Starting phenix.real_space_refine on Wed May 28 18:25:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqb_37737/05_2025/8wqb_37737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqb_37737/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqb_37737/05_2025/8wqb_37737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqb_37737/05_2025/8wqb_37737.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqb_37737/05_2025/8wqb_37737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqb_37737/05_2025/8wqb_37737.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 1, 'ASN:plan1': 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: {'TYR:plan': 1, 'ASN:plan1': 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: 15.17, per 1000 atoms: 0.58 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: 6.02 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 2.78 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: 7.83 Time building geometry restraints manager: 7.06 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: 8.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.040 Extract box with map and model: 0.980 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 59.940 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.040 ------------------------------------------------------------------------------- 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 : 7.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (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 TRP 0.022 0.002 TRP B 35 HIS 0.005 0.001 HIS J 476 PHE 0.021 0.002 PHE J 626 TYR 0.032 0.001 TYR F 542 ARG 0.007 0.000 ARG F 247 Details of bonding type rmsd hydrogen bonds : bond 0.18977 ( 1369) hydrogen bonds : angle 6.67187 ( 4044) metal coordination : bond 0.01202 ( 22) metal coordination : angle 5.59159 ( 12) covalent geometry : bond 0.00349 (26757) covalent geometry : angle 0.63856 (36157) *********************** 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 : 2.980 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: 0.7990 (mtt) REVERT: H 6 MET cc_start: 0.6907 (tmm) cc_final: 0.6422 (tmm) REVERT: I 68 CYS cc_start: 0.5595 (p) cc_final: 0.5301 (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: 0.3998 time to fit residues: 273.1245 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 : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 0.9980 chunk 242 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 152 optimal weight: 0.0770 chunk 186 optimal weight: 6.9990 chunk 290 optimal weight: 8.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 581 GLN B 590 ASN C 58 ASN C 108 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.181716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131340 restraints weight = 42095.512| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.71 r_work: 0.3559 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26779 Z= 0.148 Angle : 0.592 15.538 36169 Z= 0.309 Chirality : 0.040 0.173 4066 Planarity : 0.004 0.066 4640 Dihedral : 4.289 21.671 3545 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.97 % Allowed : 7.84 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3231 helix: 0.44 (0.12), residues: 1920 sheet: -1.66 (0.54), residues: 73 loop : -1.73 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 35 HIS 0.005 0.001 HIS B 696 PHE 0.032 0.002 PHE F 392 TYR 0.025 0.001 TYR F 349 ARG 0.005 0.000 ARG F 334 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 1369) hydrogen bonds : angle 4.70428 ( 4044) metal coordination : bond 0.00713 ( 22) metal coordination : angle 4.78123 ( 12) covalent geometry : bond 0.00337 (26757) covalent geometry : angle 0.58587 (36157) *********************** 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 343 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 315 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.8146 (t0) REVERT: A 622 MET cc_start: 0.6382 (mpp) cc_final: 0.6117 (mpp) REVERT: A 723 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7341 (tm-30) REVERT: H 6 MET cc_start: 0.7121 (tmm) cc_final: 0.6272 (tmm) REVERT: I 47 ASN cc_start: 0.6839 (m-40) cc_final: 0.6472 (m-40) REVERT: I 104 GLN cc_start: 0.6988 (mm110) cc_final: 0.6628 (mp10) REVERT: B 438 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8128 (mtm) REVERT: B 467 TYR cc_start: 0.7760 (t80) cc_final: 0.7523 (t80) REVERT: D 80 ARG cc_start: 0.6146 (ttp80) cc_final: 0.5890 (ttp80) REVERT: J 241 HIS cc_start: 0.7239 (t-90) cc_final: 0.6911 (t-170) REVERT: J 327 GLU cc_start: 0.8253 (tp30) cc_final: 0.7946 (tp30) REVERT: K -20 SER cc_start: 0.8824 (m) cc_final: 0.8301 (p) REVERT: E 105 LYS cc_start: 0.7133 (mmtm) cc_final: 0.6070 (mtpt) REVERT: F 196 GLU cc_start: 0.8111 (tt0) cc_final: 0.7847 (mt-10) REVERT: F 321 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7389 (mmp80) REVERT: F 440 TYR cc_start: 0.7502 (t80) cc_final: 0.6755 (t80) outliers start: 28 outliers final: 13 residues processed: 333 average time/residue: 0.3625 time to fit residues: 190.4423 Evaluate side-chains 298 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 283 time to evaluate : 2.748 ------------------------------------------------------------------------------- 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 578 THR Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain B residue 438 MET 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 119 optimal weight: 2.9990 chunk 84 optimal weight: 0.0060 chunk 180 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 238 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 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 113 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.182224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.132969 restraints weight = 42126.291| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.84 r_work: 0.3579 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1723 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= 0.128 Angle : 0.549 14.161 36169 Z= 0.285 Chirality : 0.039 0.165 4066 Planarity : 0.004 0.063 4640 Dihedral : 4.126 21.395 3545 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.10 % Allowed : 9.39 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3231 helix: 0.77 (0.12), residues: 1923 sheet: -1.68 (0.52), residues: 73 loop : -1.68 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 209 HIS 0.009 0.001 HIS F 300 PHE 0.029 0.001 PHE F 626 TYR 0.020 0.001 TYR F 139 ARG 0.005 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 1369) hydrogen bonds : angle 4.45625 ( 4044) metal coordination : bond 0.00695 ( 22) metal coordination : angle 4.72728 ( 12) covalent geometry : bond 0.00289 (26757) covalent geometry : angle 0.54239 (36157) *********************** 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 336 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 304 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7813 (mtp) REVERT: A 723 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7308 (tm-30) REVERT: H 6 MET cc_start: 0.7136 (tmm) cc_final: 0.6359 (tmm) REVERT: I 47 ASN cc_start: 0.7141 (m-40) cc_final: 0.6649 (m-40) REVERT: I 104 GLN cc_start: 0.6983 (mm110) cc_final: 0.6658 (mp10) REVERT: B 242 ARG cc_start: 0.7094 (mmt-90) cc_final: 0.6337 (mmm160) REVERT: B 467 TYR cc_start: 0.7729 (t80) cc_final: 0.7524 (t80) REVERT: B 597 LYS cc_start: 0.7360 (tppt) cc_final: 0.7114 (tppt) REVERT: J 241 HIS cc_start: 0.7205 (t-90) cc_final: 0.6838 (t-170) REVERT: J 327 GLU cc_start: 0.8231 (tp30) cc_final: 0.7940 (tp30) REVERT: K -20 SER cc_start: 0.8810 (m) cc_final: 0.8290 (p) REVERT: E 105 LYS cc_start: 0.7207 (mmtm) cc_final: 0.6122 (mtpt) REVERT: F 196 GLU cc_start: 0.8067 (tt0) cc_final: 0.7789 (mt-10) REVERT: F 321 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7455 (mmp80) REVERT: F 358 MET cc_start: 0.6569 (mmp) cc_final: 0.6168 (tmm) outliers start: 32 outliers final: 18 residues processed: 329 average time/residue: 0.3701 time to fit residues: 194.9137 Evaluate side-chains 303 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 284 time to evaluate : 2.763 ------------------------------------------------------------------------------- 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 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 B residue 187 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 86 SER 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 38 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 220 optimal weight: 0.7980 chunk 304 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS A 697 ASN I 41 ASN ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS B 604 GLN ** J 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.181323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131739 restraints weight = 42482.890| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.95 r_work: 0.3552 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1911 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= 0.142 Angle : 0.547 14.064 36169 Z= 0.283 Chirality : 0.039 0.169 4066 Planarity : 0.004 0.062 4640 Dihedral : 4.075 21.354 3545 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.31 % Allowed : 10.60 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3231 helix: 0.91 (0.12), residues: 1924 sheet: -1.73 (0.49), residues: 83 loop : -1.65 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 35 HIS 0.006 0.001 HIS F 476 PHE 0.027 0.001 PHE F 626 TYR 0.027 0.001 TYR A 558 ARG 0.005 0.000 ARG G 82 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 1369) hydrogen bonds : angle 4.34866 ( 4044) metal coordination : bond 0.00613 ( 22) metal coordination : angle 4.39995 ( 12) covalent geometry : bond 0.00333 (26757) covalent geometry : angle 0.54126 (36157) *********************** 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 333 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 295 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7848 (mtp) REVERT: A 723 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7305 (tm-30) REVERT: H 6 MET cc_start: 0.7103 (tmm) cc_final: 0.6042 (ttm) REVERT: I 47 ASN cc_start: 0.7114 (m-40) cc_final: 0.6542 (m-40) REVERT: I 104 GLN cc_start: 0.6990 (mm110) cc_final: 0.6681 (mp10) REVERT: B 112 PHE cc_start: 0.7978 (t80) cc_final: 0.7771 (t80) REVERT: B 242 ARG cc_start: 0.7141 (mmt-90) cc_final: 0.6389 (mmm160) REVERT: B 438 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8108 (mtm) REVERT: B 467 TYR cc_start: 0.7738 (t80) cc_final: 0.7525 (t80) REVERT: D 20 GLU cc_start: 0.4825 (mp0) cc_final: 0.4237 (mp0) REVERT: D 80 ARG cc_start: 0.6232 (ttp80) cc_final: 0.5979 (ttp80) REVERT: J 171 ARG cc_start: 0.9126 (ptm160) cc_final: 0.8766 (ptp90) REVERT: J 209 TRP cc_start: 0.7889 (t-100) cc_final: 0.7652 (t-100) REVERT: J 241 HIS cc_start: 0.7232 (t-90) cc_final: 0.6827 (t-170) REVERT: J 327 GLU cc_start: 0.8212 (tp30) cc_final: 0.7947 (tp30) REVERT: K -20 SER cc_start: 0.8774 (m) cc_final: 0.8193 (p) REVERT: E 105 LYS cc_start: 0.7246 (mmtm) cc_final: 0.6136 (mtpt) REVERT: F 196 GLU cc_start: 0.8037 (tt0) cc_final: 0.7784 (mt-10) REVERT: F 321 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7563 (mmp80) REVERT: F 358 MET cc_start: 0.6384 (mmp) cc_final: 0.6114 (tmm) outliers start: 38 outliers final: 25 residues processed: 322 average time/residue: 0.3794 time to fit residues: 192.8910 Evaluate side-chains 305 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 2.718 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 213 THR 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 578 THR 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 H residue 12 THR 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 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 438 ASP Chi-restraints excluded: chain J residue 462 GLU Chi-restraints excluded: chain J residue 586 GLU 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 231 optimal weight: 0.9980 chunk 264 optimal weight: 0.9990 chunk 159 optimal weight: 0.3980 chunk 243 optimal weight: 0.9990 chunk 279 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 171 optimal weight: 0.4980 chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.186354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134182 restraints weight = 43978.729| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.63 r_work: 0.3565 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 26779 Z= 0.131 Angle : 0.536 13.415 36169 Z= 0.278 Chirality : 0.039 0.164 4066 Planarity : 0.004 0.061 4640 Dihedral : 4.014 20.854 3545 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.45 % Allowed : 11.67 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3231 helix: 1.04 (0.12), residues: 1921 sheet: -1.72 (0.49), residues: 83 loop : -1.61 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 35 HIS 0.006 0.001 HIS F 476 PHE 0.027 0.001 PHE F 626 TYR 0.015 0.001 TYR G 76 ARG 0.005 0.000 ARG J 210 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 1369) hydrogen bonds : angle 4.25839 ( 4044) metal coordination : bond 0.00626 ( 22) metal coordination : angle 4.21071 ( 12) covalent geometry : bond 0.00304 (26757) covalent geometry : angle 0.53020 (36157) *********************** 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 332 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 MET cc_start: 0.6666 (mmp) cc_final: 0.6216 (mmp) REVERT: A 723 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7331 (tm-30) REVERT: H 6 MET cc_start: 0.7034 (tmm) cc_final: 0.6210 (ttm) REVERT: I 47 ASN cc_start: 0.7147 (m-40) cc_final: 0.6536 (m-40) REVERT: I 104 GLN cc_start: 0.6958 (mm110) cc_final: 0.6667 (mp10) REVERT: B 112 PHE cc_start: 0.8000 (t80) cc_final: 0.7776 (t80) REVERT: B 162 MET cc_start: 0.8015 (tpp) cc_final: 0.7797 (tpp) REVERT: B 242 ARG cc_start: 0.7095 (mmt-90) cc_final: 0.6392 (mmm160) REVERT: B 438 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8099 (mtm) REVERT: B 467 TYR cc_start: 0.7747 (t80) cc_final: 0.7534 (t80) REVERT: D 20 GLU cc_start: 0.4685 (mp0) cc_final: 0.4079 (mp0) REVERT: D 80 ARG cc_start: 0.6288 (ttp80) cc_final: 0.6028 (ttp80) REVERT: J 241 HIS cc_start: 0.7269 (t-90) cc_final: 0.6782 (t-170) REVERT: J 327 GLU cc_start: 0.8226 (tp30) cc_final: 0.7987 (tp30) REVERT: K -20 SER cc_start: 0.8743 (m) cc_final: 0.8126 (p) REVERT: F 196 GLU cc_start: 0.7980 (tt0) cc_final: 0.7744 (mt-10) REVERT: F 358 MET cc_start: 0.6317 (mmp) cc_final: 0.6058 (tmm) REVERT: F 501 PHE cc_start: 0.6324 (t80) cc_final: 0.6073 (t80) outliers start: 42 outliers final: 28 residues processed: 322 average time/residue: 0.3708 time to fit residues: 188.7162 Evaluate side-chains 300 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 2.657 ------------------------------------------------------------------------------- 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 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 578 THR 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 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 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 438 ASP 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 98 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 211 optimal weight: 0.7980 chunk 260 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 216 optimal weight: 0.3980 chunk 174 optimal weight: 0.7980 chunk 258 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.180652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130214 restraints weight = 42179.545| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.79 r_work: 0.3546 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26779 Z= 0.141 Angle : 0.549 13.306 36169 Z= 0.283 Chirality : 0.039 0.170 4066 Planarity : 0.004 0.060 4640 Dihedral : 4.003 20.799 3545 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.69 % Allowed : 12.78 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3231 helix: 1.09 (0.12), residues: 1918 sheet: -1.69 (0.50), residues: 83 loop : -1.59 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP J 209 HIS 0.006 0.001 HIS F 476 PHE 0.027 0.001 PHE F 626 TYR 0.028 0.001 TYR A 558 ARG 0.008 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 1369) hydrogen bonds : angle 4.23106 ( 4044) metal coordination : bond 0.00614 ( 22) metal coordination : angle 4.18215 ( 12) covalent geometry : bond 0.00332 (26757) covalent geometry : angle 0.54356 (36157) *********************** 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 335 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 688 MET cc_start: 0.6711 (mmp) cc_final: 0.6235 (mmp) REVERT: H 6 MET cc_start: 0.7112 (tmm) cc_final: 0.6333 (ttm) REVERT: I 47 ASN cc_start: 0.7114 (m-40) cc_final: 0.6511 (m-40) REVERT: I 104 GLN cc_start: 0.6905 (mm110) cc_final: 0.6625 (mp10) REVERT: B 112 PHE cc_start: 0.8048 (t80) cc_final: 0.7793 (t80) REVERT: B 162 MET cc_start: 0.8033 (tpp) cc_final: 0.7830 (tpp) REVERT: B 251 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8204 (ttm-80) REVERT: B 438 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8106 (mtm) REVERT: B 467 TYR cc_start: 0.7752 (t80) cc_final: 0.7552 (t80) REVERT: B 596 TYR cc_start: 0.7314 (t80) cc_final: 0.6807 (t80) REVERT: D 20 GLU cc_start: 0.4723 (mp0) cc_final: 0.4113 (mp0) REVERT: D 80 ARG cc_start: 0.6191 (ttp80) cc_final: 0.5937 (ttp80) REVERT: J 209 TRP cc_start: 0.7674 (t-100) cc_final: 0.7393 (t-100) REVERT: J 241 HIS cc_start: 0.7225 (t-90) cc_final: 0.6766 (t-170) REVERT: J 327 GLU cc_start: 0.8225 (tp30) cc_final: 0.7982 (tp30) REVERT: K -20 SER cc_start: 0.8700 (m) cc_final: 0.8078 (p) REVERT: F 159 MET cc_start: 0.5417 (mmp) cc_final: 0.5211 (mmt) REVERT: F 196 GLU cc_start: 0.8024 (tt0) cc_final: 0.7767 (mt-10) REVERT: F 358 MET cc_start: 0.6394 (mmp) cc_final: 0.5885 (tmm) REVERT: F 501 PHE cc_start: 0.6330 (t80) cc_final: 0.6067 (t80) outliers start: 49 outliers final: 35 residues processed: 321 average time/residue: 0.3638 time to fit residues: 186.0910 Evaluate side-chains 305 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 2.777 ------------------------------------------------------------------------------- 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 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 375 VAL 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 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 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 398 LEU 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 438 ASP Chi-restraints excluded: chain J residue 577 LEU 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 233 optimal weight: 0.7980 chunk 285 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 152 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 300 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.180255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.130052 restraints weight = 42206.125| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.71 r_work: 0.3541 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26779 Z= 0.144 Angle : 0.551 13.398 36169 Z= 0.285 Chirality : 0.039 0.182 4066 Planarity : 0.004 0.060 4640 Dihedral : 4.011 21.395 3545 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.62 % Allowed : 13.19 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.15), residues: 3231 helix: 1.11 (0.12), residues: 1918 sheet: -1.73 (0.50), residues: 83 loop : -1.60 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 209 HIS 0.006 0.001 HIS F 476 PHE 0.027 0.001 PHE F 626 TYR 0.015 0.001 TYR G 76 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1369) hydrogen bonds : angle 4.20804 ( 4044) metal coordination : bond 0.00626 ( 22) metal coordination : angle 4.17482 ( 12) covalent geometry : bond 0.00341 (26757) covalent geometry : angle 0.54563 (36157) *********************** 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 322 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7547 (mt-10) REVERT: A 297 MET cc_start: 0.8360 (tpp) cc_final: 0.8139 (tpp) REVERT: A 538 GLN cc_start: 0.8347 (mm110) cc_final: 0.8106 (mm110) REVERT: A 576 MET cc_start: 0.5481 (OUTLIER) cc_final: 0.4171 (mpp) REVERT: H 6 MET cc_start: 0.7016 (tmm) cc_final: 0.6354 (ttm) REVERT: I 104 GLN cc_start: 0.6885 (mm110) cc_final: 0.6608 (mp10) REVERT: B 112 PHE cc_start: 0.8043 (t80) cc_final: 0.7794 (t80) REVERT: B 162 MET cc_start: 0.8093 (tpp) cc_final: 0.7886 (tpp) REVERT: B 251 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8203 (ttm-80) REVERT: B 438 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8102 (mtm) REVERT: B 467 TYR cc_start: 0.7741 (t80) cc_final: 0.7541 (t80) REVERT: B 596 TYR cc_start: 0.7299 (t80) cc_final: 0.6809 (t80) REVERT: D 20 GLU cc_start: 0.4699 (mp0) cc_final: 0.4049 (mp0) REVERT: D 80 ARG cc_start: 0.6273 (ttp80) cc_final: 0.6032 (ttp80) REVERT: J 241 HIS cc_start: 0.7258 (t-90) cc_final: 0.6822 (t-170) REVERT: J 327 GLU cc_start: 0.8231 (tp30) cc_final: 0.7990 (tp30) REVERT: K -20 SER cc_start: 0.8673 (m) cc_final: 0.8025 (p) REVERT: F 196 GLU cc_start: 0.8060 (tt0) cc_final: 0.7811 (mt-10) REVERT: F 326 MET cc_start: 0.8277 (tpp) cc_final: 0.8071 (tpp) REVERT: F 358 MET cc_start: 0.6440 (mmp) cc_final: 0.6226 (ttp) outliers start: 47 outliers final: 35 residues processed: 310 average time/residue: 0.3590 time to fit residues: 178.8418 Evaluate side-chains 304 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 3.015 ------------------------------------------------------------------------------- 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 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 375 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 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 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 696 HIS Chi-restraints excluded: chain C residue 25 ASP 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 438 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 619 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 303 optimal weight: 1.9990 chunk 243 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 chunk 92 optimal weight: 0.1980 chunk 247 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 157 optimal weight: 7.9990 chunk 238 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.181129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131640 restraints weight = 42221.859| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.97 r_work: 0.3543 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26779 Z= 0.122 Angle : 0.540 16.523 36169 Z= 0.280 Chirality : 0.039 0.177 4066 Planarity : 0.004 0.060 4640 Dihedral : 3.960 21.226 3545 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.59 % Allowed : 13.54 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3231 helix: 1.21 (0.12), residues: 1915 sheet: -1.70 (0.50), residues: 83 loop : -1.58 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 209 HIS 0.005 0.001 HIS F 476 PHE 0.025 0.001 PHE J 626 TYR 0.031 0.001 TYR A 558 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 1369) hydrogen bonds : angle 4.13972 ( 4044) metal coordination : bond 0.00722 ( 22) metal coordination : angle 5.07517 ( 12) covalent geometry : bond 0.00279 (26757) covalent geometry : angle 0.53258 (36157) *********************** 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 324 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7556 (mt-10) REVERT: A 297 MET cc_start: 0.8404 (tpp) cc_final: 0.8159 (tpp) REVERT: A 538 GLN cc_start: 0.8316 (mm110) cc_final: 0.8047 (mm110) REVERT: A 576 MET cc_start: 0.5443 (OUTLIER) cc_final: 0.4146 (mpp) REVERT: H 6 MET cc_start: 0.6982 (tmm) cc_final: 0.6386 (ttm) REVERT: I 104 GLN cc_start: 0.6904 (mm110) cc_final: 0.6636 (mp10) REVERT: B 112 PHE cc_start: 0.8070 (t80) cc_final: 0.7825 (t80) REVERT: B 251 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8191 (ttm-80) REVERT: B 438 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8131 (mtm) REVERT: B 467 TYR cc_start: 0.7768 (t80) cc_final: 0.7561 (t80) REVERT: B 596 TYR cc_start: 0.7327 (t80) cc_final: 0.6825 (t80) REVERT: D 20 GLU cc_start: 0.4758 (mp0) cc_final: 0.4088 (mp0) REVERT: D 43 ARG cc_start: 0.6249 (tpp-160) cc_final: 0.6023 (tpp-160) REVERT: J 327 GLU cc_start: 0.8230 (tp30) cc_final: 0.8001 (tp30) REVERT: J 438 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8603 (m-30) REVERT: K -20 SER cc_start: 0.8665 (m) cc_final: 0.8028 (p) REVERT: F 326 MET cc_start: 0.8224 (tpp) cc_final: 0.7944 (tpp) REVERT: F 376 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8013 (mmtm) REVERT: F 392 PHE cc_start: 0.7818 (m-80) cc_final: 0.7231 (m-80) outliers start: 46 outliers final: 27 residues processed: 310 average time/residue: 0.3708 time to fit residues: 185.7274 Evaluate side-chains 297 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 2.783 ------------------------------------------------------------------------------- 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 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 G residue 71 SER 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 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 J residue 438 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 619 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 168 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 181 optimal weight: 0.5980 chunk 174 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 269 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 300 optimal weight: 8.9990 chunk 131 optimal weight: 0.7980 chunk 229 optimal weight: 0.6980 chunk 289 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 362 GLN ** 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 = 0.4390 r_free = 0.4390 target = 0.185135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134214 restraints weight = 43917.426| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.68 r_work: 0.3553 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26779 Z= 0.131 Angle : 0.551 16.785 36169 Z= 0.284 Chirality : 0.039 0.249 4066 Planarity : 0.004 0.060 4640 Dihedral : 3.974 21.723 3545 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.45 % Allowed : 13.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3231 helix: 1.22 (0.12), residues: 1917 sheet: -1.68 (0.50), residues: 83 loop : -1.57 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 209 HIS 0.005 0.001 HIS F 476 PHE 0.026 0.001 PHE F 626 TYR 0.038 0.001 TYR A 558 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 1369) hydrogen bonds : angle 4.13563 ( 4044) metal coordination : bond 0.00693 ( 22) metal coordination : angle 5.10693 ( 12) covalent geometry : bond 0.00305 (26757) covalent geometry : angle 0.54314 (36157) *********************** 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 320 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 278 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 GLN cc_start: 0.8309 (mm110) cc_final: 0.8037 (mm110) REVERT: H 6 MET cc_start: 0.6940 (tmm) cc_final: 0.6409 (ttm) REVERT: I 104 GLN cc_start: 0.6905 (mm110) cc_final: 0.6642 (mp10) REVERT: B 112 PHE cc_start: 0.8076 (t80) cc_final: 0.7832 (t80) REVERT: B 251 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8181 (ttm-80) REVERT: B 438 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8112 (mtm) REVERT: B 467 TYR cc_start: 0.7760 (t80) cc_final: 0.7555 (t80) REVERT: B 596 TYR cc_start: 0.7357 (t80) cc_final: 0.6827 (t80) REVERT: D 43 ARG cc_start: 0.6265 (tpp-160) cc_final: 0.6024 (tpp-160) REVERT: J 206 LEU cc_start: 0.8501 (mp) cc_final: 0.8280 (mp) REVERT: J 241 HIS cc_start: 0.7144 (t-90) cc_final: 0.6824 (t-170) REVERT: J 327 GLU cc_start: 0.8208 (tp30) cc_final: 0.7966 (tp30) REVERT: J 438 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8593 (m-30) REVERT: K -20 SER cc_start: 0.8634 (m) cc_final: 0.8015 (p) REVERT: F 326 MET cc_start: 0.8275 (tpp) cc_final: 0.7990 (tpp) REVERT: F 376 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8048 (mmtm) REVERT: F 565 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.6422 (m-70) outliers start: 42 outliers final: 33 residues processed: 308 average time/residue: 0.3605 time to fit residues: 180.0287 Evaluate side-chains 305 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 2.746 ------------------------------------------------------------------------------- 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 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 I residue 38 VAL 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 398 LEU Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 696 HIS Chi-restraints excluded: chain C residue 25 ASP 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 438 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 4.9990 chunk 229 optimal weight: 0.0370 chunk 228 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 121 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 312 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 overall best weight: 0.3658 ------------------------------------------------------------------------------- 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 143 ASN ** 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 = 0.4400 r_free = 0.4400 target = 0.187009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.136492 restraints weight = 43783.260| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.75 r_work: 0.3562 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26779 Z= 0.115 Angle : 0.544 15.415 36169 Z= 0.282 Chirality : 0.039 0.218 4066 Planarity : 0.003 0.059 4640 Dihedral : 3.933 22.018 3545 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.14 % Allowed : 14.16 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3231 helix: 1.30 (0.12), residues: 1915 sheet: -1.68 (0.50), residues: 83 loop : -1.56 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 35 HIS 0.005 0.001 HIS F 476 PHE 0.026 0.001 PHE J 626 TYR 0.013 0.001 TYR G 76 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 1369) hydrogen bonds : angle 4.08401 ( 4044) metal coordination : bond 0.00707 ( 22) metal coordination : angle 4.72339 ( 12) covalent geometry : bond 0.00259 (26757) covalent geometry : angle 0.53769 (36157) ********************** 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 309 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 MET cc_start: 0.7251 (tpp) cc_final: 0.6539 (tpp) REVERT: A 538 GLN cc_start: 0.8286 (mm110) cc_final: 0.8011 (mm110) REVERT: H 6 MET cc_start: 0.6898 (tmm) cc_final: 0.6392 (ttm) REVERT: I 104 GLN cc_start: 0.6815 (mm110) cc_final: 0.6584 (mp10) REVERT: B 112 PHE cc_start: 0.8034 (t80) cc_final: 0.7805 (t80) REVERT: B 438 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8113 (mtm) REVERT: B 467 TYR cc_start: 0.7753 (t80) cc_final: 0.7539 (t80) REVERT: B 596 TYR cc_start: 0.7244 (t80) cc_final: 0.6699 (t80) REVERT: D 43 ARG cc_start: 0.6455 (tpp-160) cc_final: 0.6195 (tpp-160) REVERT: J 206 LEU cc_start: 0.8483 (mp) cc_final: 0.8258 (mp) REVERT: J 241 HIS cc_start: 0.7165 (t-90) cc_final: 0.6853 (t-170) REVERT: J 327 GLU cc_start: 0.8204 (tp30) cc_final: 0.7974 (tp30) REVERT: J 438 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8565 (m-30) REVERT: K -20 SER cc_start: 0.8594 (m) cc_final: 0.7995 (p) REVERT: F 159 MET cc_start: 0.5116 (mmp) cc_final: 0.4875 (mmt) REVERT: F 326 MET cc_start: 0.8233 (tpp) cc_final: 0.7954 (tpp) REVERT: F 376 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8056 (mmtm) REVERT: F 384 ASP cc_start: 0.8123 (t0) cc_final: 0.7674 (m-30) REVERT: F 565 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.6301 (m170) outliers start: 33 outliers final: 27 residues processed: 300 average time/residue: 0.3555 time to fit residues: 172.9501 Evaluate side-chains 295 residues out of total 2901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 3.110 ------------------------------------------------------------------------------- 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 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 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 189 VAL Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain B residue 449 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 J residue 438 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 79 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 157 optimal weight: 9.9990 chunk 27 optimal weight: 0.4980 chunk 303 optimal weight: 0.9990 chunk 169 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** C 108 ASN ** 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 = 0.4380 r_free = 0.4380 target = 0.181206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132994 restraints weight = 42364.799| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 3.05 r_work: 0.3569 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26779 Z= 0.131 Angle : 0.554 15.446 36169 Z= 0.286 Chirality : 0.039 0.215 4066 Planarity : 0.004 0.060 4640 Dihedral : 3.927 22.105 3545 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.38 % Allowed : 14.30 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3231 helix: 1.28 (0.12), residues: 1915 sheet: -1.74 (0.50), residues: 83 loop : -1.56 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 209 HIS 0.005 0.001 HIS F 476 PHE 0.026 0.001 PHE J 626 TYR 0.038 0.001 TYR A 558 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 1369) hydrogen bonds : angle 4.08969 ( 4044) metal coordination : bond 0.00659 ( 22) metal coordination : angle 4.74212 ( 12) covalent geometry : bond 0.00305 (26757) covalent geometry : angle 0.54764 (36157) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14134.57 seconds wall clock time: 245 minutes 54.82 seconds (14754.82 seconds total)