm-85) outliers start: 13 outliers final: 1 residues processed: 384 average time/residue: 0.3963 time to fit residues: 221.1192 Evaluate side-chains 165 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 64 optimal weight: 0.0020 chunk 128 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 76 optimal weight: 0.0070 chunk 119 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 227 optimal weight: 0.0770 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN A 91 ASN A 251 HIS A 419 GLN A 522 ASN A 588 GLN A 635 GLN A1000 ASN B 219 HIS B 373 GLN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS C 373 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 ASN C 479 ASN D 13 HIS D 47 HIS D 88 GLN F 13 HIS F 43 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20780 Z= 0.165 Angle : 0.681 9.375 28106 Z= 0.361 Chirality : 0.045 0.210 3114 Planarity : 0.005 0.085 3646 Dihedral : 6.767 36.879 2730 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.09 % Allowed : 2.82 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 1.41 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.15), residues: 2502 helix: -0.80 (0.14), residues: 1115 sheet: -2.35 (0.28), residues: 264 loop : -3.43 (0.16), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP E 117 HIS 0.004 0.001 HIS E 313 PHE 0.018 0.001 PHE C 199 TYR 0.018 0.001 TYR F 49 ARG 0.010 0.000 ARG C 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 140 GLN cc_start: 0.8688 (mp-120) cc_final: 0.8484 (mt0) REVERT: E 181 MET cc_start: 0.8753 (ptm) cc_final: 0.8545 (ptm) REVERT: E 184 LYS cc_start: 0.7886 (tttp) cc_final: 0.7613 (ttpt) REVERT: E 314 MET cc_start: 0.7799 (tpt) cc_final: 0.7474 (mmm) REVERT: E 328 LYS cc_start: 0.5041 (tttp) cc_final: 0.4611 (ttpp) REVERT: A 252 THR cc_start: 0.9349 (m) cc_final: 0.9015 (t) REVERT: A 589 ASN cc_start: 0.6485 (p0) cc_final: 0.5572 (p0) REVERT: A 910 MET cc_start: 0.7055 (mmp) cc_final: 0.5999 (mmp) REVERT: B 136 PHE cc_start: 0.7343 (t80) cc_final: 0.6810 (t80) REVERT: B 262 LEU cc_start: 0.9401 (pp) cc_final: 0.9128 (pp) REVERT: C 37 LEU cc_start: 0.9287 (mt) cc_final: 0.9082 (mp) REVERT: C 41 PHE cc_start: 0.8271 (t80) cc_final: 0.7974 (t80) REVERT: C 223 ILE cc_start: 0.8969 (tt) cc_final: 0.8676 (mp) REVERT: C 275 ASP cc_start: 0.7317 (p0) cc_final: 0.6845 (p0) REVERT: C 377 ASP cc_start: 0.8598 (t0) cc_final: 0.8295 (t70) REVERT: C 440 MET cc_start: 0.7577 (tpt) cc_final: 0.7280 (tpp) REVERT: D 17 MET cc_start: 0.8263 (ttm) cc_final: 0.8021 (ttm) REVERT: D 48 TYR cc_start: 0.6537 (m-80) cc_final: 0.6058 (m-80) REVERT: D 79 ARG cc_start: 0.8920 (mmt90) cc_final: 0.8586 (mmm-85) outliers start: 2 outliers final: 0 residues processed: 248 average time/residue: 0.3363 time to fit residues: 126.8412 Evaluate side-chains 156 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 228 optimal weight: 0.6980 chunk 246 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 ASN B 21 ASN B 244 HIS ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN F 8 ASN F 43 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20780 Z= 0.190 Angle : 0.660 8.866 28106 Z= 0.350 Chirality : 0.044 0.245 3114 Planarity : 0.005 0.069 3646 Dihedral : 6.059 35.397 2730 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 1.41 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.16), residues: 2502 helix: 0.04 (0.15), residues: 1116 sheet: -2.05 (0.30), residues: 265 loop : -3.20 (0.16), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E 117 HIS 0.005 0.001 HIS E 313 PHE 0.026 0.001 PHE C 41 TYR 0.023 0.001 TYR C 363 ARG 0.009 0.001 ARG A 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 181 MET cc_start: 0.8814 (ptm) cc_final: 0.8566 (ptm) REVERT: E 297 MET cc_start: 0.7711 (mtm) cc_final: 0.7426 (mtt) REVERT: E 314 MET cc_start: 0.7777 (tpt) cc_final: 0.7513 (mmm) REVERT: E 379 ILE cc_start: 0.9507 (mt) cc_final: 0.9285 (mt) REVERT: A 683 MET cc_start: 0.6447 (ptt) cc_final: 0.6237 (ptt) REVERT: B 436 ILE cc_start: 0.8059 (pt) cc_final: 0.7475 (mp) REVERT: C 37 LEU cc_start: 0.9428 (mt) cc_final: 0.9128 (mp) REVERT: C 265 MET cc_start: 0.8789 (mtm) cc_final: 0.8447 (mtm) REVERT: C 275 ASP cc_start: 0.7635 (p0) cc_final: 0.7056 (p0) REVERT: C 440 MET cc_start: 0.7599 (tpt) cc_final: 0.7270 (tpp) REVERT: D 17 MET cc_start: 0.8285 (ttm) cc_final: 0.8039 (ttm) REVERT: D 48 TYR cc_start: 0.7035 (m-80) cc_final: 0.6641 (m-80) REVERT: D 55 VAL cc_start: 0.8935 (p) cc_final: 0.8684 (m) REVERT: D 79 ARG cc_start: 0.8907 (mmt90) cc_final: 0.8565 (mmm-85) REVERT: F 5 MET cc_start: 0.6748 (mtm) cc_final: 0.6455 (mtm) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.2905 time to fit residues: 88.2580 Evaluate side-chains 134 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 25 optimal weight: 30.0000 chunk 108 optimal weight: 0.1980 chunk 153 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 64 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 ASN A 192 ASN A 402 GLN A 459 HIS ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS F 43 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20780 Z= 0.213 Angle : 0.661 9.174 28106 Z= 0.348 Chirality : 0.045 0.290 3114 Planarity : 0.004 0.066 3646 Dihedral : 5.855 33.882 2730 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2502 helix: 0.43 (0.16), residues: 1122 sheet: -2.01 (0.29), residues: 276 loop : -3.07 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP E 117 HIS 0.007 0.001 HIS E 313 PHE 0.019 0.002 PHE B 362 TYR 0.015 0.001 TYR C 363 ARG 0.005 0.000 ARG A 989 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 297 MET cc_start: 0.7868 (mtm) cc_final: 0.7356 (mtt) REVERT: E 314 MET cc_start: 0.7829 (tpt) cc_final: 0.7418 (mmm) REVERT: A 254 LEU cc_start: 0.9441 (tt) cc_final: 0.9128 (pp) REVERT: A 350 TYR cc_start: 0.7726 (m-80) cc_final: 0.7467 (m-80) REVERT: A 683 MET cc_start: 0.6702 (ptt) cc_final: 0.6450 (ptt) REVERT: A 910 MET cc_start: 0.7120 (mmm) cc_final: 0.5605 (mmp) REVERT: A 994 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7392 (tt0) REVERT: B 82 LYS cc_start: 0.7658 (tptt) cc_final: 0.7411 (tptp) REVERT: C 316 THR cc_start: 0.7834 (t) cc_final: 0.7466 (m) REVERT: C 440 MET cc_start: 0.7897 (tpt) cc_final: 0.7604 (tpp) REVERT: D 55 VAL cc_start: 0.9068 (p) cc_final: 0.8797 (m) REVERT: D 79 ARG cc_start: 0.8955 (mmt90) cc_final: 0.8444 (mmm-85) REVERT: D 86 TYR cc_start: 0.9016 (t80) cc_final: 0.8604 (t80) REVERT: F 8 ASN cc_start: 0.9358 (m-40) cc_final: 0.9129 (m-40) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.3101 time to fit residues: 87.0724 Evaluate side-chains 111 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 123 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 64 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN A 192 ASN A 370 ASN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN C 102 ASN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20780 Z= 0.340 Angle : 0.765 9.200 28106 Z= 0.407 Chirality : 0.047 0.246 3114 Planarity : 0.005 0.064 3646 Dihedral : 6.354 36.985 2730 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.16), residues: 2502 helix: 0.16 (0.15), residues: 1135 sheet: -2.19 (0.31), residues: 266 loop : -3.07 (0.17), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP E 117 HIS 0.007 0.002 HIS E 313 PHE 0.025 0.002 PHE B 422 TYR 0.031 0.002 TYR A 30 ARG 0.007 0.001 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 VAL cc_start: 0.8811 (m) cc_final: 0.8474 (p) REVERT: E 117 TRP cc_start: 0.6982 (m-90) cc_final: 0.6777 (m-90) REVERT: E 297 MET cc_start: 0.8062 (mtm) cc_final: 0.7510 (mtt) REVERT: E 314 MET cc_start: 0.7816 (tpt) cc_final: 0.7524 (mmm) REVERT: A 309 THR cc_start: 0.7378 (m) cc_final: 0.7163 (t) REVERT: A 344 TYR cc_start: 0.8955 (t80) cc_final: 0.8497 (t80) REVERT: A 604 MET cc_start: 0.7756 (pmm) cc_final: 0.7480 (pmm) REVERT: A 994 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7469 (tt0) REVERT: B 141 ASN cc_start: 0.6068 (t0) cc_final: 0.5683 (m-40) REVERT: B 436 ILE cc_start: 0.8261 (pt) cc_final: 0.8044 (pt) REVERT: B 440 MET cc_start: 0.7700 (tpt) cc_final: 0.7335 (tmm) REVERT: D 17 MET cc_start: 0.8366 (ttm) cc_final: 0.8165 (ttm) REVERT: D 79 ARG cc_start: 0.9097 (mmt90) cc_final: 0.8478 (mmm-85) REVERT: F 89 LEU cc_start: 0.9381 (mm) cc_final: 0.9162 (mm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.3037 time to fit residues: 73.5043 Evaluate side-chains 102 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 242 optimal weight: 9.9990 chunk 201 optimal weight: 0.0870 chunk 112 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN A 57 GLN A 104 HIS A 192 ASN A 504 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN C 244 HIS ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN F 43 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20780 Z= 0.156 Angle : 0.641 9.494 28106 Z= 0.334 Chirality : 0.044 0.253 3114 Planarity : 0.004 0.061 3646 Dihedral : 5.697 33.454 2730 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.68 (0.17), residues: 2502 helix: 0.65 (0.16), residues: 1117 sheet: -2.12 (0.30), residues: 269 loop : -2.79 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 17 HIS 0.007 0.001 HIS E 313 PHE 0.032 0.001 PHE B 277 TYR 0.021 0.001 TYR A 30 ARG 0.005 0.000 ARG A 989 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 ASP cc_start: 0.5182 (t0) cc_final: 0.4600 (p0) REVERT: E 140 GLN cc_start: 0.8733 (mt0) cc_final: 0.8400 (mm-40) REVERT: A 344 TYR cc_start: 0.9008 (t80) cc_final: 0.8470 (t80) REVERT: A 604 MET cc_start: 0.7638 (pmm) cc_final: 0.7389 (pmm) REVERT: A 910 MET cc_start: 0.7457 (mmm) cc_final: 0.5643 (mmp) REVERT: B 82 LYS cc_start: 0.7848 (tptt) cc_final: 0.7457 (tmtt) REVERT: D 79 ARG cc_start: 0.9028 (mmt90) cc_final: 0.8599 (mmm-85) REVERT: D 88 GLN cc_start: 0.9392 (tp40) cc_final: 0.8598 (tp40) REVERT: F 15 TYR cc_start: 0.8422 (t80) cc_final: 0.8099 (t80) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.3060 time to fit residues: 80.2103 Evaluate side-chains 93 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 204 optimal weight: 0.2980 chunk 135 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN A 57 GLN A 104 HIS A 192 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 HIS B 345 ASN B 373 GLN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 102 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20780 Z= 0.245 Angle : 0.687 8.435 28106 Z= 0.361 Chirality : 0.045 0.270 3114 Planarity : 0.004 0.062 3646 Dihedral : 5.829 32.607 2730 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 2502 helix: 0.58 (0.16), residues: 1115 sheet: -2.18 (0.30), residues: 280 loop : -2.82 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP E 117 HIS 0.009 0.001 HIS E 313 PHE 0.037 0.002 PHE B 277 TYR 0.025 0.002 TYR F 15 ARG 0.011 0.001 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 ASP cc_start: 0.4630 (t0) cc_final: 0.4007 (p0) REVERT: E 140 GLN cc_start: 0.8709 (mt0) cc_final: 0.8265 (mm-40) REVERT: E 181 MET cc_start: 0.8869 (ppp) cc_final: 0.8619 (ppp) REVERT: E 239 MET cc_start: 0.1989 (mmp) cc_final: 0.1577 (tpp) REVERT: A 309 THR cc_start: 0.7372 (m) cc_final: 0.7168 (t) REVERT: A 390 MET cc_start: 0.8293 (ttp) cc_final: 0.7987 (ttm) REVERT: A 604 MET cc_start: 0.7870 (pmm) cc_final: 0.7532 (pmm) REVERT: A 753 MET cc_start: 0.8350 (mmm) cc_final: 0.8101 (mpp) REVERT: A 994 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7345 (tt0) REVERT: B 436 ILE cc_start: 0.8379 (pt) cc_final: 0.7811 (mp) REVERT: B 440 MET cc_start: 0.7901 (tpt) cc_final: 0.7547 (tmm) REVERT: C 136 PHE cc_start: 0.6808 (p90) cc_final: 0.5914 (p90) REVERT: D 56 MET cc_start: 0.8909 (tpt) cc_final: 0.8322 (tpp) REVERT: D 79 ARG cc_start: 0.8983 (mmt90) cc_final: 0.8529 (mmm-85) REVERT: D 88 GLN cc_start: 0.9450 (tp40) cc_final: 0.9172 (tp40) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3075 time to fit residues: 69.8596 Evaluate side-chains 98 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 164 optimal weight: 0.0470 chunk 119 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN D 13 HIS ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20780 Z= 0.155 Angle : 0.643 10.345 28106 Z= 0.333 Chirality : 0.044 0.279 3114 Planarity : 0.004 0.060 3646 Dihedral : 5.539 32.424 2730 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.05 % Allowed : 1.28 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.49 (0.17), residues: 2502 helix: 0.77 (0.16), residues: 1113 sheet: -2.11 (0.30), residues: 282 loop : -2.62 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP E 117 HIS 0.009 0.001 HIS E 313 PHE 0.025 0.001 PHE B 277 TYR 0.037 0.001 TYR E 310 ARG 0.003 0.000 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 ASP cc_start: 0.4502 (t0) cc_final: 0.3897 (p0) REVERT: E 140 GLN cc_start: 0.8687 (mt0) cc_final: 0.8361 (mm-40) REVERT: E 181 MET cc_start: 0.8860 (ppp) cc_final: 0.8622 (ppp) REVERT: E 239 MET cc_start: 0.1359 (mmp) cc_final: 0.1085 (tpp) REVERT: A 344 TYR cc_start: 0.8778 (t80) cc_final: 0.8274 (t80) REVERT: A 390 MET cc_start: 0.8359 (ttp) cc_final: 0.8071 (ttm) REVERT: A 589 ASN cc_start: 0.6864 (p0) cc_final: 0.6638 (p0) REVERT: A 604 MET cc_start: 0.7814 (pmm) cc_final: 0.7471 (pmm) REVERT: B 436 ILE cc_start: 0.8196 (pt) cc_final: 0.7641 (mp) REVERT: B 440 MET cc_start: 0.7785 (tpt) cc_final: 0.7454 (tmm) REVERT: C 37 LEU cc_start: 0.9531 (mt) cc_final: 0.9240 (mp) REVERT: C 265 MET cc_start: 0.8861 (mtm) cc_final: 0.8540 (mtt) REVERT: C 275 ASP cc_start: 0.7086 (p0) cc_final: 0.6464 (p0) REVERT: D 56 MET cc_start: 0.8960 (tpt) cc_final: 0.8356 (tpp) REVERT: D 79 ARG cc_start: 0.8973 (mmt90) cc_final: 0.8520 (mmm-85) REVERT: D 88 GLN cc_start: 0.9481 (tp40) cc_final: 0.9198 (tt0) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.3277 time to fit residues: 79.1157 Evaluate side-chains 106 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 135 optimal weight: 0.0770 chunk 98 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS B 102 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 HIS ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.7354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20780 Z= 0.190 Angle : 0.650 8.613 28106 Z= 0.338 Chirality : 0.044 0.267 3114 Planarity : 0.004 0.061 3646 Dihedral : 5.521 32.665 2730 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.05 % Allowed : 0.91 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.43 (0.17), residues: 2502 helix: 0.82 (0.16), residues: 1112 sheet: -2.03 (0.30), residues: 283 loop : -2.59 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP E 117 HIS 0.008 0.001 HIS E 64 PHE 0.030 0.002 PHE C 362 TYR 0.028 0.001 TYR F 15 ARG 0.005 0.000 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 ASP cc_start: 0.4433 (t0) cc_final: 0.3885 (p0) REVERT: E 140 GLN cc_start: 0.8648 (mt0) cc_final: 0.8274 (mm-40) REVERT: A 390 MET cc_start: 0.8357 (ttp) cc_final: 0.8048 (ttm) REVERT: A 604 MET cc_start: 0.7878 (pmm) cc_final: 0.7508 (pmm) REVERT: A 753 MET cc_start: 0.8312 (mmm) cc_final: 0.8112 (mpp) REVERT: A 910 MET cc_start: 0.7526 (mmp) cc_final: 0.7226 (mmm) REVERT: B 436 ILE cc_start: 0.8330 (pt) cc_final: 0.7816 (mp) REVERT: C 136 PHE cc_start: 0.7154 (p90) cc_final: 0.6370 (p90) REVERT: C 265 MET cc_start: 0.8952 (mtm) cc_final: 0.8598 (mtt) REVERT: C 275 ASP cc_start: 0.7231 (p0) cc_final: 0.6612 (p0) REVERT: D 56 MET cc_start: 0.8945 (tpt) cc_final: 0.8234 (tpp) REVERT: D 79 ARG cc_start: 0.8961 (mmt90) cc_final: 0.8594 (mmm-85) REVERT: D 88 GLN cc_start: 0.9476 (tp40) cc_final: 0.8840 (tp40) REVERT: F 15 TYR cc_start: 0.8404 (t80) cc_final: 0.8191 (t80) REVERT: F 89 LEU cc_start: 0.9337 (mm) cc_final: 0.9134 (mm) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.3053 time to fit residues: 73.2603 Evaluate side-chains 102 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 199 optimal weight: 0.0010 chunk 20 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 ASN A 104 HIS A 443 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 HIS ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.7533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20780 Z= 0.181 Angle : 0.651 8.899 28106 Z= 0.335 Chirality : 0.044 0.266 3114 Planarity : 0.004 0.061 3646 Dihedral : 5.432 32.425 2730 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.05 % Allowed : 0.36 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.39 (0.17), residues: 2502 helix: 0.80 (0.16), residues: 1127 sheet: -1.97 (0.31), residues: 280 loop : -2.56 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP E 117 HIS 0.008 0.001 HIS E 313 PHE 0.025 0.001 PHE B 277 TYR 0.030 0.001 TYR F 104 ARG 0.006 0.000 ARG B 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 ASP cc_start: 0.4448 (t0) cc_final: 0.3982 (p0) REVERT: E 140 GLN cc_start: 0.8664 (mt0) cc_final: 0.8304 (mm-40) REVERT: A 390 MET cc_start: 0.8345 (ttp) cc_final: 0.8016 (ttm) REVERT: A 589 ASN cc_start: 0.7243 (p0) cc_final: 0.6980 (p0) REVERT: A 604 MET cc_start: 0.7897 (pmm) cc_final: 0.7493 (pmm) REVERT: A 753 MET cc_start: 0.8293 (mmm) cc_final: 0.8085 (mpp) REVERT: B 436 ILE cc_start: 0.8301 (pt) cc_final: 0.7811 (mp) REVERT: C 136 PHE cc_start: 0.7088 (p90) cc_final: 0.6274 (p90) REVERT: C 265 MET cc_start: 0.8905 (mtm) cc_final: 0.8555 (mtt) REVERT: C 275 ASP cc_start: 0.7061 (p0) cc_final: 0.6437 (p0) REVERT: D 56 MET cc_start: 0.8937 (tpt) cc_final: 0.8214 (tpp) REVERT: D 79 ARG cc_start: 0.8947 (mmt90) cc_final: 0.8573 (mmm-85) REVERT: D 88 GLN cc_start: 0.9466 (tp40) cc_final: 0.8851 (tp40) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.2964 time to fit residues: 67.5262 Evaluate side-chains 98 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 199 optimal weight: 0.0170 chunk 83 optimal weight: 4.9990 chunk 204 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 0.4980 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN A 684 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN C 102 ASN ** C 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 HIS F 43 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.079657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.057781 restraints weight = 111624.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.059320 restraints weight = 64741.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.060251 restraints weight = 45851.706| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.7702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20780 Z= 0.156 Angle : 0.632 8.918 28106 Z= 0.324 Chirality : 0.043 0.268 3114 Planarity : 0.004 0.060 3646 Dihedral : 5.254 32.947 2730 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.05 % Allowed : 0.55 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 2.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2502 helix: 0.92 (0.16), residues: 1123 sheet: -1.91 (0.30), residues: 280 loop : -2.52 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP E 117 HIS 0.009 0.001 HIS D 13 PHE 0.024 0.001 PHE B 199 TYR 0.032 0.001 TYR F 15 ARG 0.003 0.000 ARG E 241 =============================================================================== Job complete usr+sys time: 3460.03 seconds wall clock time: 66 minutes 33.40 seconds (3993.40 seconds total)