Starting phenix.real_space_refine on Mon Aug 25 21:54:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqb_37737/08_2025/8wqb_37737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqb_37737/08_2025/8wqb_37737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wqb_37737/08_2025/8wqb_37737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqb_37737/08_2025/8wqb_37737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wqb_37737/08_2025/8wqb_37737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqb_37737/08_2025/8wqb_37737.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.017 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 6261 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 182 5.16 5 C 16611 2.51 5 N 4551 2.21 5 O 4905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26255 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "H" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 618 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 5947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5947 Classifications: {'peptide': 725} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 705} Chain breaks: 1 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "K" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 126 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain breaks: 1 Chain: "E" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 703 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "I" 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} Chain: "E" 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 7735 SG CYS I 53 103.659 99.167 73.146 1.00 33.05 S ATOM 7758 SG CYS I 56 100.393 100.093 75.291 1.00 35.63 S ATOM 7786 SG CYS I 68 102.200 102.733 73.158 1.00 41.56 S ATOM 7649 SG CYS I 42 106.908 100.807 67.043 1.00 41.43 S ATOM 7668 SG CYS I 45 105.382 97.346 67.872 1.00 36.76 S ATOM 7904 SG CYS I 83 107.476 99.182 70.511 1.00 41.10 S ATOM 7836 SG CYS I 75 115.460 110.314 62.975 1.00 52.57 S ATOM 8000 SG CYS I 94 116.994 107.706 64.380 1.00 53.00 S ATOM 20888 SG CYS E 53 113.543 39.862 57.765 1.00 47.67 S ATOM 20911 SG CYS E 56 117.289 39.079 58.168 1.00 56.45 S ATOM 20995 SG CYS E 68 115.317 40.503 61.124 1.00 52.68 S ATOM 20802 SG CYS E 42 106.645 43.331 58.516 1.00 23.20 S ATOM 20821 SG CYS E 45 107.952 40.098 56.989 1.00 23.41 S ATOM 21113 SG CYS E 83 110.063 42.724 56.845 1.00 32.42 S ATOM 21045 SG CYS E 75 102.292 55.377 58.301 1.00 12.95 S ATOM 21209 SG CYS E 94 102.538 52.655 55.474 1.00 11.46 S Time building chain proxies: 5.14, per 1000 atoms: 0.20 Number of scatterers: 26255 At special positions: 0 Unit cell: (145.14, 166.46, 201.72, 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 6 29.99 S 182 16.00 O 4905 8.00 N 4551 7.00 C 16611 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 - 3.00 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: 1.74 Conformation dependent library (CDL) restraints added in 999.9 milliseconds Enol-peptide restraints added in 1.7 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 200 " pdb="ZN ZN E 200 " - pdb=" ND1 HIS E 82 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 56 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 68 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 53 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 45 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 83 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 42 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 94 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 75 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 77 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" ND1 HIS I 82 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 68 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 56 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 53 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 80 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 45 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 83 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 94 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 77 " Number of angles added : 12 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6282 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 15 sheets defined 61.7% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.527A pdb=" N THR A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 53 through 79 Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.500A pdb=" N MET A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 138 through 148 removed outlier: 3.745A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 172 removed outlier: 3.623A pdb=" N ILE A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.828A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 202 through 207 removed outlier: 3.506A pdb=" N PHE A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 227 removed outlier: 3.638A pdb=" N GLN A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 254 removed outlier: 3.761A pdb=" N MET A 236 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) 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 271 removed outlier: 3.563A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.731A pdb=" N VAL A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 327 removed outlier: 4.049A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 357 removed outlier: 3.748A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.539A pdb=" N ALA A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 400 removed outlier: 3.602A pdb=" N CYS A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 450 through 470 removed outlier: 3.754A pdb=" N GLU A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N TYR A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N GLU A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 469 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 497 removed outlier: 3.518A pdb=" N ARG A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 removed outlier: 3.635A pdb=" N VAL A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 542 " --> pdb=" O GLN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 580 No H-bonds generated for 'chain 'A' and resid 578 through 580' Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 587 through 590 removed outlier: 3.996A pdb=" N ASN A 590 " --> pdb=" O ALA A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.663A pdb=" N LEU A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 600 " --> pdb=" O TYR A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 600' Processing helix chain 'A' and resid 606 through 619 removed outlier: 3.924A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A 619 " --> pdb=" O LYS A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 689 removed outlier: 3.906A pdb=" N ASP A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 707 removed outlier: 3.586A pdb=" N ILE A 700 " --> pdb=" O HIS A 696 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 728 Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 39 through 47 removed outlier: 3.862A pdb=" N LYS G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 83 removed outlier: 3.717A pdb=" N LEU G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'H' and resid 23 through 36 removed outlier: 4.391A pdb=" N LEU H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE H 34 " --> pdb=" O ILE H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 49 Processing helix chain 'H' and resid 57 through 61 Processing helix chain 'I' and resid 81 through 91 Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.731A pdb=" N THR B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 53 through 79 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 138 through 152 Processing helix chain 'B' and resid 155 through 173 Processing helix chain 'B' and resid 177 through 189 removed outlier: 3.715A pdb=" N ILE B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 4.374A pdb=" N TYR B 194 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 207 through 230 Processing helix chain 'B' and resid 231 through 254 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 268 removed outlier: 3.526A pdb=" N VAL B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.584A pdb=" N LEU B 278 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 304 Processing helix chain 'B' and resid 308 through 328 Processing helix chain 'B' and resid 334 through 358 removed outlier: 3.756A pdb=" N LEU B 338 " --> pdb=" O ASN B 334 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 340 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 377 Processing helix chain 'B' and resid 386 through 400 Processing helix chain 'B' and resid 407 through 423 removed outlier: 4.109A pdb=" N THR B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 445 removed outlier: 3.583A pdb=" N PHE B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 465 Processing helix chain 'B' and resid 470 through 496 removed outlier: 4.633A pdb=" N ALA B 484 " --> pdb=" O MET B 480 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP B 485 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 547 removed outlier: 3.938A pdb=" N SER B 536 " --> pdb=" O GLU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 570 removed outlier: 3.555A pdb=" N GLY B 570 " --> pdb=" O ASN B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 567 through 570' Processing helix chain 'B' and resid 579 through 591 removed outlier: 3.727A pdb=" N VAL B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 604 Processing helix chain 'B' and resid 606 through 619 Processing helix chain 'B' and resid 661 through 692 Processing helix chain 'B' and resid 695 through 707 Processing helix chain 'B' and resid 714 through 728 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 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'D' and resid 24 through 36 Processing helix chain 'D' and resid 38 through 42 removed outlier: 4.133A pdb=" N GLU D 41 " --> pdb=" O PRO D 38 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 42 " --> pdb=" O PRO D 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 38 through 42' Processing helix chain 'J' and resid 2 through 14 removed outlier: 3.612A pdb=" N GLU J 14 " --> pdb=" O LYS J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 24 Processing helix chain 'J' and resid 28 through 37 removed outlier: 4.023A pdb=" N ILE J 32 " --> pdb=" O SER J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 56 removed outlier: 3.609A pdb=" N ASN J 56 " --> pdb=" O ILE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 69 removed outlier: 4.085A pdb=" N VAL J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 98 removed outlier: 3.636A pdb=" N CYS J 94 " --> pdb=" O THR J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 110 removed outlier: 3.559A pdb=" N VAL J 104 " --> pdb=" O HIS J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 132 removed outlier: 3.868A pdb=" N ALA J 127 " --> pdb=" O THR J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 143 removed outlier: 3.532A pdb=" N VAL J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 164 Processing helix chain 'J' and resid 166 through 176 removed outlier: 3.662A pdb=" N VAL J 170 " --> pdb=" O HIS J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 195 Processing helix chain 'J' and resid 199 through 209 Processing helix chain 'J' and resid 221 through 229 Processing helix chain 'J' and resid 231 through 239 Processing helix chain 'J' and resid 245 through 262 removed outlier: 3.581A pdb=" N ALA J 261 " --> pdb=" O GLY J 257 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN J 262 " --> pdb=" O ALA J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 284 Processing helix chain 'J' and resid 299 through 303 Processing helix chain 'J' and resid 310 through 317 Processing helix chain 'J' and resid 320 through 337 Processing helix chain 'J' and resid 344 through 357 Processing helix chain 'J' and resid 360 through 377 Processing helix chain 'J' and resid 381 through 398 removed outlier: 3.515A pdb=" N HIS J 397 " --> pdb=" O SER J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 403 through 428 Processing helix chain 'J' and resid 432 through 456 Processing helix chain 'J' and resid 460 through 476 Processing helix chain 'J' and resid 486 through 493 removed outlier: 3.813A pdb=" N ALA J 491 " --> pdb=" O LEU J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 501 through 506 Processing helix chain 'J' and resid 511 through 521 Processing helix chain 'J' and resid 534 through 541 removed outlier: 3.561A pdb=" N ILE J 538 " --> pdb=" O SER J 534 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN J 541 " --> pdb=" O HIS J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 563 Processing helix chain 'J' and resid 577 through 581 removed outlier: 4.397A pdb=" N THR J 581 " --> pdb=" O ASP J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 593 Processing helix chain 'J' and resid 596 through 609 Processing helix chain 'J' and resid 617 through 627 removed outlier: 3.986A pdb=" N GLU J 622 " --> pdb=" O ARG J 618 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE J 623 " --> pdb=" O THR J 619 " (cutoff:3.500A) Processing helix chain 'K' and resid -22 through -17 removed outlier: 3.547A pdb=" N LEU K -17 " --> pdb=" O HIS K -21 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.873A pdb=" N ALA E 58 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 17 through 23 removed outlier: 3.507A pdb=" N ALA F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 37 removed outlier: 3.845A pdb=" N ILE F 32 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 56 removed outlier: 3.588A pdb=" N ILE F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 56 " --> pdb=" O ILE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.860A pdb=" N VAL F 62 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 98 removed outlier: 3.884A pdb=" N CYS F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 110 removed outlier: 3.660A pdb=" N VAL F 104 " --> pdb=" O HIS F 100 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 107 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 132 removed outlier: 3.972A pdb=" N ALA F 127 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 142 Processing helix chain 'F' and resid 156 through 164 Processing helix chain 'F' and resid 166 through 175 removed outlier: 3.789A pdb=" N VAL F 170 " --> pdb=" O HIS F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 195 Processing helix chain 'F' and resid 199 through 209 removed outlier: 3.533A pdb=" N VAL F 203 " --> pdb=" O HIS F 199 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS F 204 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU F 206 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 229 Processing helix chain 'F' and resid 231 through 239 removed outlier: 3.507A pdb=" N LEU F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 262 removed outlier: 3.540A pdb=" N ILE F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU F 251 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA F 252 " --> pdb=" O SER F 248 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 284 removed outlier: 3.714A pdb=" N TYR F 273 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 316 Processing helix chain 'F' and resid 320 through 337 removed outlier: 3.533A pdb=" N LEU F 324 " --> pdb=" O ASP F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 357 Processing helix chain 'F' and resid 360 through 377 Processing helix chain 'F' and resid 381 through 398 Processing helix chain 'F' and resid 403 through 428 Processing helix chain 'F' and resid 432 through 456 Processing helix chain 'F' and resid 460 through 476 Processing helix chain 'F' and resid 486 through 493 removed outlier: 3.649A pdb=" N ALA F 491 " --> pdb=" O LEU F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 507 removed outlier: 3.974A pdb=" N VAL F 506 " --> pdb=" O HIS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 522 Processing helix chain 'F' and resid 534 through 540 removed outlier: 3.699A pdb=" N ILE F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 563 removed outlier: 3.953A pdb=" N SER F 558 " --> pdb=" O SER F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 593 Processing helix chain 'F' and resid 596 through 608 Processing helix chain 'F' and resid 617 through 627 removed outlier: 3.799A pdb=" N GLU F 622 " --> pdb=" O ARG F 618 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE F 623 " --> pdb=" O THR F 619 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 513 removed outlier: 4.269A pdb=" N VAL I 30 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA3, first strand: chain 'A' and resid 732 through 733 Processing sheet with id=AA4, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AA5, first strand: chain 'H' and resid 13 through 18 removed outlier: 3.564A pdb=" N GLY H 76 " --> pdb=" O TYR H 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'B' and resid 509 through 513 removed outlier: 6.028A pdb=" N TYR B 510 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TRP E 33 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 512 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N TRP E 35 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 11.827A pdb=" N ASN E 28 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N TYR B 558 " --> pdb=" O ASN E 28 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL E 30 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 509 through 513 removed outlier: 6.028A pdb=" N TYR B 510 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TRP E 33 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 512 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N TRP E 35 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 11.827A pdb=" N ASN E 28 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N TYR B 558 " --> pdb=" O ASN E 28 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL E 30 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 623 through 625 removed outlier: 3.726A pdb=" N ASN B 624 " --> pdb=" O SER B 639 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER B 639 " --> pdb=" O ASN B 624 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 731 through 733 removed outlier: 3.565A pdb=" N GLU B 732 " --> pdb=" O SER B 742 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 61 removed outlier: 5.013A pdb=" N LYS C 32 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N ASP D 17 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 40 through 42 Processing sheet with id=AB4, first strand: chain 'E' and resid 41 through 42 removed outlier: 3.626A pdb=" N ASN E 47 " --> pdb=" O CYS E 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 70 through 72 Processing sheet with id=AB6, first strand: chain 'F' and resid 40 through 42 1374 hydrogen bonds defined for protein. 4044 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: 3.60 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8670 1.34 - 1.46: 4616 1.46 - 1.58: 13187 1.58 - 1.69: 0 1.69 - 1.81: 284 Bond restraints: 26757 Sorted by residual: bond pdb=" C LEU A 308 " pdb=" N PRO A 309 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.08e-02 8.57e+03 9.75e+00 bond pdb=" CG1 ILE B 614 " pdb=" CD1 ILE B 614 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" CG1 ILE B 722 " pdb=" CD1 ILE B 722 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" CA ASP B 426 " pdb=" CB ASP B 426 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.64e+00 bond pdb=" CB ASP B 426 " pdb=" CG ASP B 426 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.58e+00 ... (remaining 26752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 35472 2.02 - 4.05: 564 4.05 - 6.07: 101 6.07 - 8.10: 18 8.10 - 10.12: 2 Bond angle restraints: 36157 Sorted by residual: angle pdb=" N VAL B 152 " pdb=" CA VAL B 152 " pdb=" C VAL B 152 " ideal model delta sigma weight residual 113.71 109.31 4.40 9.50e-01 1.11e+00 2.15e+01 angle pdb=" N VAL F 492 " pdb=" CA VAL F 492 " pdb=" C VAL F 492 " ideal model delta sigma weight residual 112.96 108.33 4.63 1.00e+00 1.00e+00 2.15e+01 angle pdb=" C ILE B 425 " pdb=" N ASP B 426 " pdb=" CA ASP B 426 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C GLU G 54 " pdb=" N ASN G 55 " pdb=" CA ASN G 55 " ideal model delta sigma weight residual 122.46 128.01 -5.55 1.41e+00 5.03e-01 1.55e+01 angle pdb=" C TYR J 84 " pdb=" N VAL J 85 " pdb=" CA VAL J 85 " ideal model delta sigma weight residual 121.97 128.70 -6.73 1.80e+00 3.09e-01 1.40e+01 ... (remaining 36152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 14561 17.57 - 35.14: 1399 35.14 - 52.70: 226 52.70 - 70.27: 63 70.27 - 87.84: 39 Dihedral angle restraints: 16288 sinusoidal: 6632 harmonic: 9656 Sorted by residual: dihedral pdb=" CA ARG B 38 " pdb=" C ARG B 38 " pdb=" N PHE B 39 " pdb=" CA PHE B 39 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA VAL A 47 " pdb=" C VAL A 47 " pdb=" N ALA A 48 " pdb=" CA ALA A 48 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS F 476 " pdb=" C HIS F 476 " pdb=" N LEU F 477 " pdb=" CA LEU F 477 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 16285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2774 0.038 - 0.077: 1008 0.077 - 0.115: 223 0.115 - 0.154: 52 0.154 - 0.192: 9 Chirality restraints: 4066 Sorted by residual: chirality pdb=" CB VAL B 620 " pdb=" CA VAL B 620 " pdb=" CG1 VAL B 620 " pdb=" CG2 VAL B 620 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CA VAL B 189 " pdb=" N VAL B 189 " pdb=" C VAL B 189 " pdb=" CB VAL B 189 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA ASN G 55 " pdb=" N ASN G 55 " pdb=" C ASN G 55 " pdb=" CB ASN G 55 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 4063 not shown) Planarity restraints: 4640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 255 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO B 256 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 256 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 256 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 65 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO C 66 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 66 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 66 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 661 " -0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 662 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " -0.031 5.00e-02 4.00e+02 ... (remaining 4637 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 230 2.61 - 3.19: 22792 3.19 - 3.76: 42351 3.76 - 4.33: 56187 4.33 - 4.90: 93276 Nonbonded interactions: 214836 Sorted by model distance: nonbonded pdb=" OD1 ASP E 97 " pdb="ZN ZN E 202 " model vdw 2.043 2.230 nonbonded pdb=" OG SER D 22 " pdb=" OE2 GLU D 26 " model vdw 2.112 3.040 nonbonded pdb=" OH TYR J 275 " pdb=" O ILE F 546 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR G 79 " pdb=" O PRO G 91 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR C 79 " pdb=" O PRO C 91 " model vdw 2.224 3.040 ... (remaining 214831 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' and (resid 1 through 115 or resid 135 through 744)) selection = (chain 'B' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 744)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 22 through 59 or resid 68 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 104 or r \ esid 200 through 202)) selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } 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: 0.000 Normalize map: mean=0, sd=1: 8.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.010 Find NCS groups from input model: 0.410 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26779 Z= 0.155 Angle : 0.647 18.026 36169 Z= 0.339 Chirality : 0.042 0.192 4066 Planarity : 0.005 0.081 4640 Dihedral : 14.726 87.839 10006 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.14), residues: 3231 helix: -0.41 (0.11), residues: 1879 sheet: -1.32 (0.57), residues: 62 loop : -1.82 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 247 TYR 0.032 0.001 TYR F 542 PHE 0.021 0.002 PHE J 626 TRP 0.022 0.002 TRP B 35 HIS 0.005 0.001 HIS J 476 Details of bonding type rmsd covalent geometry : bond 0.00349 (26757) covalent geometry : angle 0.63856 (36157) hydrogen bonds : bond 0.18977 ( 1369) hydrogen bonds : angle 6.67187 ( 4044) metal coordination : bond 0.01202 ( 22) metal coordination : angle 5.59159 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 45 MET cc_start: 0.8312 (mtt) cc_final: 0.7991 (mtt) REVERT: H 6 MET cc_start: 0.6907 (tmm) cc_final: 0.6421 (tmm) REVERT: I 68 CYS cc_start: 0.5595 (p) cc_final: 0.5302 (p) REVERT: B 363 HIS cc_start: 0.7164 (m90) cc_final: 0.6894 (m170) REVERT: B 467 TYR cc_start: 0.7512 (t80) cc_final: 0.7301 (t80) REVERT: B 577 VAL cc_start: 0.8592 (p) cc_final: 0.8345 (t) REVERT: J 241 HIS cc_start: 0.6542 (t-90) cc_final: 0.6302 (t-170) REVERT: J 327 GLU cc_start: 0.7496 (tp30) cc_final: 0.7126 (tp30) REVERT: K -20 SER cc_start: 0.8512 (m) cc_final: 0.8216 (p) REVERT: F 440 TYR cc_start: 0.7287 (t80) cc_final: 0.6687 (t80) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.1730 time to fit residues: 118.1871 Evaluate side-chains 293 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 204 GLN A 292 ASN A 377 ASN A 409 ASN A 463 GLN A 496 ASN A 567 ASN A 697 ASN A 712 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 ASN B 190 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN B 581 GLN B 590 ASN C 58 ASN D 42 GLN ** J 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 GLN J 511 ASN K -4 HIS F 113 ASN ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.182394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.149500 restraints weight = 42166.664| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 3.54 r_work: 0.3483 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26779 Z= 0.158 Angle : 0.597 15.788 36169 Z= 0.311 Chirality : 0.040 0.178 4066 Planarity : 0.004 0.067 4640 Dihedral : 4.298 21.770 3545 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.97 % Allowed : 7.98 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.15), residues: 3231 helix: 0.43 (0.12), residues: 1918 sheet: -1.68 (0.54), residues: 73 loop : -1.75 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 247 TYR 0.025 0.002 TYR F 349 PHE 0.033 0.002 PHE F 392 TRP 0.018 0.002 TRP B 35 HIS 0.005 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00367 (26757) covalent geometry : angle 0.59034 (36157) hydrogen bonds : bond 0.04556 ( 1369) hydrogen bonds : angle 4.72895 ( 4044) metal coordination : bond 0.00749 ( 22) metal coordination : angle 4.85242 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 311 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8153 (t0) REVERT: A 576 MET cc_start: 0.5233 (OUTLIER) cc_final: 0.3894 (mpp) REVERT: A 622 MET cc_start: 0.6303 (mpp) cc_final: 0.6090 (mpp) REVERT: A 723 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7376 (tm-30) REVERT: H 6 MET cc_start: 0.7285 (tmm) cc_final: 0.6442 (tmm) REVERT: I 47 ASN cc_start: 0.6902 (m-40) cc_final: 0.6458 (m-40) REVERT: I 104 GLN cc_start: 0.7011 (mm110) cc_final: 0.6638 (mp10) REVERT: B 467 TYR cc_start: 0.7910 (t80) cc_final: 0.7672 (t80) REVERT: D 80 ARG cc_start: 0.6249 (ttp80) cc_final: 0.5981 (ttp80) REVERT: J 241 HIS cc_start: 0.7404 (t-90) cc_final: 0.7009 (t-170) REVERT: J 327 GLU cc_start: 0.8420 (tp30) cc_final: 0.8141 (tp30) REVERT: K -20 SER cc_start: 0.8860 (m) cc_final: 0.8321 (p) REVERT: E 105 LYS cc_start: 0.7207 (mmtm) cc_final: 0.6100 (mtpt) REVERT: F 196 GLU cc_start: 0.8106 (tt0) cc_final: 0.7830 (mt-10) REVERT: F 440 TYR cc_start: 0.7608 (t80) cc_final: 0.6819 (t80) outliers start: 28 outliers final: 14 residues processed: 330 average time/residue: 0.1635 time to fit residues: 84.8083 Evaluate side-chains 299 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 283 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain J residue 438 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 322 ASP Chi-restraints excluded: chain F residue 434 HIS Chi-restraints excluded: chain F residue 619 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 288 optimal weight: 5.9990 chunk 187 optimal weight: 0.2980 chunk 268 optimal weight: 6.9990 chunk 201 optimal weight: 0.2980 chunk 191 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 314 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 101 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS A 492 ASN A 697 ASN ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS C 58 ASN ** J 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 HIS ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.182330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.132725 restraints weight = 42253.344| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.92 r_work: 0.3585 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26779 Z= 0.125 Angle : 0.546 14.229 36169 Z= 0.284 Chirality : 0.039 0.165 4066 Planarity : 0.004 0.063 4640 Dihedral : 4.132 21.398 3545 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.14 % Allowed : 9.25 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.15), residues: 3231 helix: 0.77 (0.12), residues: 1923 sheet: -1.71 (0.52), residues: 73 loop : -1.68 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 161 TYR 0.019 0.001 TYR J 472 PHE 0.029 0.001 PHE F 626 TRP 0.026 0.002 TRP J 209 HIS 0.009 0.001 HIS F 300 Details of bonding type rmsd covalent geometry : bond 0.00280 (26757) covalent geometry : angle 0.53982 (36157) hydrogen bonds : bond 0.04101 ( 1369) hydrogen bonds : angle 4.46257 ( 4044) metal coordination : bond 0.00881 ( 22) metal coordination : angle 4.70173 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7353 (tm-30) REVERT: G 45 MET cc_start: 0.8348 (mtt) cc_final: 0.8060 (mtt) REVERT: H 6 MET cc_start: 0.7209 (tmm) cc_final: 0.5856 (ttm) REVERT: I 47 ASN cc_start: 0.7217 (m-40) cc_final: 0.6699 (m-40) REVERT: I 104 GLN cc_start: 0.6954 (mm110) cc_final: 0.6632 (mp10) REVERT: B 242 ARG cc_start: 0.7127 (mmt-90) cc_final: 0.6373 (mmm160) REVERT: B 438 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8080 (mtm) REVERT: B 597 LYS cc_start: 0.7346 (tppt) cc_final: 0.7086 (tppt) REVERT: J 209 TRP cc_start: 0.7778 (t-100) cc_final: 0.7530 (t-100) REVERT: J 241 HIS cc_start: 0.7204 (t-90) cc_final: 0.6843 (t-170) REVERT: J 327 GLU cc_start: 0.8210 (tp30) cc_final: 0.7927 (tp30) REVERT: K -20 SER cc_start: 0.8820 (m) cc_final: 0.8320 (p) REVERT: E 105 LYS cc_start: 0.7250 (mmtm) cc_final: 0.6172 (mtpt) REVERT: F 196 GLU cc_start: 0.8096 (tt0) cc_final: 0.7802 (mt-10) REVERT: F 358 MET cc_start: 0.6466 (mmp) cc_final: 0.6173 (tmm) REVERT: F 440 TYR cc_start: 0.7520 (t80) cc_final: 0.6799 (t80) outliers start: 33 outliers final: 17 residues processed: 326 average time/residue: 0.1467 time to fit residues: 77.3577 Evaluate side-chains 297 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 279 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 438 ASP Chi-restraints excluded: chain J residue 586 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 619 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 93 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 242 optimal weight: 0.2980 chunk 244 optimal weight: 0.9980 chunk 282 optimal weight: 0.0010 chunk 114 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN I 41 ASN ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.182041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.131760 restraints weight = 42212.463| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.71 r_work: 0.3571 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26779 Z= 0.125 Angle : 0.538 14.155 36169 Z= 0.279 Chirality : 0.039 0.164 4066 Planarity : 0.004 0.061 4640 Dihedral : 4.049 21.316 3545 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.31 % Allowed : 10.46 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.15), residues: 3231 helix: 0.95 (0.12), residues: 1924 sheet: -1.72 (0.49), residues: 83 loop : -1.65 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.028 0.001 TYR A 558 PHE 0.027 0.001 PHE F 626 TRP 0.016 0.001 TRP B 35 HIS 0.006 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00284 (26757) covalent geometry : angle 0.53253 (36157) hydrogen bonds : bond 0.03827 ( 1369) hydrogen bonds : angle 4.32640 ( 4044) metal coordination : bond 0.00583 ( 22) metal coordination : angle 4.25203 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 293 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7769 (mtp) REVERT: A 297 MET cc_start: 0.8364 (tpp) cc_final: 0.8116 (tpp) REVERT: A 566 MET cc_start: 0.0232 (mmm) cc_final: -0.0077 (mpp) REVERT: A 576 MET cc_start: 0.5351 (OUTLIER) cc_final: 0.4028 (mpp) REVERT: A 723 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7328 (tm-30) REVERT: H 6 MET cc_start: 0.7110 (tmm) cc_final: 0.6062 (ttm) REVERT: I 47 ASN cc_start: 0.7056 (m-40) cc_final: 0.6503 (m-40) REVERT: I 104 GLN cc_start: 0.6935 (mm110) cc_final: 0.6632 (mp10) REVERT: B 242 ARG cc_start: 0.7113 (mmt-90) cc_final: 0.6387 (mmm160) REVERT: B 438 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8073 (mtm) REVERT: B 576 MET cc_start: 0.7786 (mpp) cc_final: 0.7549 (mmt) REVERT: D 20 GLU cc_start: 0.4835 (mp0) cc_final: 0.4242 (mp0) REVERT: D 80 ARG cc_start: 0.6235 (ttp80) cc_final: 0.5977 (ttp80) REVERT: J 171 ARG cc_start: 0.9130 (ptm160) cc_final: 0.8780 (ptp90) REVERT: J 209 TRP cc_start: 0.7870 (t-100) cc_final: 0.7617 (t-100) REVERT: J 241 HIS cc_start: 0.7182 (t-90) cc_final: 0.6799 (t-170) REVERT: J 327 GLU cc_start: 0.8197 (tp30) cc_final: 0.7920 (tp30) REVERT: K -20 SER cc_start: 0.8766 (m) cc_final: 0.8190 (p) REVERT: E 105 LYS cc_start: 0.7241 (mmtm) cc_final: 0.6141 (mtpt) REVERT: F 196 GLU cc_start: 0.8040 (tt0) cc_final: 0.7785 (mt-10) REVERT: F 358 MET cc_start: 0.6436 (mmp) cc_final: 0.6131 (tmm) REVERT: F 565 HIS cc_start: 0.7832 (m-70) cc_final: 0.6738 (m170) outliers start: 38 outliers final: 19 residues processed: 321 average time/residue: 0.1491 time to fit residues: 76.7979 Evaluate side-chains 294 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 272 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 438 ASP Chi-restraints excluded: chain F residue 619 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 266 optimal weight: 20.0000 chunk 111 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 244 optimal weight: 0.5980 chunk 84 optimal weight: 0.0030 chunk 30 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 ASN J 443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.179156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127904 restraints weight = 41818.314| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.60 r_work: 0.3515 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26779 Z= 0.176 Angle : 0.573 14.480 36169 Z= 0.297 Chirality : 0.041 0.181 4066 Planarity : 0.004 0.062 4640 Dihedral : 4.082 20.929 3545 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.69 % Allowed : 11.74 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.15), residues: 3231 helix: 0.97 (0.12), residues: 1919 sheet: -1.77 (0.49), residues: 83 loop : -1.64 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 210 TYR 0.019 0.001 TYR F 542 PHE 0.029 0.002 PHE F 626 TRP 0.016 0.002 TRP B 35 HIS 0.007 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00421 (26757) covalent geometry : angle 0.56690 (36157) hydrogen bonds : bond 0.03937 ( 1369) hydrogen bonds : angle 4.34019 ( 4044) metal coordination : bond 0.00769 ( 22) metal coordination : angle 4.51119 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 284 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7790 (mtp) REVERT: A 297 MET cc_start: 0.8455 (tpp) cc_final: 0.8222 (tpp) REVERT: A 365 MET cc_start: 0.8593 (mmm) cc_final: 0.8306 (mmm) REVERT: A 688 MET cc_start: 0.6645 (mmp) cc_final: 0.6178 (mmp) REVERT: H 6 MET cc_start: 0.7121 (tmm) cc_final: 0.6282 (ttm) REVERT: I 47 ASN cc_start: 0.7158 (m-40) cc_final: 0.6597 (m-40) REVERT: B 162 MET cc_start: 0.8055 (tpp) cc_final: 0.7833 (tpp) REVERT: B 438 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8080 (mtm) REVERT: D 20 GLU cc_start: 0.4677 (mp0) cc_final: 0.4074 (mp0) REVERT: D 80 ARG cc_start: 0.6170 (ttp80) cc_final: 0.5924 (ttp80) REVERT: J 241 HIS cc_start: 0.7292 (t-90) cc_final: 0.6795 (t-170) REVERT: J 327 GLU cc_start: 0.8255 (tp30) cc_final: 0.8024 (tp30) REVERT: K -20 SER cc_start: 0.8705 (m) cc_final: 0.8192 (p) REVERT: K -18 ASP cc_start: 0.8518 (t0) cc_final: 0.8311 (t0) REVERT: F 196 GLU cc_start: 0.8023 (tt0) cc_final: 0.7780 (mt-10) REVERT: F 358 MET cc_start: 0.6490 (mmp) cc_final: 0.6145 (tmm) outliers start: 49 outliers final: 37 residues processed: 320 average time/residue: 0.1627 time to fit residues: 82.8647 Evaluate side-chains 304 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 438 ASP Chi-restraints excluded: chain J residue 462 GLU Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain J residue 586 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 619 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 103 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 170 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 293 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN F 241 HIS ** F 565 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 = 0.4376 r_free = 0.4376 target = 0.180822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130681 restraints weight = 42030.802| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.76 r_work: 0.3544 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26779 Z= 0.129 Angle : 0.540 13.528 36169 Z= 0.280 Chirality : 0.039 0.161 4066 Planarity : 0.004 0.061 4640 Dihedral : 4.016 21.431 3545 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.66 % Allowed : 12.88 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.15), residues: 3231 helix: 1.09 (0.12), residues: 1917 sheet: -1.75 (0.49), residues: 83 loop : -1.61 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 165 TYR 0.027 0.001 TYR A 558 PHE 0.026 0.001 PHE F 626 TRP 0.038 0.002 TRP J 209 HIS 0.006 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00296 (26757) covalent geometry : angle 0.53422 (36157) hydrogen bonds : bond 0.03709 ( 1369) hydrogen bonds : angle 4.22361 ( 4044) metal coordination : bond 0.00637 ( 22) metal coordination : angle 4.24134 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.5533 (OUTLIER) cc_final: 0.4200 (mpp) REVERT: H 6 MET cc_start: 0.7134 (tmm) cc_final: 0.6378 (ttm) REVERT: I 47 ASN cc_start: 0.7106 (m-40) cc_final: 0.6508 (m-40) REVERT: I 104 GLN cc_start: 0.6891 (mm110) cc_final: 0.6609 (mp10) REVERT: B 162 MET cc_start: 0.8035 (tpp) cc_final: 0.7834 (tpp) REVERT: B 438 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8109 (mtm) REVERT: B 596 TYR cc_start: 0.7303 (t80) cc_final: 0.6814 (t80) REVERT: D 20 GLU cc_start: 0.4660 (mp0) cc_final: 0.4031 (mp0) REVERT: D 80 ARG cc_start: 0.6311 (ttp80) cc_final: 0.6055 (ttp80) REVERT: J 241 HIS cc_start: 0.7262 (t-90) cc_final: 0.6788 (t-170) REVERT: J 327 GLU cc_start: 0.8216 (tp30) cc_final: 0.7979 (tp30) REVERT: K -20 SER cc_start: 0.8727 (m) cc_final: 0.8188 (p) REVERT: F 196 GLU cc_start: 0.7997 (tt0) cc_final: 0.7713 (mm-30) REVERT: F 358 MET cc_start: 0.6439 (mmp) cc_final: 0.5923 (tmm) outliers start: 48 outliers final: 27 residues processed: 310 average time/residue: 0.1616 time to fit residues: 81.5918 Evaluate side-chains 298 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain F residue 619 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 297 optimal weight: 0.6980 chunk 215 optimal weight: 0.0980 chunk 90 optimal weight: 7.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS F 143 ASN F 241 HIS ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.181263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131063 restraints weight = 42075.602| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.94 r_work: 0.3555 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26779 Z= 0.122 Angle : 0.535 12.896 36169 Z= 0.278 Chirality : 0.039 0.184 4066 Planarity : 0.003 0.060 4640 Dihedral : 3.978 21.269 3545 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.62 % Allowed : 13.09 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.15), residues: 3231 helix: 1.19 (0.12), residues: 1914 sheet: -1.74 (0.49), residues: 83 loop : -1.60 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 165 TYR 0.017 0.001 TYR G 76 PHE 0.026 0.001 PHE J 626 TRP 0.020 0.001 TRP J 209 HIS 0.006 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00277 (26757) covalent geometry : angle 0.53040 (36157) hydrogen bonds : bond 0.03632 ( 1369) hydrogen bonds : angle 4.17159 ( 4044) metal coordination : bond 0.00631 ( 22) metal coordination : angle 4.02721 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7573 (mt-10) REVERT: A 297 MET cc_start: 0.8363 (tpp) cc_final: 0.8056 (tpp) REVERT: A 576 MET cc_start: 0.5457 (OUTLIER) cc_final: 0.4145 (mpp) REVERT: H 6 MET cc_start: 0.7044 (tmm) cc_final: 0.6387 (ttm) REVERT: I 47 ASN cc_start: 0.7112 (m-40) cc_final: 0.6497 (m-40) REVERT: I 104 GLN cc_start: 0.6933 (mm110) cc_final: 0.6655 (mp10) REVERT: B 162 MET cc_start: 0.8084 (tpp) cc_final: 0.7870 (tpp) REVERT: B 438 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8091 (mtm) REVERT: B 596 TYR cc_start: 0.7323 (t80) cc_final: 0.6806 (t80) REVERT: D 20 GLU cc_start: 0.4728 (mp0) cc_final: 0.4086 (mp0) REVERT: D 41 GLU cc_start: 0.7671 (mp0) cc_final: 0.7432 (mp0) REVERT: D 43 ARG cc_start: 0.6169 (tpp-160) cc_final: 0.5876 (tpp-160) REVERT: D 80 ARG cc_start: 0.6364 (ttp80) cc_final: 0.6103 (ttp80) REVERT: J 241 HIS cc_start: 0.7300 (t-90) cc_final: 0.6837 (t-170) REVERT: J 327 GLU cc_start: 0.8216 (tp30) cc_final: 0.7985 (tp30) REVERT: K -20 SER cc_start: 0.8699 (m) cc_final: 0.8131 (p) REVERT: F 196 GLU cc_start: 0.8025 (tt0) cc_final: 0.7737 (mm-30) REVERT: F 326 MET cc_start: 0.8272 (tpp) cc_final: 0.8034 (tpp) REVERT: F 358 MET cc_start: 0.6393 (mmp) cc_final: 0.6169 (ttp) REVERT: F 565 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.6559 (m-70) outliers start: 47 outliers final: 26 residues processed: 304 average time/residue: 0.1735 time to fit residues: 85.5078 Evaluate side-chains 290 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 462 GLU Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 619 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 91 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 chunk 233 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 260 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 GLN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.179747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129449 restraints weight = 42251.909| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.73 r_work: 0.3524 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26779 Z= 0.155 Angle : 0.564 17.113 36169 Z= 0.290 Chirality : 0.040 0.251 4066 Planarity : 0.004 0.060 4640 Dihedral : 4.016 21.147 3545 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.66 % Allowed : 13.57 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.15), residues: 3231 helix: 1.14 (0.12), residues: 1917 sheet: -1.24 (0.60), residues: 53 loop : -1.60 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 165 TYR 0.018 0.001 TYR G 76 PHE 0.027 0.001 PHE F 626 TRP 0.020 0.001 TRP J 209 HIS 0.006 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00368 (26757) covalent geometry : angle 0.55558 (36157) hydrogen bonds : bond 0.03720 ( 1369) hydrogen bonds : angle 4.19691 ( 4044) metal coordination : bond 0.00796 ( 22) metal coordination : angle 5.27887 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7563 (mt-10) REVERT: A 576 MET cc_start: 0.5496 (OUTLIER) cc_final: 0.4176 (mpp) REVERT: H 6 MET cc_start: 0.6973 (tmm) cc_final: 0.6435 (ttm) REVERT: I 47 ASN cc_start: 0.7189 (m-40) cc_final: 0.6974 (m-40) REVERT: B 162 MET cc_start: 0.8084 (tpp) cc_final: 0.7863 (tpp) REVERT: B 251 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8198 (ttm-80) REVERT: B 438 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8102 (mtm) REVERT: B 596 TYR cc_start: 0.7357 (t80) cc_final: 0.6819 (t80) REVERT: D 20 GLU cc_start: 0.4792 (mp0) cc_final: 0.4119 (mp0) REVERT: D 41 GLU cc_start: 0.7718 (mp0) cc_final: 0.7470 (mp0) REVERT: D 43 ARG cc_start: 0.6266 (tpp-160) cc_final: 0.5975 (tpp-160) REVERT: D 80 ARG cc_start: 0.6359 (ttp80) cc_final: 0.6101 (ttp80) REVERT: K -20 SER cc_start: 0.8676 (m) cc_final: 0.8039 (p) REVERT: F 326 MET cc_start: 0.8214 (tpp) cc_final: 0.7908 (tpp) REVERT: F 358 MET cc_start: 0.6423 (mmp) cc_final: 0.6208 (ttp) REVERT: F 376 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8037 (mmtm) REVERT: F 392 PHE cc_start: 0.7804 (m-80) cc_final: 0.7162 (m-80) REVERT: F 565 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.6467 (m-70) outliers start: 48 outliers final: 33 residues processed: 305 average time/residue: 0.1792 time to fit residues: 88.1962 Evaluate side-chains 301 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 401 THR Chi-restraints excluded: chain J residue 462 GLU Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 619 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 114 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 311 optimal weight: 0.0370 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 HIS ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.180887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.130921 restraints weight = 42217.579| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.70 r_work: 0.3543 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26779 Z= 0.128 Angle : 0.549 16.961 36169 Z= 0.283 Chirality : 0.039 0.206 4066 Planarity : 0.003 0.059 4640 Dihedral : 3.991 21.940 3545 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.38 % Allowed : 13.98 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.15), residues: 3231 helix: 1.21 (0.12), residues: 1917 sheet: -1.17 (0.61), residues: 53 loop : -1.58 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 82 TYR 0.016 0.001 TYR G 76 PHE 0.025 0.001 PHE J 626 TRP 0.017 0.001 TRP J 209 HIS 0.005 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00295 (26757) covalent geometry : angle 0.54086 (36157) hydrogen bonds : bond 0.03614 ( 1369) hydrogen bonds : angle 4.16236 ( 4044) metal coordination : bond 0.00699 ( 22) metal coordination : angle 5.17137 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7535 (mt-10) REVERT: H 6 MET cc_start: 0.6945 (tmm) cc_final: 0.6455 (ttm) REVERT: I 47 ASN cc_start: 0.7265 (m-40) cc_final: 0.7019 (m-40) REVERT: I 104 GLN cc_start: 0.6837 (mm110) cc_final: 0.6558 (mp10) REVERT: B 251 ARG cc_start: 0.8410 (ttp80) cc_final: 0.8170 (ttm-80) REVERT: B 438 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8117 (mtm) REVERT: B 596 TYR cc_start: 0.7318 (t80) cc_final: 0.6795 (t80) REVERT: D 43 ARG cc_start: 0.6273 (tpp-160) cc_final: 0.6063 (tpp-160) REVERT: D 80 ARG cc_start: 0.6182 (ttp80) cc_final: 0.5936 (ttp80) REVERT: J 206 LEU cc_start: 0.8487 (mp) cc_final: 0.8254 (mp) REVERT: J 241 HIS cc_start: 0.7209 (t-90) cc_final: 0.6888 (t-170) REVERT: K -20 SER cc_start: 0.8614 (m) cc_final: 0.7993 (p) REVERT: F 326 MET cc_start: 0.8232 (tpp) cc_final: 0.7903 (tpp) REVERT: F 376 LYS cc_start: 0.8669 (mmmt) cc_final: 0.7997 (mmtm) REVERT: F 565 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.6515 (m-70) outliers start: 40 outliers final: 33 residues processed: 302 average time/residue: 0.1773 time to fit residues: 87.0917 Evaluate side-chains 298 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 462 GLU Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 619 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 141 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 188 optimal weight: 0.0670 chunk 129 optimal weight: 0.5980 chunk 279 optimal weight: 20.0000 chunk 260 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 227 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 565 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 = 0.4395 r_free = 0.4395 target = 0.186631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136265 restraints weight = 43879.855| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.98 r_work: 0.3579 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26779 Z= 0.117 Angle : 0.546 15.846 36169 Z= 0.283 Chirality : 0.039 0.238 4066 Planarity : 0.004 0.059 4640 Dihedral : 3.955 22.213 3545 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.35 % Allowed : 14.23 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 3231 helix: 1.28 (0.12), residues: 1909 sheet: -1.16 (0.61), residues: 53 loop : -1.55 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 82 TYR 0.035 0.001 TYR A 558 PHE 0.026 0.001 PHE J 626 TRP 0.018 0.001 TRP B 35 HIS 0.005 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00266 (26757) covalent geometry : angle 0.53911 (36157) hydrogen bonds : bond 0.03556 ( 1369) hydrogen bonds : angle 4.11834 ( 4044) metal coordination : bond 0.00720 ( 22) metal coordination : angle 4.86624 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6462 Ramachandran restraints generated. 3231 Oldfield, 0 Emsley, 3231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7692 (mt-10) REVERT: A 406 MET cc_start: 0.7197 (tpp) cc_final: 0.6445 (tpp) REVERT: H 6 MET cc_start: 0.6963 (tmm) cc_final: 0.6583 (ttm) REVERT: I 47 ASN cc_start: 0.7143 (m-40) cc_final: 0.6861 (m-40) REVERT: I 104 GLN cc_start: 0.6805 (mm110) cc_final: 0.6570 (mp10) REVERT: B 438 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8270 (mtm) REVERT: B 596 TYR cc_start: 0.7263 (t80) cc_final: 0.6724 (t80) REVERT: D 43 ARG cc_start: 0.6363 (tpp-160) cc_final: 0.6064 (tpp-160) REVERT: J 206 LEU cc_start: 0.8478 (mp) cc_final: 0.8237 (mp) REVERT: J 241 HIS cc_start: 0.7579 (t-90) cc_final: 0.7096 (t-170) REVERT: K -20 SER cc_start: 0.8605 (m) cc_final: 0.7957 (p) REVERT: F 326 MET cc_start: 0.8224 (tpp) cc_final: 0.7882 (tpp) REVERT: F 376 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8083 (mmtm) REVERT: F 384 ASP cc_start: 0.8359 (t0) cc_final: 0.7757 (m-30) REVERT: F 565 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.6674 (m-70) outliers start: 39 outliers final: 32 residues processed: 294 average time/residue: 0.1712 time to fit residues: 82.1032 Evaluate side-chains 295 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain J residue 93 TRP Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 462 GLU Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 619 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 259 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 209 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 357 ASN ** F 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 565 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 = 0.4370 r_free = 0.4370 target = 0.180267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129767 restraints weight = 41974.896| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.59 r_work: 0.3546 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26779 Z= 0.144 Angle : 0.562 16.360 36169 Z= 0.292 Chirality : 0.040 0.233 4066 Planarity : 0.004 0.060 4640 Dihedral : 3.980 22.093 3545 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.45 % Allowed : 14.54 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.15), residues: 3231 helix: 1.23 (0.12), residues: 1910 sheet: -1.73 (0.53), residues: 73 loop : -1.53 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 165 TYR 0.036 0.001 TYR A 558 PHE 0.026 0.001 PHE F 626 TRP 0.017 0.001 TRP J 209 HIS 0.006 0.001 HIS F 476 Details of bonding type rmsd covalent geometry : bond 0.00340 (26757) covalent geometry : angle 0.55472 (36157) hydrogen bonds : bond 0.03648 ( 1369) hydrogen bonds : angle 4.13659 ( 4044) metal coordination : bond 0.00698 ( 22) metal coordination : angle 5.01949 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6918.48 seconds wall clock time: 119 minutes 30.29 seconds (7170.29 seconds total)