Starting phenix.real_space_refine on Fri Mar 15 14:13:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/03_2024/7ksr_23024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/03_2024/7ksr_23024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/03_2024/7ksr_23024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/03_2024/7ksr_23024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/03_2024/7ksr_23024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ksr_23024/03_2024/7ksr_23024.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 87 5.16 5 C 7499 2.51 5 N 2106 2.21 5 O 2164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 686": "NH1" <-> "NH2" Residue "A ASP 706": "OD1" <-> "OD2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C ASP 198": "OD1" <-> "OD2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 360": "NH1" <-> "NH2" Residue "C ASP 446": "OD1" <-> "OD2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11863 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3098 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 19, 'TRANS': 375} Chain breaks: 4 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2909 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2932 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 15, 'TRANS': 381} Chain breaks: 9 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 502 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 227 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2917 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 352} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 911 SG CYS A 299 60.232 45.699 88.425 1.00 77.53 S ATOM 939 SG CYS A 302 57.071 45.555 86.837 0.99 75.84 S ATOM 985 SG CYS A 307 59.522 45.519 84.292 0.87 75.70 S ATOM 1591 SG CYS A 531 70.136 60.350 100.152 1.00112.25 S ATOM 1734 SG CYS A 550 66.043 57.750 100.459 1.00102.41 S ATOM 1534 SG CYS A 524 70.650 56.219 95.707 1.00105.16 S ATOM 1719 SG CYS A 548 66.859 55.656 97.184 1.00 97.15 S ATOM 1973 SG CYS A 581 48.139 64.118 91.620 1.00100.74 S ATOM 2031 SG CYS A 589 45.612 62.751 95.386 1.00111.99 S ATOM 1819 SG CYS A 561 48.886 66.206 95.929 1.00 97.71 S ATOM 1973 SG CYS A 581 48.139 64.118 91.620 1.00100.74 S ATOM 1973 SG CYS A 581 48.139 64.118 91.620 1.00100.74 S ATOM 2031 SG CYS A 589 45.612 62.751 95.386 1.00111.99 S ATOM 2110 SG CYS A 602 44.703 63.403 90.988 1.00106.02 S Time building chain proxies: 6.38, per 1000 atoms: 0.54 Number of scatterers: 11863 At special positions: 0 Unit cell: (90.45, 170.1, 132.3, 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) Zn 7 29.99 S 87 16.00 O 2164 8.00 N 2106 7.00 C 7499 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: 3.85 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 307 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 302 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 299 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb="ZN ZN A 803 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 531 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 550 " pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb="ZN ZN A 804 " pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 524 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 548 " pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 589 " pdb="ZN ZN A 805 " - pdb="ZN ZN A 807 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 581 " pdb=" ZN A 806 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 581 " pdb="ZN ZN A 806 " - pdb=" SG CYS A 561 " pdb=" ZN A 807 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 581 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 589 " pdb="ZN ZN A 807 " - pdb=" SG CYS A 602 " 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 22 sheets defined 20.4% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 34 through 63 removed outlier: 3.759A pdb=" N LYS A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 435 through 450 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 464 through 474 Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.852A pdb=" N MET A 539 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 removed outlier: 3.850A pdb=" N ALA A 577 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'D' and resid 12 through 28 Processing helix chain 'D' and resid 355 through 362 removed outlier: 4.058A pdb=" N ASP D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.184A pdb=" N TYR D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 107 Proline residue: C 93 - end of helix removed outlier: 3.537A pdb=" N ILE C 96 " --> pdb=" O LYS C 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 115 removed outlier: 3.506A pdb=" N LEU C 115 " --> pdb=" O HIS C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.533A pdb=" N LEU C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 602 removed outlier: 3.931A pdb=" N ARG C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 600 " --> pdb=" O THR C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 624 Processing helix chain 'C' and resid 631 through 649 removed outlier: 4.139A pdb=" N MET C 637 " --> pdb=" O ASN C 633 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 641 " --> pdb=" O MET C 637 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS C 646 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 removed outlier: 3.707A pdb=" N PHE C 666 " --> pdb=" O SER C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 686 Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.642A pdb=" N LYS B 342 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE B 343 " --> pdb=" O ILE B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'B' and resid 395 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 5.865A pdb=" N SER A 115 " --> pdb=" O GLY A 682 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 removed outlier: 6.617A pdb=" N PHE A 121 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 619 Processing sheet with id=AA5, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.785A pdb=" N PHE A 638 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 713 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 377 through 382 removed outlier: 3.718A pdb=" N LEU D 34 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL D 35 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 529 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 47 through 54 removed outlier: 5.463A pdb=" N ARG D 65 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASP D 52 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE D 63 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR D 54 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE D 61 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASN D 77 " --> pdb=" O ASN D 122 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN D 122 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU D 79 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS D 120 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE D 81 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AA9, first strand: chain 'D' and resid 183 through 185 removed outlier: 3.603A pdb=" N SER D 197 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 230 through 235 removed outlier: 3.809A pdb=" N LYS D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 276 through 281 removed outlier: 3.886A pdb=" N THR D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS D 311 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 320 through 322 removed outlier: 7.074A pdb=" N SER D 336 " --> pdb=" O PHE D 321 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP D 346 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU D 366 " --> pdb=" O ASP D 346 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 160 through 161 removed outlier: 4.156A pdb=" N LEU C 355 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 317 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE C 357 " --> pdb=" O TYR C 315 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR C 315 " --> pdb=" O PHE C 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 203 through 210 removed outlier: 4.303A pdb=" N ARG C 204 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 190 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 208 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL C 186 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU C 185 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 187 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 250 " --> pdb=" O MET C 299 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 297 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 437 through 441 removed outlier: 4.212A pdb=" N ARG C 439 " --> pdb=" O PHE C 432 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE C 432 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLN C 441 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N TYR C 430 " --> pdb=" O GLN C 441 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.358A pdb=" N CYS B 84 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP B 438 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 86 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 98 through 101 removed outlier: 4.064A pdb=" N GLY B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 136 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 125 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU B 134 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 147 through 154 removed outlier: 4.448A pdb=" N THR B 149 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 166 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 167 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 184 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN B 176 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N CYS B 182 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 193 through 198 removed outlier: 3.670A pdb=" N GLU B 195 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 215 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE B 228 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 217 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N GLN B 292 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL B 226 " --> pdb=" O GLN B 292 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 239 through 244 Processing sheet with id=AC3, first strand: chain 'B' and resid 312 through 315 removed outlier: 7.226A pdb=" N LYS B 332 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE B 352 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 368 through 369 385 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3911 1.35 - 1.46: 2795 1.46 - 1.58: 5305 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 12131 Sorted by residual: bond pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.26e+00 bond pdb=" CB ILE A 456 " pdb=" CG2 ILE A 456 " ideal model delta sigma weight residual 1.521 1.565 -0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" C ASN D 186 " pdb=" N PRO D 187 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.74e+00 bond pdb=" C ASN D 282 " pdb=" N PRO D 283 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.69e+00 bond pdb=" C SER D 326 " pdb=" N PRO D 327 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.62e+00 ... (remaining 12126 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.98: 397 106.98 - 113.73: 6600 113.73 - 120.48: 4495 120.48 - 127.24: 4764 127.24 - 133.99: 187 Bond angle restraints: 16443 Sorted by residual: angle pdb=" N THR D 28 " pdb=" CA THR D 28 " pdb=" C THR D 28 " ideal model delta sigma weight residual 109.81 116.61 -6.80 2.21e+00 2.05e-01 9.48e+00 angle pdb=" CA THR D 28 " pdb=" C THR D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 118.44 122.81 -4.37 1.59e+00 3.96e-01 7.55e+00 angle pdb=" C LYS C 587 " pdb=" N ASP C 588 " pdb=" CA ASP C 588 " ideal model delta sigma weight residual 121.80 128.43 -6.63 2.44e+00 1.68e-01 7.39e+00 angle pdb=" CA LYS C 92 " pdb=" C LYS C 92 " pdb=" N PRO C 93 " ideal model delta sigma weight residual 118.44 122.75 -4.31 1.59e+00 3.96e-01 7.36e+00 angle pdb=" N SER D 184 " pdb=" CA SER D 184 " pdb=" C SER D 184 " ideal model delta sigma weight residual 108.32 112.42 -4.10 1.64e+00 3.72e-01 6.25e+00 ... (remaining 16438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6781 17.54 - 35.08: 390 35.08 - 52.61: 51 52.61 - 70.15: 13 70.15 - 87.69: 8 Dihedral angle restraints: 7243 sinusoidal: 2773 harmonic: 4470 Sorted by residual: dihedral pdb=" CA TYR B 244 " pdb=" C TYR B 244 " pdb=" N ASP B 245 " pdb=" CA ASP B 245 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA LYS D 251 " pdb=" C LYS D 251 " pdb=" N LEU D 252 " pdb=" CA LEU D 252 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA THR D 297 " pdb=" C THR D 297 " pdb=" N VAL D 298 " pdb=" CA VAL D 298 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 7240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1146 0.035 - 0.071: 459 0.071 - 0.106: 117 0.106 - 0.142: 77 0.142 - 0.177: 16 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CA VAL D 298 " pdb=" N VAL D 298 " pdb=" C VAL D 298 " pdb=" CB VAL D 298 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA THR D 28 " pdb=" N THR D 28 " pdb=" C THR D 28 " pdb=" CB THR D 28 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE D 81 " pdb=" N ILE D 81 " pdb=" C ILE D 81 " pdb=" CB ILE D 81 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1812 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 201 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO C 202 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 202 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 202 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 28 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO D 29 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 86 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO D 87 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " -0.024 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 756 2.74 - 3.28: 11601 3.28 - 3.82: 17769 3.82 - 4.36: 21450 4.36 - 4.90: 37885 Nonbonded interactions: 89461 Sorted by model distance: nonbonded pdb=" OG SER D 147 " pdb=" O HIS D 176 " model vdw 2.200 2.440 nonbonded pdb=" O ASP C 136 " pdb=" OG SER C 139 " model vdw 2.216 2.440 nonbonded pdb=" OG SER D 285 " pdb=" OD1 ASP C 135 " model vdw 2.218 2.440 nonbonded pdb=" OD1 ASP B 431 " pdb=" OG SER B 433 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR A 315 " pdb=" OD1 ASN A 317 " model vdw 2.308 2.440 ... (remaining 89456 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.20 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.350 Check model and map are aligned: 0.210 Set scattering table: 0.110 Process input model: 33.650 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 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 : 0.004 0.054 12131 Z= 0.289 Angle : 0.697 8.135 16443 Z= 0.366 Chirality : 0.047 0.177 1815 Planarity : 0.004 0.047 2118 Dihedral : 11.737 87.689 4319 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -4.46 (0.16), residues: 1484 helix: -2.26 (0.21), residues: 274 sheet: -3.18 (0.23), residues: 303 loop : -3.26 (0.16), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 345 HIS 0.003 0.001 HIS B 397 PHE 0.013 0.001 PHE D 243 TYR 0.014 0.001 TYR B 244 ARG 0.002 0.000 ARG D 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 1.331 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: A 97 MET cc_start: 0.6874 (tpt) cc_final: 0.6538 (tpp) REVERT: A 278 ASP cc_start: 0.7469 (m-30) cc_final: 0.7039 (t0) REVERT: A 615 LEU cc_start: 0.8909 (mt) cc_final: 0.8695 (mp) REVERT: A 645 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7123 (mt-10) REVERT: A 670 LEU cc_start: 0.7509 (tp) cc_final: 0.7222 (tt) REVERT: D 15 ARG cc_start: 0.7544 (mpt180) cc_final: 0.7198 (mmt180) REVERT: D 24 TRP cc_start: 0.8146 (t60) cc_final: 0.7928 (t60) REVERT: D 38 HIS cc_start: 0.6880 (t70) cc_final: 0.5720 (t-90) REVERT: D 49 TRP cc_start: 0.6467 (m100) cc_final: 0.5281 (m100) REVERT: D 55 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7467 (mpp80) REVERT: D 85 GLN cc_start: 0.7178 (mt0) cc_final: 0.6704 (mp10) REVERT: D 313 PHE cc_start: 0.7518 (m-80) cc_final: 0.7310 (m-80) REVERT: D 354 GLN cc_start: 0.7328 (pm20) cc_final: 0.6625 (pt0) REVERT: D 380 PHE cc_start: 0.7542 (p90) cc_final: 0.7213 (p90) REVERT: D 403 GLN cc_start: 0.7353 (tt0) cc_final: 0.6991 (tm-30) REVERT: C 453 CYS cc_start: 0.4715 (t) cc_final: 0.3308 (t) REVERT: C 528 ILE cc_start: 0.8350 (pt) cc_final: 0.8123 (mp) REVERT: B 144 ASP cc_start: 0.7324 (p0) cc_final: 0.6966 (p0) REVERT: B 211 LYS cc_start: 0.8457 (tttt) cc_final: 0.7968 (tmtt) REVERT: B 252 MET cc_start: 0.8541 (tpp) cc_final: 0.8334 (ttt) REVERT: B 272 ASN cc_start: 0.8524 (p0) cc_final: 0.8215 (m-40) REVERT: B 319 ILE cc_start: 0.8832 (mm) cc_final: 0.7749 (mm) REVERT: B 372 PHE cc_start: 0.8177 (t80) cc_final: 0.7631 (t80) outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.2686 time to fit residues: 180.8380 Evaluate side-chains 237 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 ASN A 556 ASN D 188 ASN C 104 ASN C 440 GLN C 624 HIS C 634 HIS C 664 HIS B 104 HIS B 194 ASN B 204 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12131 Z= 0.238 Angle : 0.589 7.394 16443 Z= 0.311 Chirality : 0.045 0.224 1815 Planarity : 0.004 0.058 2118 Dihedral : 4.428 20.352 1617 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.24 % Allowed : 3.47 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.19), residues: 1484 helix: -0.60 (0.27), residues: 290 sheet: -2.34 (0.25), residues: 318 loop : -2.67 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.011 0.001 HIS C 659 PHE 0.019 0.002 PHE B 101 TYR 0.017 0.002 TYR C 434 ARG 0.006 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 1.435 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: A 660 ASP cc_start: 0.7070 (m-30) cc_final: 0.6868 (m-30) REVERT: A 727 TYR cc_start: 0.5051 (p90) cc_final: 0.3138 (t80) REVERT: D 55 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7608 (mpp80) REVERT: D 85 GLN cc_start: 0.7021 (mt0) cc_final: 0.6179 (mp10) REVERT: D 86 LEU cc_start: 0.7753 (mp) cc_final: 0.7071 (tt) REVERT: D 153 ASP cc_start: 0.7292 (t0) cc_final: 0.6022 (p0) REVERT: D 154 TYR cc_start: 0.6070 (p90) cc_final: 0.5776 (p90) REVERT: D 354 GLN cc_start: 0.7642 (pm20) cc_final: 0.6997 (pt0) REVERT: D 366 LEU cc_start: 0.9049 (tp) cc_final: 0.8743 (tp) REVERT: C 467 LEU cc_start: 0.8996 (mp) cc_final: 0.8718 (mt) REVERT: B 139 VAL cc_start: 0.8170 (t) cc_final: 0.7781 (p) REVERT: B 144 ASP cc_start: 0.7455 (p0) cc_final: 0.7253 (p0) REVERT: B 172 ILE cc_start: 0.9203 (mt) cc_final: 0.8895 (tt) REVERT: B 237 ASP cc_start: 0.7873 (t0) cc_final: 0.7629 (t0) REVERT: B 243 ASP cc_start: 0.8416 (t0) cc_final: 0.8080 (t0) REVERT: B 252 MET cc_start: 0.9080 (tpp) cc_final: 0.8560 (ttt) REVERT: B 271 MET cc_start: 0.9434 (mmt) cc_final: 0.9132 (mmt) REVERT: B 319 ILE cc_start: 0.8877 (mm) cc_final: 0.8038 (mm) outliers start: 3 outliers final: 0 residues processed: 252 average time/residue: 0.2179 time to fit residues: 80.4063 Evaluate side-chains 175 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 37 optimal weight: 0.0470 chunk 136 optimal weight: 0.6980 chunk 147 optimal weight: 0.0060 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN D 272 HIS ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 HIS B 415 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12131 Z= 0.145 Angle : 0.518 7.010 16443 Z= 0.272 Chirality : 0.043 0.165 1815 Planarity : 0.003 0.038 2118 Dihedral : 4.149 18.247 1617 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: -2.55 (0.19), residues: 1484 helix: 0.12 (0.30), residues: 291 sheet: -1.80 (0.25), residues: 339 loop : -2.38 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 345 HIS 0.006 0.001 HIS C 471 PHE 0.022 0.001 PHE B 101 TYR 0.026 0.001 TYR B 124 ARG 0.005 0.001 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.444 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: A 97 MET cc_start: 0.6607 (tpt) cc_final: 0.6361 (tpp) REVERT: A 545 GLU cc_start: 0.7939 (tp30) cc_final: 0.7714 (mm-30) REVERT: A 660 ASP cc_start: 0.7127 (m-30) cc_final: 0.6907 (m-30) REVERT: A 727 TYR cc_start: 0.4675 (p90) cc_final: 0.3244 (t80) REVERT: D 20 GLU cc_start: 0.8379 (tp30) cc_final: 0.7910 (tp30) REVERT: D 38 HIS cc_start: 0.6863 (t70) cc_final: 0.6652 (t-90) REVERT: D 55 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7661 (mpp80) REVERT: D 85 GLN cc_start: 0.7151 (mt0) cc_final: 0.6325 (mp10) REVERT: D 153 ASP cc_start: 0.7075 (t0) cc_final: 0.6649 (p0) REVERT: D 354 GLN cc_start: 0.7417 (pm20) cc_final: 0.6904 (pt0) REVERT: D 366 LEU cc_start: 0.9105 (tp) cc_final: 0.8905 (mm) REVERT: C 441 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 612 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7856 (tp30) REVERT: B 139 VAL cc_start: 0.8264 (t) cc_final: 0.8033 (p) REVERT: B 144 ASP cc_start: 0.7516 (p0) cc_final: 0.7148 (p0) REVERT: B 172 ILE cc_start: 0.9214 (mt) cc_final: 0.8850 (tt) REVERT: B 243 ASP cc_start: 0.8268 (t0) cc_final: 0.7827 (t0) REVERT: B 252 MET cc_start: 0.9082 (tpp) cc_final: 0.8730 (ttt) REVERT: B 271 MET cc_start: 0.9382 (mmt) cc_final: 0.9106 (mmt) REVERT: B 308 TYR cc_start: 0.6548 (m-80) cc_final: 0.6339 (m-80) REVERT: B 319 ILE cc_start: 0.8915 (mm) cc_final: 0.8063 (mm) REVERT: B 372 PHE cc_start: 0.8566 (t80) cc_final: 0.7696 (t80) REVERT: B 391 LEU cc_start: 0.8607 (tp) cc_final: 0.7995 (tp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.2396 time to fit residues: 84.2390 Evaluate side-chains 172 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0060 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 91 optimal weight: 0.0270 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.4654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS D 316 HIS ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 194 ASN B 235 HIS B 397 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12131 Z= 0.145 Angle : 0.516 7.100 16443 Z= 0.271 Chirality : 0.043 0.168 1815 Planarity : 0.003 0.049 2118 Dihedral : 4.084 18.358 1617 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.08 % Allowed : 2.74 % Favored : 97.18 % 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: -2.06 (0.20), residues: 1484 helix: 0.43 (0.31), residues: 284 sheet: -1.28 (0.27), residues: 341 loop : -2.11 (0.19), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 437 HIS 0.006 0.001 HIS A 594 PHE 0.021 0.001 PHE A 471 TYR 0.053 0.001 TYR A 42 ARG 0.009 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.6610 (tpt) cc_final: 0.6334 (tpp) REVERT: A 608 GLN cc_start: 0.8160 (mt0) cc_final: 0.7876 (mt0) REVERT: A 660 ASP cc_start: 0.7319 (m-30) cc_final: 0.7093 (m-30) REVERT: D 20 GLU cc_start: 0.8396 (tp30) cc_final: 0.7954 (tp30) REVERT: D 55 ARG cc_start: 0.8091 (mtt-85) cc_final: 0.7636 (mpp80) REVERT: D 85 GLN cc_start: 0.7188 (mt0) cc_final: 0.6363 (mp10) REVERT: D 153 ASP cc_start: 0.7096 (t0) cc_final: 0.6658 (p0) REVERT: D 256 ASP cc_start: 0.7062 (t0) cc_final: 0.6835 (t0) REVERT: D 354 GLN cc_start: 0.7287 (pm20) cc_final: 0.6835 (pt0) REVERT: C 612 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8143 (tp30) REVERT: B 140 ASP cc_start: 0.6223 (p0) cc_final: 0.6008 (p0) REVERT: B 142 ASP cc_start: 0.7743 (p0) cc_final: 0.6888 (p0) REVERT: B 144 ASP cc_start: 0.7514 (p0) cc_final: 0.7034 (p0) REVERT: B 172 ILE cc_start: 0.9218 (mt) cc_final: 0.8842 (tt) REVERT: B 243 ASP cc_start: 0.8221 (t0) cc_final: 0.7672 (t0) REVERT: B 252 MET cc_start: 0.9099 (tpp) cc_final: 0.8825 (ttt) REVERT: B 256 MET cc_start: 0.8889 (ttm) cc_final: 0.8549 (ttt) REVERT: B 271 MET cc_start: 0.9357 (mmt) cc_final: 0.9054 (mmt) REVERT: B 296 PHE cc_start: 0.8385 (m-80) cc_final: 0.8177 (m-80) REVERT: B 308 TYR cc_start: 0.6318 (m-80) cc_final: 0.5780 (m-80) REVERT: B 319 ILE cc_start: 0.8816 (mm) cc_final: 0.8180 (mm) REVERT: B 372 PHE cc_start: 0.8511 (t80) cc_final: 0.7823 (t80) outliers start: 1 outliers final: 1 residues processed: 239 average time/residue: 0.2025 time to fit residues: 72.9402 Evaluate side-chains 171 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 707 HIS D 38 HIS ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12131 Z= 0.317 Angle : 0.630 6.977 16443 Z= 0.336 Chirality : 0.046 0.251 1815 Planarity : 0.004 0.044 2118 Dihedral : 4.686 24.561 1617 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: -1.85 (0.21), residues: 1484 helix: 0.54 (0.31), residues: 285 sheet: -1.10 (0.27), residues: 364 loop : -1.98 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 235 HIS 0.013 0.002 HIS B 213 PHE 0.022 0.002 PHE A 471 TYR 0.033 0.002 TYR A 42 ARG 0.007 0.001 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.6965 (tpt) cc_final: 0.6722 (tpp) REVERT: A 99 MET cc_start: 0.7299 (tpp) cc_final: 0.6970 (ttm) REVERT: A 645 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7773 (mt-10) REVERT: A 660 ASP cc_start: 0.7908 (m-30) cc_final: 0.7597 (m-30) REVERT: A 680 ARG cc_start: 0.7272 (mtm-85) cc_final: 0.6790 (mtm180) REVERT: D 20 GLU cc_start: 0.8457 (tp30) cc_final: 0.8072 (tp30) REVERT: D 38 HIS cc_start: 0.7243 (t70) cc_final: 0.6789 (t70) REVERT: D 85 GLN cc_start: 0.7307 (mt0) cc_final: 0.6104 (mp10) REVERT: D 86 LEU cc_start: 0.7831 (mp) cc_final: 0.7151 (tt) REVERT: C 612 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8263 (tp30) REVERT: B 144 ASP cc_start: 0.7453 (p0) cc_final: 0.7062 (p0) REVERT: B 172 ILE cc_start: 0.9318 (mt) cc_final: 0.8911 (tt) REVERT: B 237 ASP cc_start: 0.8500 (t70) cc_final: 0.8274 (t70) REVERT: B 243 ASP cc_start: 0.8189 (t0) cc_final: 0.7673 (t0) REVERT: B 252 MET cc_start: 0.9331 (tpp) cc_final: 0.8712 (ttt) REVERT: B 256 MET cc_start: 0.8879 (ttm) cc_final: 0.8439 (ttp) REVERT: B 308 TYR cc_start: 0.7039 (m-80) cc_final: 0.6461 (m-80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1812 time to fit residues: 51.2291 Evaluate side-chains 144 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 704 ASN ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS D 277 ASN D 311 HIS ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12131 Z= 0.167 Angle : 0.534 7.469 16443 Z= 0.282 Chirality : 0.044 0.219 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.409 22.893 1617 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.08 % Allowed : 1.21 % Favored : 98.71 % 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: -1.63 (0.21), residues: 1484 helix: 0.69 (0.32), residues: 281 sheet: -0.80 (0.28), residues: 349 loop : -1.89 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 345 HIS 0.011 0.001 HIS B 258 PHE 0.018 0.001 PHE A 46 TYR 0.027 0.001 TYR A 42 ARG 0.005 0.000 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.6862 (tpt) cc_final: 0.6602 (tpp) REVERT: A 586 CYS cc_start: 0.6285 (m) cc_final: 0.5978 (m) REVERT: A 660 ASP cc_start: 0.7962 (m-30) cc_final: 0.7624 (m-30) REVERT: A 726 ASP cc_start: 0.8007 (t0) cc_final: 0.7652 (m-30) REVERT: D 20 GLU cc_start: 0.8505 (tp30) cc_final: 0.8284 (tp30) REVERT: D 85 GLN cc_start: 0.7285 (mt0) cc_final: 0.6276 (mp10) REVERT: D 153 ASP cc_start: 0.7436 (t0) cc_final: 0.6730 (p0) REVERT: D 253 MET cc_start: 0.8053 (pmm) cc_final: 0.7836 (pmm) REVERT: D 373 HIS cc_start: 0.6728 (m-70) cc_final: 0.6368 (m-70) REVERT: C 594 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7014 (tm-30) REVERT: C 612 GLU cc_start: 0.8652 (mm-30) cc_final: 0.7939 (tp30) REVERT: B 142 ASP cc_start: 0.7972 (p0) cc_final: 0.7275 (p0) REVERT: B 144 ASP cc_start: 0.7519 (p0) cc_final: 0.7022 (p0) REVERT: B 252 MET cc_start: 0.9182 (tpp) cc_final: 0.8953 (ttm) REVERT: B 271 MET cc_start: 0.9322 (mmt) cc_final: 0.9099 (mmt) REVERT: B 310 ASP cc_start: 0.8129 (m-30) cc_final: 0.7858 (m-30) outliers start: 1 outliers final: 1 residues processed: 184 average time/residue: 0.1791 time to fit residues: 52.4119 Evaluate side-chains 138 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.7980 chunk 82 optimal weight: 40.0000 chunk 105 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 0.2980 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 HIS ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12131 Z= 0.167 Angle : 0.526 6.986 16443 Z= 0.278 Chirality : 0.044 0.193 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.296 22.915 1617 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -1.46 (0.21), residues: 1484 helix: 0.73 (0.32), residues: 283 sheet: -0.73 (0.28), residues: 355 loop : -1.72 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 345 HIS 0.007 0.001 HIS B 213 PHE 0.019 0.001 PHE A 46 TYR 0.024 0.001 TYR A 42 ARG 0.005 0.000 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.6773 (tpt) cc_final: 0.6494 (tpp) REVERT: A 638 PHE cc_start: 0.8956 (t80) cc_final: 0.8272 (t80) REVERT: A 660 ASP cc_start: 0.7938 (m-30) cc_final: 0.7610 (m-30) REVERT: A 726 ASP cc_start: 0.8132 (t0) cc_final: 0.7835 (m-30) REVERT: D 20 GLU cc_start: 0.8517 (tp30) cc_final: 0.8305 (tp30) REVERT: D 85 GLN cc_start: 0.7292 (mt0) cc_final: 0.6240 (mp10) REVERT: D 153 ASP cc_start: 0.7464 (t0) cc_final: 0.6785 (p0) REVERT: D 179 GLU cc_start: 0.6457 (pt0) cc_final: 0.6048 (pm20) REVERT: D 253 MET cc_start: 0.7944 (pmm) cc_final: 0.7723 (pmm) REVERT: C 441 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7438 (tm-30) REVERT: C 572 LEU cc_start: 0.9177 (mm) cc_final: 0.8966 (mm) REVERT: C 594 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7191 (tm-30) REVERT: C 612 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8258 (tp30) REVERT: B 237 ASP cc_start: 0.8740 (t70) cc_final: 0.8523 (t70) REVERT: B 271 MET cc_start: 0.9317 (mmt) cc_final: 0.9058 (mmt) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1707 time to fit residues: 47.4361 Evaluate side-chains 140 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 0.0070 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN D 272 HIS D 316 HIS B 213 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12131 Z= 0.135 Angle : 0.506 7.002 16443 Z= 0.267 Chirality : 0.043 0.181 1815 Planarity : 0.003 0.036 2118 Dihedral : 4.133 21.414 1617 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.08 % Allowed : 0.73 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.21), residues: 1484 helix: 0.78 (0.32), residues: 282 sheet: -0.56 (0.28), residues: 357 loop : -1.64 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 345 HIS 0.006 0.001 HIS B 213 PHE 0.017 0.001 PHE A 46 TYR 0.022 0.001 TYR A 42 ARG 0.004 0.000 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 PHE cc_start: 0.8921 (t80) cc_final: 0.8377 (t80) REVERT: A 660 ASP cc_start: 0.7893 (m-30) cc_final: 0.7555 (m-30) REVERT: D 85 GLN cc_start: 0.7237 (mt0) cc_final: 0.6087 (mp10) REVERT: D 86 LEU cc_start: 0.7943 (mp) cc_final: 0.7197 (tt) REVERT: D 153 ASP cc_start: 0.7427 (t0) cc_final: 0.6781 (p0) REVERT: D 179 GLU cc_start: 0.6492 (pt0) cc_final: 0.6162 (pm20) REVERT: D 253 MET cc_start: 0.7954 (pmm) cc_final: 0.7726 (pmm) REVERT: C 441 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7589 (tm-30) REVERT: C 570 THR cc_start: 0.9535 (p) cc_final: 0.9256 (p) REVERT: C 572 LEU cc_start: 0.9141 (mm) cc_final: 0.8919 (mm) REVERT: C 594 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7266 (tm-30) REVERT: C 612 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8170 (tp30) REVERT: B 206 LEU cc_start: 0.9081 (tp) cc_final: 0.8775 (mt) REVERT: B 243 ASP cc_start: 0.8280 (t0) cc_final: 0.7574 (t0) REVERT: B 252 MET cc_start: 0.9256 (ttm) cc_final: 0.8875 (ttm) REVERT: B 310 ASP cc_start: 0.8078 (m-30) cc_final: 0.7799 (m-30) REVERT: B 319 ILE cc_start: 0.8774 (mm) cc_final: 0.8309 (mm) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1978 time to fit residues: 56.4823 Evaluate side-chains 144 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12131 Z= 0.254 Angle : 0.591 8.500 16443 Z= 0.313 Chirality : 0.045 0.195 1815 Planarity : 0.004 0.037 2118 Dihedral : 4.532 25.111 1617 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.42 (0.21), residues: 1484 helix: 0.56 (0.31), residues: 288 sheet: -0.65 (0.27), residues: 384 loop : -1.68 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 345 HIS 0.019 0.001 HIS B 213 PHE 0.024 0.002 PHE A 312 TYR 0.021 0.002 TYR A 42 ARG 0.005 0.001 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.431 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: A 539 MET cc_start: 0.8782 (mmm) cc_final: 0.8549 (mmt) REVERT: A 660 ASP cc_start: 0.7991 (m-30) cc_final: 0.7721 (m-30) REVERT: D 38 HIS cc_start: 0.7063 (t70) cc_final: 0.6700 (t70) REVERT: D 179 GLU cc_start: 0.6428 (pt0) cc_final: 0.6120 (pm20) REVERT: D 253 MET cc_start: 0.7813 (pmm) cc_final: 0.7469 (pmm) REVERT: C 441 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7679 (tm-30) REVERT: B 252 MET cc_start: 0.9320 (ttm) cc_final: 0.8885 (ttt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1772 time to fit residues: 46.5273 Evaluate side-chains 130 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 91 optimal weight: 20.0000 chunk 72 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.6917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12131 Z= 0.147 Angle : 0.550 11.341 16443 Z= 0.285 Chirality : 0.043 0.181 1815 Planarity : 0.003 0.035 2118 Dihedral : 4.299 22.549 1617 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.21 (0.21), residues: 1484 helix: 0.74 (0.31), residues: 283 sheet: -0.32 (0.29), residues: 342 loop : -1.60 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 345 HIS 0.004 0.001 HIS B 160 PHE 0.022 0.001 PHE D 152 TYR 0.022 0.001 TYR A 42 ARG 0.004 0.000 ARG D 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 638 PHE cc_start: 0.8957 (t80) cc_final: 0.8387 (t80) REVERT: A 660 ASP cc_start: 0.7948 (m-30) cc_final: 0.7670 (m-30) REVERT: D 153 ASP cc_start: 0.7526 (t0) cc_final: 0.6650 (p0) REVERT: D 253 MET cc_start: 0.7833 (pmm) cc_final: 0.7569 (pmm) REVERT: D 319 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8115 (tt0) REVERT: C 84 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 441 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7629 (tm-30) REVERT: C 594 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7336 (tm-30) REVERT: C 614 MET cc_start: 0.8946 (mmm) cc_final: 0.8642 (mmt) REVERT: B 206 LEU cc_start: 0.9049 (tp) cc_final: 0.8793 (mt) REVERT: B 243 ASP cc_start: 0.8198 (t0) cc_final: 0.7602 (t0) REVERT: B 252 MET cc_start: 0.9436 (ttm) cc_final: 0.9023 (ttt) REVERT: B 296 PHE cc_start: 0.8200 (m-80) cc_final: 0.7818 (m-80) REVERT: B 319 ILE cc_start: 0.8821 (mm) cc_final: 0.8341 (mm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1822 time to fit residues: 48.5356 Evaluate side-chains 138 residues out of total 1387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 86 optimal weight: 0.0010 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN D 272 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.128509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097291 restraints weight = 29919.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099815 restraints weight = 16901.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.101469 restraints weight = 11422.600| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12131 Z= 0.144 Angle : 0.525 7.256 16443 Z= 0.274 Chirality : 0.043 0.175 1815 Planarity : 0.003 0.035 2118 Dihedral : 4.184 22.501 1617 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -1.11 (0.22), residues: 1484 helix: 0.90 (0.31), residues: 283 sheet: -0.38 (0.27), residues: 378 loop : -1.53 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 345 HIS 0.004 0.001 HIS B 160 PHE 0.026 0.001 PHE A 312 TYR 0.020 0.001 TYR B 124 ARG 0.004 0.000 ARG D 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.52 seconds wall clock time: 46 minutes 54.33 seconds (2814.33 seconds total)