Starting phenix.real_space_refine on Fri Sep 27 18:56:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl6_25192/09_2024/7sl6_25192_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl6_25192/09_2024/7sl6_25192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl6_25192/09_2024/7sl6_25192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl6_25192/09_2024/7sl6_25192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl6_25192/09_2024/7sl6_25192_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl6_25192/09_2024/7sl6_25192_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3460 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 112 5.16 5 C 8892 2.51 5 N 2406 2.21 5 O 2594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14004 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6623 Classifications: {'peptide': 819} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 773} Chain breaks: 6 Chain: "B" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6623 Classifications: {'peptide': 819} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 773} Chain breaks: 6 Chain: "E" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 217 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "F" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 217 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 162 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 8.24, per 1000 atoms: 0.59 Number of scatterers: 14004 At special positions: 0 Unit cell: (147.96, 100.44, 173.88, 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 112 16.00 O 2594 8.00 N 2406 7.00 C 8892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.04 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.16 Conformation dependent library (CDL) restraints added in 1.7 seconds 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 33 sheets defined 18.5% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.788A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.954A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.653A pdb=" N ARG A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.915A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.805A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.735A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.631A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 378 through 382 removed outlier: 4.480A pdb=" N PHE A 381 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 382 " --> pdb=" O LEU A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 382' Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.592A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.654A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.597A pdb=" N PHE A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 716 removed outlier: 3.500A pdb=" N ILE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 695 " --> pdb=" O ASP A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.960A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 3.922A pdb=" N ARG B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 48' Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.644A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.930A pdb=" N CYS B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.797A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 318 removed outlier: 3.737A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 315 through 318' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.647A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.490A pdb=" N PHE B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.602A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.621A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.673A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 640 through 645' Processing helix chain 'B' and resid 690 through 716 removed outlier: 3.751A pdb=" N LEU B 695 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'E' and resid 8 through 19 Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.714A pdb=" N VAL F 12 " --> pdb=" O GLY F 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 14 through 20 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 14 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.964A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE A 145 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU A 120 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A 147 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.603A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.507A pdb=" N ASN A 337 " --> pdb=" O CYS A 312 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321 removed outlier: 7.160A pdb=" N LEU A 368 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU A 403 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 370 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 479 through 480 Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.692A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 567 " --> pdb=" O PHE A 506 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 508 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 601 through 607 removed outlier: 6.274A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 764 removed outlier: 3.697A pdb=" N GLU A 762 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 632 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 821 through 824 Processing sheet with id=AB7, first strand: chain 'A' and resid 858 through 864 removed outlier: 3.838A pdb=" N LEU A 846 " --> pdb=" O THR A 891 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 12 through 14 removed outlier: 6.977A pdb=" N GLN B 34 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 63 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 36 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG B 65 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 145 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU B 120 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU B 147 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.566A pdb=" N VAL B 179 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 182 through 184 removed outlier: 6.463A pdb=" N HIS B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.626A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 246 through 248 Processing sheet with id=AC5, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.510A pdb=" N ASN B 337 " --> pdb=" O CYS B 312 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 319 through 321 removed outlier: 7.130A pdb=" N LEU B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU B 403 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 370 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD1, first strand: chain 'B' and resid 479 through 480 Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.517A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 567 " --> pdb=" O PHE B 506 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.704A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.679A pdb=" N GLU B 762 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD6, first strand: chain 'B' and resid 858 through 864 removed outlier: 3.891A pdb=" N LEU B 846 " --> pdb=" O THR B 891 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 873 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: 4.78 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4587 1.34 - 1.46: 3346 1.46 - 1.58: 6277 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14346 Sorted by residual: bond pdb=" CA TYR B 581 " pdb=" CB TYR B 581 " ideal model delta sigma weight residual 1.530 1.553 -0.022 1.69e-02 3.50e+03 1.75e+00 bond pdb=" CG GLU A 697 " pdb=" CD GLU A 697 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.30e+00 bond pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.26e+00 bond pdb=" CG GLU E 13 " pdb=" CD GLU E 13 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" C SER A 792 " pdb=" N PRO A 793 " ideal model delta sigma weight residual 1.340 1.369 -0.029 2.76e-02 1.31e+03 1.10e+00 ... (remaining 14341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 19253 2.33 - 4.66: 172 4.66 - 6.98: 13 6.98 - 9.31: 4 9.31 - 11.64: 2 Bond angle restraints: 19444 Sorted by residual: angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 133.18 -11.64 1.91e+00 2.74e-01 3.71e+01 angle pdb=" CA TYR B 581 " pdb=" CB TYR B 581 " pdb=" CG TYR B 581 " ideal model delta sigma weight residual 113.90 122.94 -9.04 1.80e+00 3.09e-01 2.52e+01 angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 130.92 -9.38 1.91e+00 2.74e-01 2.41e+01 angle pdb=" N TYR A 581 " pdb=" CA TYR A 581 " pdb=" CB TYR A 581 " ideal model delta sigma weight residual 110.49 118.58 -8.09 1.69e+00 3.50e-01 2.29e+01 angle pdb=" N GLU A 697 " pdb=" CA GLU A 697 " pdb=" CB GLU A 697 " ideal model delta sigma weight residual 110.28 115.75 -5.47 1.55e+00 4.16e-01 1.25e+01 ... (remaining 19439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 7844 17.36 - 34.72: 695 34.72 - 52.07: 124 52.07 - 69.43: 27 69.43 - 86.79: 14 Dihedral angle restraints: 8704 sinusoidal: 3638 harmonic: 5066 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 155 " pdb=" CB CYS B 155 " ideal model delta sinusoidal sigma weight residual -86.00 -150.13 64.13 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 155 " pdb=" CB CYS A 155 " ideal model delta sinusoidal sigma weight residual -86.00 -147.73 61.73 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 149.10 -56.10 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 8701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1383 0.034 - 0.068: 471 0.068 - 0.102: 161 0.102 - 0.136: 83 0.136 - 0.169: 10 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CB VAL B 572 " pdb=" CA VAL B 572 " pdb=" CG1 VAL B 572 " pdb=" CG2 VAL B 572 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CB THR B 690 " pdb=" CA THR B 690 " pdb=" OG1 THR B 690 " pdb=" CG2 THR B 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CB THR A 690 " pdb=" CA THR A 690 " pdb=" OG1 THR A 690 " pdb=" CG2 THR A 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 2105 not shown) Planarity restraints: 2514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C THR B 580 " 0.052 2.00e-02 2.50e+03 pdb=" O THR B 580 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR B 581 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 581 " 0.007 2.00e-02 2.50e+03 1.65e-02 5.43e+00 pdb=" CG TYR A 581 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 581 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 581 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 581 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 581 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 581 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 581 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 836 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 837 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 837 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 837 " -0.018 5.00e-02 4.00e+02 ... (remaining 2511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1069 2.74 - 3.28: 13867 3.28 - 3.82: 22763 3.82 - 4.36: 26995 4.36 - 4.90: 46368 Nonbonded interactions: 111062 Sorted by model distance: nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.201 3.040 nonbonded pdb=" OG SER C 12 " pdb=" OE1 GLN C 15 " model vdw 2.202 3.040 nonbonded pdb=" O ARG A 776 " pdb=" OG1 THR A 779 " model vdw 2.241 3.040 nonbonded pdb=" O GLU A 826 " pdb=" OH TYR A 910 " model vdw 2.255 3.040 nonbonded pdb=" O GLU B 826 " pdb=" OH TYR B 910 " model vdw 2.270 3.040 ... (remaining 111057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.700 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14346 Z= 0.178 Angle : 0.552 11.641 19444 Z= 0.292 Chirality : 0.043 0.169 2108 Planarity : 0.003 0.032 2514 Dihedral : 13.379 86.791 5312 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.48 % Favored : 93.29 % Rotamer: Outliers : 0.25 % Allowed : 0.25 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.21), residues: 1698 helix: 0.30 (0.37), residues: 206 sheet: 0.56 (0.32), residues: 316 loop : -0.92 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 414 HIS 0.003 0.001 HIS B 440 PHE 0.009 0.001 PHE A 381 TYR 0.038 0.001 TYR A 581 ARG 0.007 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 58 average time/residue: 0.2652 time to fit residues: 24.3231 Evaluate side-chains 39 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 0.0470 chunk 154 optimal weight: 7.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 GLN A 867 HIS B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14346 Z= 0.268 Angle : 0.565 7.192 19444 Z= 0.300 Chirality : 0.044 0.166 2108 Planarity : 0.004 0.030 2514 Dihedral : 4.460 18.173 1894 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.38 % Allowed : 4.87 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1698 helix: 0.49 (0.38), residues: 210 sheet: 0.57 (0.30), residues: 338 loop : -0.91 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 834 HIS 0.005 0.001 HIS B 440 PHE 0.013 0.001 PHE A 381 TYR 0.020 0.001 TYR B 847 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 1.647 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.2256 time to fit residues: 19.7468 Evaluate side-chains 44 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 128 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 154 optimal weight: 0.3980 chunk 167 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14346 Z= 0.222 Angle : 0.531 8.459 19444 Z= 0.279 Chirality : 0.043 0.174 2108 Planarity : 0.003 0.032 2514 Dihedral : 4.432 18.526 1894 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.57 % Allowed : 8.29 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.21), residues: 1698 helix: 0.61 (0.38), residues: 212 sheet: 0.52 (0.30), residues: 338 loop : -0.88 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 634 HIS 0.004 0.001 HIS A 831 PHE 0.011 0.001 PHE B 381 TYR 0.027 0.001 TYR A 847 ARG 0.004 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 1.650 Fit side-chains REVERT: A 300 MET cc_start: 0.7843 (tpp) cc_final: 0.7611 (tpp) REVERT: B 300 MET cc_start: 0.7868 (tpp) cc_final: 0.7621 (tpp) REVERT: B 834 TRP cc_start: 0.3027 (p90) cc_final: 0.2441 (p90) outliers start: 9 outliers final: 5 residues processed: 50 average time/residue: 0.2241 time to fit residues: 19.0687 Evaluate side-chains 46 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 155 optimal weight: 0.1980 chunk 164 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 111 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS A 295 ASN B 90 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 295 ASN B 612 GLN ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 14346 Z= 0.572 Angle : 0.766 8.759 19444 Z= 0.397 Chirality : 0.049 0.186 2108 Planarity : 0.005 0.049 2514 Dihedral : 5.512 18.065 1894 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.89 % Favored : 91.05 % Rotamer: Outliers : 1.33 % Allowed : 11.33 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.32 (0.20), residues: 1698 helix: -0.59 (0.33), residues: 236 sheet: 0.16 (0.29), residues: 340 loop : -1.34 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 634 HIS 0.010 0.002 HIS A 185 PHE 0.027 0.002 PHE B 381 TYR 0.018 0.002 TYR B 507 ARG 0.005 0.001 ARG B 865 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 45 time to evaluate : 1.835 Fit side-chains REVERT: A 651 LYS cc_start: 0.8106 (mttt) cc_final: 0.7448 (ptmm) REVERT: B 651 LYS cc_start: 0.8314 (mttt) cc_final: 0.7706 (ptmm) outliers start: 21 outliers final: 14 residues processed: 66 average time/residue: 0.2181 time to fit residues: 24.1592 Evaluate side-chains 54 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14346 Z= 0.166 Angle : 0.552 10.363 19444 Z= 0.286 Chirality : 0.043 0.170 2108 Planarity : 0.003 0.035 2514 Dihedral : 4.787 20.805 1894 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.07 % Favored : 93.88 % Rotamer: Outliers : 0.95 % Allowed : 12.78 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1698 helix: 0.19 (0.36), residues: 224 sheet: 0.06 (0.29), residues: 362 loop : -0.95 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 414 HIS 0.004 0.001 HIS A 831 PHE 0.012 0.001 PHE A 707 TYR 0.016 0.001 TYR B 581 ARG 0.003 0.000 ARG A 782 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: B 634 TRP cc_start: 0.7610 (OUTLIER) cc_final: 0.7240 (m-90) outliers start: 15 outliers final: 8 residues processed: 55 average time/residue: 0.2268 time to fit residues: 21.1117 Evaluate side-chains 45 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 76 optimal weight: 0.0040 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14346 Z= 0.152 Angle : 0.524 11.678 19444 Z= 0.272 Chirality : 0.043 0.173 2108 Planarity : 0.003 0.032 2514 Dihedral : 4.477 26.042 1894 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.33 % Allowed : 13.42 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.21), residues: 1698 helix: 0.29 (0.37), residues: 224 sheet: 0.34 (0.29), residues: 352 loop : -0.93 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 834 HIS 0.004 0.001 HIS A 831 PHE 0.013 0.001 PHE A 574 TYR 0.029 0.001 TYR A 581 ARG 0.003 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 41 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.8102 (mmm) cc_final: 0.7853 (mmm) REVERT: A 634 TRP cc_start: 0.7325 (OUTLIER) cc_final: 0.6981 (m-90) REVERT: A 812 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7717 (mmmt) REVERT: B 634 TRP cc_start: 0.7579 (OUTLIER) cc_final: 0.7251 (m-90) outliers start: 21 outliers final: 10 residues processed: 60 average time/residue: 0.2506 time to fit residues: 24.2963 Evaluate side-chains 52 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 812 LYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 138 optimal weight: 0.0020 chunk 91 optimal weight: 6.9990 chunk 163 optimal weight: 0.0070 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.9010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 550 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14346 Z= 0.209 Angle : 0.525 8.389 19444 Z= 0.271 Chirality : 0.043 0.169 2108 Planarity : 0.003 0.033 2514 Dihedral : 4.484 20.317 1894 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.54 % Favored : 93.40 % Rotamer: Outliers : 1.20 % Allowed : 13.42 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1698 helix: 0.34 (0.37), residues: 224 sheet: 0.41 (0.29), residues: 362 loop : -0.91 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 634 HIS 0.004 0.001 HIS A 831 PHE 0.014 0.001 PHE A 778 TYR 0.015 0.001 TYR B 581 ARG 0.002 0.000 ARG B 776 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 38 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.8198 (mmm) cc_final: 0.7977 (mmm) REVERT: A 634 TRP cc_start: 0.7346 (OUTLIER) cc_final: 0.6960 (m-90) REVERT: A 812 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7701 (mmmt) REVERT: B 634 TRP cc_start: 0.7605 (OUTLIER) cc_final: 0.7254 (m-90) outliers start: 19 outliers final: 13 residues processed: 56 average time/residue: 0.2256 time to fit residues: 21.2029 Evaluate side-chains 53 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 37 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 812 LYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 128 optimal weight: 0.0670 chunk 149 optimal weight: 9.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14346 Z= 0.160 Angle : 0.512 8.142 19444 Z= 0.262 Chirality : 0.042 0.167 2108 Planarity : 0.003 0.032 2514 Dihedral : 4.363 21.126 1894 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.65 % Favored : 93.29 % Rotamer: Outliers : 1.46 % Allowed : 13.42 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1698 helix: 0.36 (0.37), residues: 224 sheet: 0.45 (0.29), residues: 354 loop : -0.90 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 634 HIS 0.004 0.001 HIS A 831 PHE 0.012 0.001 PHE A 567 TYR 0.017 0.001 TYR B 851 ARG 0.002 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 38 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 634 TRP cc_start: 0.7316 (OUTLIER) cc_final: 0.6991 (m-90) REVERT: A 812 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7698 (mmmt) REVERT: B 634 TRP cc_start: 0.7601 (OUTLIER) cc_final: 0.7267 (m-90) outliers start: 23 outliers final: 15 residues processed: 60 average time/residue: 0.2296 time to fit residues: 22.9594 Evaluate side-chains 55 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 37 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 812 LYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 144 optimal weight: 0.2980 chunk 100 optimal weight: 0.0970 chunk 161 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14346 Z= 0.206 Angle : 0.534 8.134 19444 Z= 0.272 Chirality : 0.043 0.168 2108 Planarity : 0.003 0.033 2514 Dihedral : 4.408 21.017 1894 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.89 % Favored : 93.05 % Rotamer: Outliers : 1.39 % Allowed : 13.61 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1698 helix: 0.36 (0.37), residues: 224 sheet: 0.46 (0.29), residues: 352 loop : -0.90 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 634 HIS 0.004 0.001 HIS A 831 PHE 0.011 0.001 PHE B 567 TYR 0.019 0.001 TYR B 581 ARG 0.002 0.000 ARG B 776 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 38 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 634 TRP cc_start: 0.7360 (OUTLIER) cc_final: 0.6972 (m-90) REVERT: A 812 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7709 (mmmt) REVERT: B 634 TRP cc_start: 0.7611 (OUTLIER) cc_final: 0.7260 (m-90) outliers start: 22 outliers final: 15 residues processed: 58 average time/residue: 0.2208 time to fit residues: 21.7475 Evaluate side-chains 55 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 37 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 812 LYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 0.0020 chunk 134 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14346 Z= 0.212 Angle : 0.552 16.948 19444 Z= 0.277 Chirality : 0.044 0.389 2108 Planarity : 0.003 0.032 2514 Dihedral : 4.429 19.818 1894 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.83 % Favored : 93.11 % Rotamer: Outliers : 1.20 % Allowed : 13.92 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.21), residues: 1698 helix: 0.31 (0.36), residues: 226 sheet: 0.46 (0.29), residues: 352 loop : -0.93 (0.20), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 634 HIS 0.004 0.001 HIS A 831 PHE 0.011 0.001 PHE B 567 TYR 0.025 0.001 TYR B 581 ARG 0.002 0.000 ARG B 776 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3396 Ramachandran restraints generated. 1698 Oldfield, 0 Emsley, 1698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 37 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 634 TRP cc_start: 0.7408 (OUTLIER) cc_final: 0.7032 (m-90) REVERT: B 11 MET cc_start: 0.8288 (pmm) cc_final: 0.8027 (pmm) REVERT: B 634 TRP cc_start: 0.7647 (OUTLIER) cc_final: 0.7286 (m-90) outliers start: 19 outliers final: 17 residues processed: 55 average time/residue: 0.2078 time to fit residues: 19.9089 Evaluate side-chains 55 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 36 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 687 CYS Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 803 VAL Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain F residue 13 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.063385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045557 restraints weight = 72551.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.046659 restraints weight = 41907.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047362 restraints weight = 29809.033| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14346 Z= 0.258 Angle : 0.563 14.987 19444 Z= 0.285 Chirality : 0.044 0.322 2108 Planarity : 0.003 0.033 2514 Dihedral : 4.550 19.409 1894 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.42 % Favored : 92.52 % Rotamer: Outliers : 1.20 % Allowed : 13.99 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1698 helix: 0.31 (0.37), residues: 224 sheet: 0.25 (0.28), residues: 362 loop : -0.90 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 634 HIS 0.004 0.001 HIS A 831 PHE 0.012 0.001 PHE A 778 TYR 0.022 0.001 TYR B 581 ARG 0.003 0.000 ARG B 776 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2235.08 seconds wall clock time: 41 minutes 23.77 seconds (2483.77 seconds total)