Starting phenix.real_space_refine on Wed Nov 15 03:54:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shk_25127/11_2023/7shk_25127.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shk_25127/11_2023/7shk_25127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shk_25127/11_2023/7shk_25127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shk_25127/11_2023/7shk_25127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shk_25127/11_2023/7shk_25127.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7shk_25127/11_2023/7shk_25127.pdb" } resolution = 3.1 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= 1.000 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 4 6.06 5 S 82 5.16 5 C 6689 2.51 5 N 1761 2.21 5 O 1949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 143": "OD1" <-> "OD2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 258": "OE1" <-> "OE2" Residue "L PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 324": "OE1" <-> "OE2" Residue "L ASP 357": "OD1" <-> "OD2" Residue "L TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 10485 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 6100 Classifications: {'peptide': 744} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 723} Chain: "B" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 770 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "C" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2228 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 264} Chain: "R" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9419 SG CYS L 356 45.915 26.856 135.856 1.00 90.44 S ATOM 9433 SG CYS L 358 47.271 23.972 137.907 1.00 94.83 S ATOM 9746 SG CYS L 400 49.660 26.302 136.190 1.00 90.30 S ATOM 9773 SG CYS L 404 47.414 23.969 134.046 1.00 93.77 S ATOM 10111 SG CYS R 53 41.482 36.616 58.649 1.00265.35 S ATOM 10131 SG CYS R 56 43.220 33.958 60.783 1.00263.20 S ATOM 10157 SG CYS R 68 42.592 33.335 57.039 1.00270.24 S ATOM 10043 SG CYS R 42 37.367 38.588 51.529 1.00257.20 S ATOM 10062 SG CYS R 45 39.843 39.804 53.987 1.00256.03 S ATOM 10275 SG CYS R 83 38.002 37.462 55.913 1.00272.17 S ATOM 10207 SG CYS R 75 30.111 32.093 44.690 1.00279.86 S ATOM 10367 SG CYS R 94 28.909 35.299 46.659 1.00288.30 S Time building chain proxies: 5.74, per 1000 atoms: 0.55 Number of scatterers: 10485 At special positions: 0 Unit cell: (113.025, 101.475, 177.375, 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 4 29.99 S 82 16.00 O 1949 8.00 N 1761 7.00 C 6689 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: 4.13 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" SG CYS L 356 " pdb="ZN ZN L 501 " - pdb=" SG CYS L 358 " pdb="ZN ZN L 501 " - pdb=" SG CYS L 400 " pdb="ZN ZN L 501 " - pdb=" SG CYS L 404 " pdb=" ZN R 200 " pdb="ZN ZN R 200 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 200 " - pdb=" SG CYS R 68 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " Number of angles added : 12 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2518 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 53.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.685A pdb=" N THR A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.709A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.694A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 155 through 172 removed outlier: 3.680A pdb=" N ILE A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.740A pdb=" N ILE A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 200 through 208 Processing helix chain 'A' and resid 208 through 230 Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 268 removed outlier: 3.803A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 274 through 287 removed outlier: 3.623A pdb=" N GLU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.948A pdb=" N ALA A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 4.666A pdb=" N HIS A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 357 Processing helix chain 'A' and resid 361 through 377 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.704A pdb=" N VAL A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 446 removed outlier: 3.879A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.972A pdb=" N GLU A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 497 removed outlier: 4.180A pdb=" N THR A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 548 removed outlier: 4.552A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 removed outlier: 3.910A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 606 through 620 removed outlier: 3.792A pdb=" N VAL A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 692 Processing helix chain 'A' and resid 696 through 708 Processing helix chain 'A' and resid 714 through 728 Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.704A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.698A pdb=" N ASP B 41 " --> pdb=" O PRO B 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 83 removed outlier: 4.087A pdb=" N LYS C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'L' and resid 169 through 174 removed outlier: 3.888A pdb=" N LEU L 174 " --> pdb=" O MET L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 219 removed outlier: 3.613A pdb=" N CYS L 218 " --> pdb=" O GLU L 214 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER L 219 " --> pdb=" O VAL L 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 214 through 219' Processing helix chain 'L' and resid 220 through 225 removed outlier: 3.776A pdb=" N ARG L 223 " --> pdb=" O THR L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 246 Processing helix chain 'L' and resid 263 through 269 removed outlier: 4.339A pdb=" N GLY L 267 " --> pdb=" O PHE L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 292 removed outlier: 3.685A pdb=" N LYS L 290 " --> pdb=" O ASN L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 321 through 333 Processing helix chain 'L' and resid 343 through 352 removed outlier: 3.516A pdb=" N SER L 351 " --> pdb=" O CYS L 347 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU L 352 " --> pdb=" O GLN L 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 415 removed outlier: 3.603A pdb=" N SER L 406 " --> pdb=" O LEU L 402 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN L 407 " --> pdb=" O THR L 403 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE L 408 " --> pdb=" O CYS L 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 89 removed outlier: 3.512A pdb=" N LYS R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 506 through 513 removed outlier: 6.108A pdb=" N SER A 506 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA R 29 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN A 508 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA R 31 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR A 510 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TRP R 33 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 512 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N TRP R 35 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 506 through 513 removed outlier: 6.108A pdb=" N SER A 506 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA R 29 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN A 508 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA R 31 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR A 510 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TRP R 33 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 512 " --> pdb=" O TRP R 33 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N TRP R 35 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL R 24 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LYS A 565 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS R 26 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 593 through 595 Processing sheet with id=AA4, first strand: chain 'A' and resid 693 through 695 removed outlier: 4.158A pdb=" N LEU A 694 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR A 741 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.635A pdb=" N ALA B 73 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR B 13 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N LYS C 32 " --> pdb=" O THR B 13 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N PHE B 15 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL C 60 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS C 20 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AA7, first strand: chain 'L' and resid 135 through 138 removed outlier: 6.604A pdb=" N LEU L 136 " --> pdb=" O GLN L 158 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER L 160 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE L 138 " --> pdb=" O SER L 160 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU L 180 " --> pdb=" O ILE L 204 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP L 230 " --> pdb=" O LEU L 203 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU L 229 " --> pdb=" O LYS L 253 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU L 275 " --> pdb=" O ASP L 298 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU L 295 " --> pdb=" O THR L 381 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL L 383 " --> pdb=" O GLU L 295 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU L 297 " --> pdb=" O VAL L 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 313 through 314 removed outlier: 3.617A pdb=" N ASP L 313 " --> pdb=" O GLN L 368 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN L 368 " --> pdb=" O ASP L 313 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 354 through 355 removed outlier: 3.807A pdb=" N LYS L 354 " --> pdb=" O CYS L 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 78 through 80 Processing sheet with id=AB2, first strand: chain 'R' and resid 93 through 94 507 hydrogen bonds defined for protein. 1455 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: 3.73 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1739 1.30 - 1.43: 2669 1.43 - 1.55: 6158 1.55 - 1.68: 4 1.68 - 1.81: 125 Bond restraints: 10695 Sorted by residual: bond pdb=" C LEU L 322 " pdb=" O LEU L 322 " ideal model delta sigma weight residual 1.237 1.167 0.070 1.17e-02 7.31e+03 3.60e+01 bond pdb=" C PRO L 343 " pdb=" O PRO L 343 " ideal model delta sigma weight residual 1.233 1.167 0.066 1.19e-02 7.06e+03 3.04e+01 bond pdb=" C PRO L 321 " pdb=" O PRO L 321 " ideal model delta sigma weight residual 1.233 1.175 0.058 1.19e-02 7.06e+03 2.37e+01 bond pdb=" N PRO L 321 " pdb=" CA PRO L 321 " ideal model delta sigma weight residual 1.466 1.413 0.053 1.24e-02 6.50e+03 1.84e+01 bond pdb=" N THR L 325 " pdb=" CA THR L 325 " ideal model delta sigma weight residual 1.459 1.512 -0.053 1.23e-02 6.61e+03 1.83e+01 ... (remaining 10690 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.25: 211 105.25 - 112.43: 5423 112.43 - 119.62: 3658 119.62 - 126.80: 5047 126.80 - 133.99: 116 Bond angle restraints: 14455 Sorted by residual: angle pdb=" N ALA L 326 " pdb=" CA ALA L 326 " pdb=" C ALA L 326 " ideal model delta sigma weight residual 111.36 102.85 8.51 1.09e+00 8.42e-01 6.10e+01 angle pdb=" N ARG L 328 " pdb=" CA ARG L 328 " pdb=" C ARG L 328 " ideal model delta sigma weight residual 111.71 103.69 8.02 1.15e+00 7.56e-01 4.86e+01 angle pdb=" N MET C 105 " pdb=" CA MET C 105 " pdb=" C MET C 105 " ideal model delta sigma weight residual 111.28 104.00 7.28 1.09e+00 8.42e-01 4.46e+01 angle pdb=" N GLU C 102 " pdb=" CA GLU C 102 " pdb=" C GLU C 102 " ideal model delta sigma weight residual 111.28 104.40 6.88 1.09e+00 8.42e-01 3.98e+01 angle pdb=" C THR L 345 " pdb=" CA THR L 345 " pdb=" CB THR L 345 " ideal model delta sigma weight residual 110.88 101.16 9.72 1.57e+00 4.06e-01 3.84e+01 ... (remaining 14450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5873 17.99 - 35.98: 554 35.98 - 53.97: 98 53.97 - 71.96: 17 71.96 - 89.96: 4 Dihedral angle restraints: 6546 sinusoidal: 2683 harmonic: 3863 Sorted by residual: dihedral pdb=" CA MET A 605 " pdb=" C MET A 605 " pdb=" N ASN A 606 " pdb=" CA ASN A 606 " ideal model delta harmonic sigma weight residual 180.00 -154.05 -25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" C TYR L 337 " pdb=" N TYR L 337 " pdb=" CA TYR L 337 " pdb=" CB TYR L 337 " ideal model delta harmonic sigma weight residual -122.60 -110.54 -12.06 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" C THR L 345 " pdb=" N THR L 345 " pdb=" CA THR L 345 " pdb=" CB THR L 345 " ideal model delta harmonic sigma weight residual -122.00 -110.67 -11.33 0 2.50e+00 1.60e-01 2.05e+01 ... (remaining 6543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1351 0.056 - 0.112: 234 0.112 - 0.168: 32 0.168 - 0.225: 6 0.225 - 0.281: 8 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CB VAL A 665 " pdb=" CA VAL A 665 " pdb=" CG1 VAL A 665 " pdb=" CG2 VAL A 665 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA TYR L 337 " pdb=" N TYR L 337 " pdb=" C TYR L 337 " pdb=" CB TYR L 337 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ILE L 335 " pdb=" N ILE L 335 " pdb=" C ILE L 335 " pdb=" CB ILE L 335 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1628 not shown) Planarity restraints: 1838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 68 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO B 69 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO B 69 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 69 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 348 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLN L 348 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN L 348 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP L 349 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 104 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C LEU C 104 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU C 104 " 0.020 2.00e-02 2.50e+03 pdb=" N MET C 105 " 0.018 2.00e-02 2.50e+03 ... (remaining 1835 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 895 2.74 - 3.28: 11163 3.28 - 3.82: 17362 3.82 - 4.36: 20504 4.36 - 4.90: 34403 Nonbonded interactions: 84327 Sorted by model distance: nonbonded pdb=" OH TYR A 298 " pdb=" OD2 ASP A 361 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR A 407 " pdb=" OE1 GLU A 410 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASN L 287 " pdb=" NZ LYS L 290 " model vdw 2.244 2.520 nonbonded pdb=" O VAL A 184 " pdb=" OG SER A 187 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP A 396 " pdb=" NH1 ARG A 442 " model vdw 2.269 2.520 ... (remaining 84322 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.740 Construct map_model_manager: 0.000 Extract box with map and model: 6.790 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 32.740 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.005 0.107 10695 Z= 0.326 Angle : 0.819 9.725 14455 Z= 0.495 Chirality : 0.047 0.281 1631 Planarity : 0.006 0.109 1838 Dihedral : 14.182 89.956 4028 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.25 % Allowed : 0.68 % Favored : 99.07 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 3.92 % 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: -0.23 (0.24), residues: 1285 helix: 0.62 (0.21), residues: 603 sheet: -0.44 (0.63), residues: 77 loop : -0.86 (0.26), residues: 605 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 222 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 225 average time/residue: 0.3044 time to fit residues: 93.7401 Evaluate side-chains 171 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1827 time to fit residues: 2.2950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN A 317 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 GLN C 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10695 Z= 0.291 Angle : 0.657 8.322 14455 Z= 0.339 Chirality : 0.043 0.168 1631 Planarity : 0.005 0.073 1838 Dihedral : 4.540 27.798 1401 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.46 % Allowed : 8.75 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.10 (0.24), residues: 1285 helix: 0.87 (0.21), residues: 613 sheet: -0.76 (0.60), residues: 86 loop : -0.92 (0.26), residues: 586 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 204 average time/residue: 0.2130 time to fit residues: 62.5409 Evaluate side-chains 186 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1085 time to fit residues: 4.9983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 95 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 92 optimal weight: 0.0670 overall best weight: 0.4500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 313 GLN A 317 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10695 Z= 0.176 Angle : 0.595 9.323 14455 Z= 0.301 Chirality : 0.041 0.213 1631 Planarity : 0.004 0.061 1838 Dihedral : 4.364 29.788 1401 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.02 % Allowed : 12.49 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.23 (0.24), residues: 1285 helix: 1.16 (0.21), residues: 606 sheet: -0.59 (0.61), residues: 86 loop : -0.76 (0.26), residues: 593 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 198 average time/residue: 0.2344 time to fit residues: 66.4272 Evaluate side-chains 177 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0944 time to fit residues: 2.4575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.0670 chunk 86 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 115 optimal weight: 0.5980 chunk 122 optimal weight: 0.2980 chunk 60 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.2518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10695 Z= 0.167 Angle : 0.590 8.722 14455 Z= 0.299 Chirality : 0.040 0.167 1631 Planarity : 0.004 0.055 1838 Dihedral : 4.249 28.812 1401 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.19 % Allowed : 13.51 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.31 (0.24), residues: 1285 helix: 1.17 (0.21), residues: 612 sheet: -0.58 (0.53), residues: 108 loop : -0.64 (0.27), residues: 565 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 189 average time/residue: 0.2407 time to fit residues: 65.3158 Evaluate side-chains 169 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1081 time to fit residues: 2.7096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.0050 chunk 104 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 30 optimal weight: 0.0670 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10695 Z= 0.168 Angle : 0.583 7.992 14455 Z= 0.296 Chirality : 0.040 0.184 1631 Planarity : 0.004 0.052 1838 Dihedral : 4.179 27.816 1401 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.68 % Allowed : 15.21 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.27 (0.24), residues: 1285 helix: 1.10 (0.21), residues: 619 sheet: -0.54 (0.54), residues: 108 loop : -0.66 (0.27), residues: 558 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.569 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 184 average time/residue: 0.2235 time to fit residues: 59.3789 Evaluate side-chains 168 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1131 time to fit residues: 2.3686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10695 Z= 0.183 Angle : 0.612 13.087 14455 Z= 0.305 Chirality : 0.040 0.163 1631 Planarity : 0.004 0.050 1838 Dihedral : 4.215 27.548 1401 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.02 % Allowed : 15.72 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.32 (0.24), residues: 1285 helix: 1.13 (0.21), residues: 612 sheet: -0.58 (0.54), residues: 108 loop : -0.58 (0.27), residues: 565 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 183 average time/residue: 0.2392 time to fit residues: 63.0686 Evaluate side-chains 176 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1047 time to fit residues: 2.9772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 0.0570 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10695 Z= 0.175 Angle : 0.608 9.812 14455 Z= 0.300 Chirality : 0.040 0.143 1631 Planarity : 0.004 0.049 1838 Dihedral : 4.164 27.184 1401 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.51 % Allowed : 17.08 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.36 (0.24), residues: 1285 helix: 1.17 (0.21), residues: 608 sheet: -0.59 (0.54), residues: 108 loop : -0.54 (0.28), residues: 569 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 176 average time/residue: 0.2404 time to fit residues: 59.9631 Evaluate side-chains 169 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0982 time to fit residues: 2.3762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10695 Z= 0.193 Angle : 0.644 11.281 14455 Z= 0.318 Chirality : 0.041 0.210 1631 Planarity : 0.004 0.048 1838 Dihedral : 4.210 27.168 1401 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.25 % Allowed : 17.93 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.28 (0.24), residues: 1285 helix: 1.08 (0.21), residues: 611 sheet: -0.59 (0.54), residues: 108 loop : -0.58 (0.27), residues: 566 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 175 average time/residue: 0.2354 time to fit residues: 59.5719 Evaluate side-chains 169 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0988 time to fit residues: 2.2224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.0670 chunk 117 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.0070 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 113 optimal weight: 0.1980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 313 GLN A 317 ASN A 459 ASN A 508 GLN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10695 Z= 0.175 Angle : 0.654 10.529 14455 Z= 0.322 Chirality : 0.040 0.197 1631 Planarity : 0.004 0.048 1838 Dihedral : 4.231 28.032 1401 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.34 % Allowed : 18.01 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.32 (0.24), residues: 1285 helix: 1.12 (0.21), residues: 609 sheet: -0.58 (0.54), residues: 108 loop : -0.55 (0.28), residues: 568 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 176 average time/residue: 0.2356 time to fit residues: 59.5948 Evaluate side-chains 170 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.403 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0976 time to fit residues: 2.1473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 4.9990 chunk 120 optimal weight: 0.1980 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 chunk 61 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN A 264 HIS A 459 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10695 Z= 0.183 Angle : 0.669 10.488 14455 Z= 0.332 Chirality : 0.041 0.193 1631 Planarity : 0.004 0.048 1838 Dihedral : 4.223 25.911 1401 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.25 % Allowed : 18.52 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.24 (0.24), residues: 1285 helix: 1.06 (0.21), residues: 616 sheet: -0.46 (0.57), residues: 97 loop : -0.68 (0.27), residues: 572 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2570 Ramachandran restraints generated. 1285 Oldfield, 0 Emsley, 1285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 170 average time/residue: 0.2259 time to fit residues: 55.2428 Evaluate side-chains 166 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1152 time to fit residues: 2.1663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.0970 chunk 107 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 chunk 100 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.2972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN A 264 HIS A 459 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.133114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.106397 restraints weight = 22284.593| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.03 r_work: 0.3860 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10695 Z= 0.177 Angle : 0.686 10.881 14455 Z= 0.340 Chirality : 0.041 0.196 1631 Planarity : 0.004 0.048 1838 Dihedral : 4.255 24.831 1401 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.08 % Allowed : 18.95 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.25 (0.24), residues: 1285 helix: 1.07 (0.21), residues: 616 sheet: -0.48 (0.57), residues: 97 loop : -0.66 (0.27), residues: 572 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2797.48 seconds wall clock time: 51 minutes 33.69 seconds (3093.69 seconds total)