Starting phenix.real_space_refine on Thu Mar 5 21:22:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tg9_10495/03_2026/6tg9_10495.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tg9_10495/03_2026/6tg9_10495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tg9_10495/03_2026/6tg9_10495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tg9_10495/03_2026/6tg9_10495.map" model { file = "/net/cci-nas-00/data/ceres_data/6tg9_10495/03_2026/6tg9_10495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tg9_10495/03_2026/6tg9_10495.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 48 7.16 5 P 14 5.49 5 S 232 5.16 5 C 15818 2.51 5 N 4546 2.21 5 O 4752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25412 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7261 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 55, 'TRANS': 893} Chain: "B" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3645 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 30, 'TRANS': 462} Chain: "G" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1076 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "D" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 505 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 8, 'TRANS': 60} Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 131 Ad-hoc single atom residues: {'6MO': 1} Unusual residues: {'FES': 1, 'H2S': 1, 'MGD': 2, 'SF4': 4} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 1 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2875 SG CYS A 386 117.182 70.640 77.272 1.00 7.54 S ATOM 368 SG CYS A 57 89.637 94.653 56.321 1.00 3.56 S ATOM 442 SG CYS A 68 85.866 95.047 55.342 1.00 3.19 S ATOM 467 SG CYS A 71 85.021 98.459 59.082 1.00 6.31 S ATOM 568 SG CYS A 85 88.693 99.076 59.391 1.00 7.88 S ATOM 909 SG CYS A 130 84.111 81.763 52.937 1.00 3.17 S ATOM 852 SG CYS A 121 79.595 79.452 48.578 1.00 16.27 S ATOM 873 SG CYS A 124 85.380 76.133 49.472 1.00 4.70 S ATOM 1347 SG CYS A 185 91.443 88.462 53.256 1.00 4.93 S ATOM 1326 SG CYS A 182 93.268 86.268 47.471 1.00 5.76 S ATOM 1698 SG CYS A 234 92.098 82.196 52.783 1.00 16.27 S ATOM 1372 SG CYS A 188 97.400 86.449 52.275 1.00 5.12 S ATOM 1671 SG CYS A 230 99.486 80.178 55.402 1.00 6.94 S ATOM 1637 SG CYS A 224 104.914 78.460 54.122 1.00 7.72 S ATOM 1656 SG CYS A 227 103.209 80.005 60.480 1.00 16.27 S ATOM 1401 SG CYS A 192 104.854 84.620 56.440 1.00 3.35 S ATOM 1879 SG CYS A 258 103.168 70.723 70.038 1.00 5.48 S ATOM 2135 SG CYS A 293 105.565 73.915 65.834 1.00 16.27 S ATOM 1902 SG CYS A 261 108.688 74.919 71.417 1.00 5.21 S ATOM 1923 SG CYS A 265 103.038 77.511 70.955 1.00 5.41 S ATOM 10736 SG CYS B 471 92.222 106.680 46.250 1.00 7.07 S ATOM 10464 SG CYS B 433 90.747 101.868 42.412 1.00 3.44 S ATOM 10444 SG CYS B 430 89.010 101.057 48.203 1.00 3.21 S ATOM 10427 SG CYS B 427 95.285 100.838 46.917 1.00 4.74 S ATOM 11482 SG CYS G 77 99.187 111.666 27.782 1.00 19.46 S ATOM 11518 SG CYS G 82 98.825 114.152 25.823 1.00 19.75 S ATOM 11763 SG CYS G 116 100.317 114.663 31.851 1.00 17.51 S ATOM 11789 SG CYS G 120 98.921 117.866 30.579 1.00 20.46 S Restraints were copied for chains: E, F, C, H Time building chain proxies: 10.77, per 1000 atoms: 0.42 Number of scatterers: 25412 At special positions: 0 Unit cell: (155.15, 157.29, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mo 2 41.97 Fe 48 26.01 S 232 16.00 P 14 15.00 O 4752 8.00 N 4546 7.00 C 15818 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: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1004 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 68 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 85 " pdb="FE1 FES A1004 " - pdb=" SG CYS A 57 " pdb="FE2 FES A1004 " - pdb=" SG CYS A 71 " pdb=" FES C 201 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 82 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 77 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 120 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 116 " pdb=" FES E1004 " pdb="FE1 FES E1004 " - pdb=" SG CYS E 68 " pdb="FE2 FES E1004 " - pdb=" SG CYS E 85 " pdb="FE1 FES E1004 " - pdb=" SG CYS E 57 " pdb="FE2 FES E1004 " - pdb=" SG CYS E 71 " pdb=" FES G 201 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 82 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 77 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 120 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 116 " pdb=" SF4 A1005 " pdb="FE2 SF4 A1005 " - pdb=" SG CYS A 121 " pdb="FE4 SF4 A1005 " - pdb=" NE2 HIS A 117 " pdb="FE3 SF4 A1005 " - pdb=" SG CYS A 124 " pdb="FE1 SF4 A1005 " - pdb=" SG CYS A 130 " pdb=" SF4 A1006 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 182 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 234 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 185 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 188 " pdb=" SF4 A1007 " pdb="FE2 SF4 A1007 " - pdb=" SG CYS A 224 " pdb="FE4 SF4 A1007 " - pdb=" SG CYS A 192 " pdb="FE3 SF4 A1007 " - pdb=" SG CYS A 227 " pdb="FE1 SF4 A1007 " - pdb=" SG CYS A 230 " pdb=" SF4 A1008 " pdb="FE2 SF4 A1008 " - pdb=" SG CYS A 293 " pdb="FE3 SF4 A1008 " - pdb=" SG CYS A 261 " pdb="FE4 SF4 A1008 " - pdb=" SG CYS A 265 " pdb="FE1 SF4 A1008 " - pdb=" SG CYS A 258 " pdb=" SF4 B 602 " pdb="FE3 SF4 B 602 " - pdb=" SG CYS B 430 " pdb="FE4 SF4 B 602 " - pdb=" SG CYS B 427 " pdb="FE1 SF4 B 602 " - pdb=" SG CYS B 471 " pdb="FE2 SF4 B 602 " - pdb=" SG CYS B 433 " pdb=" SF4 E1005 " pdb="FE2 SF4 E1005 " - pdb=" SG CYS E 121 " pdb="FE4 SF4 E1005 " - pdb=" NE2 HIS E 117 " pdb="FE3 SF4 E1005 " - pdb=" SG CYS E 124 " pdb="FE1 SF4 E1005 " - pdb=" SG CYS E 130 " pdb=" SF4 E1006 " pdb="FE2 SF4 E1006 " - pdb=" SG CYS E 182 " pdb="FE3 SF4 E1006 " - pdb=" SG CYS E 234 " pdb="FE1 SF4 E1006 " - pdb=" SG CYS E 185 " pdb="FE4 SF4 E1006 " - pdb=" SG CYS E 188 " pdb=" SF4 E1007 " pdb="FE2 SF4 E1007 " - pdb=" SG CYS E 224 " pdb="FE4 SF4 E1007 " - pdb=" SG CYS E 192 " pdb="FE3 SF4 E1007 " - pdb=" SG CYS E 227 " pdb="FE1 SF4 E1007 " - pdb=" SG CYS E 230 " pdb=" SF4 E1008 " pdb="FE2 SF4 E1008 " - pdb=" SG CYS E 293 " pdb="FE3 SF4 E1008 " - pdb=" SG CYS E 261 " pdb="FE4 SF4 E1008 " - pdb=" SG CYS E 265 " pdb="FE1 SF4 E1008 " - pdb=" SG CYS E 258 " pdb=" SF4 F 602 " pdb="FE3 SF4 F 602 " - pdb=" SG CYS F 430 " pdb="FE4 SF4 F 602 " - pdb=" SG CYS F 427 " pdb="FE1 SF4 F 602 " - pdb=" SG CYS F 471 " pdb="FE2 SF4 F 602 " - pdb=" SG CYS F 433 " Number of angles added : 138 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6008 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 32 sheets defined 43.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 41 through 49 Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 132 through 139 removed outlier: 3.616A pdb=" N VAL A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.528A pdb=" N HIS A 305 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 345 removed outlier: 3.876A pdb=" N ALA A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 359 through 372 removed outlier: 3.502A pdb=" N THR A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.547A pdb=" N ARG A 384 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 removed outlier: 4.200A pdb=" N LYS A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 427 through 439 removed outlier: 3.712A pdb=" N ARG A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 removed outlier: 3.830A pdb=" N MET A 477 " --> pdb=" O ASN A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 499 removed outlier: 3.631A pdb=" N ILE A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.774A pdb=" N ASP A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 516 removed outlier: 3.521A pdb=" N TYR A 516 " --> pdb=" O ASN A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 516' Processing helix chain 'A' and resid 517 through 526 removed outlier: 5.450A pdb=" N SER A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 542 removed outlier: 3.859A pdb=" N LEU A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.818A pdb=" N THR A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 550 through 555' Processing helix chain 'A' and resid 559 through 574 Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 613 through 625 removed outlier: 3.632A pdb=" N LEU A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 646 Processing helix chain 'A' and resid 664 through 674 removed outlier: 3.524A pdb=" N ALA A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 692 removed outlier: 3.551A pdb=" N ASN A 690 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 749 through 761 removed outlier: 3.995A pdb=" N ILE A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 843 through 847 removed outlier: 3.996A pdb=" N THR A 846 " --> pdb=" O THR A 843 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 847 " --> pdb=" O GLU A 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 843 through 847' Processing helix chain 'A' and resid 858 through 863 removed outlier: 4.382A pdb=" N THR A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 950 removed outlier: 3.814A pdb=" N ASP A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 15 through 30 Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.622A pdb=" N LEU B 47 " --> pdb=" O MET B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 90 through 95 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.532A pdb=" N ARG B 125 " --> pdb=" O TRP B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.713A pdb=" N SER B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 183 through 191 Processing helix chain 'B' and resid 193 through 208 removed outlier: 3.574A pdb=" N VAL B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 234 Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.628A pdb=" N GLU B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 294 through 308 removed outlier: 4.003A pdb=" N VAL B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.571A pdb=" N TYR B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 377 through 383 removed outlier: 4.359A pdb=" N HIS B 382 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 393 Processing helix chain 'B' and resid 410 through 425 removed outlier: 3.689A pdb=" N MET B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 450 removed outlier: 3.945A pdb=" N GLY B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 437 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 Processing helix chain 'B' and resid 477 through 488 removed outlier: 4.134A pdb=" N VAL B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 14 Processing helix chain 'G' and resid 20 through 33 Processing helix chain 'G' and resid 36 through 39 Processing helix chain 'G' and resid 40 through 48 removed outlier: 3.627A pdb=" N ALA G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 61 Processing helix chain 'G' and resid 79 through 85 Processing helix chain 'G' and resid 86 through 98 removed outlier: 4.072A pdb=" N VAL G 90 " --> pdb=" O GLY G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 147 removed outlier: 3.887A pdb=" N GLY G 143 " --> pdb=" O ALA G 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 19 removed outlier: 4.324A pdb=" N VAL D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'D' and resid 56 through 63 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'E' and resid 41 through 49 Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 132 through 139 removed outlier: 3.616A pdb=" N VAL E 139 " --> pdb=" O MET E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 182 Processing helix chain 'E' and resid 186 through 195 Processing helix chain 'E' and resid 228 through 234 Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 293 through 298 Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.528A pdb=" N HIS E 305 " --> pdb=" O TYR E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 345 removed outlier: 3.875A pdb=" N ALA E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 350 Processing helix chain 'E' and resid 359 through 372 removed outlier: 3.502A pdb=" N THR E 363 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 385 removed outlier: 3.547A pdb=" N ARG E 384 " --> pdb=" O THR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 398 removed outlier: 4.199A pdb=" N LYS E 395 " --> pdb=" O GLY E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'E' and resid 427 through 439 removed outlier: 3.713A pdb=" N ARG E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG E 437 " --> pdb=" O ARG E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 487 removed outlier: 3.831A pdb=" N MET E 477 " --> pdb=" O ASN E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 499 removed outlier: 3.631A pdb=" N ILE E 495 " --> pdb=" O ASP E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 512 removed outlier: 3.773A pdb=" N ASP E 506 " --> pdb=" O ASP E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 516 removed outlier: 3.521A pdb=" N TYR E 516 " --> pdb=" O ASN E 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 513 through 516' Processing helix chain 'E' and resid 517 through 526 removed outlier: 5.450A pdb=" N SER E 523 " --> pdb=" O GLU E 519 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 542 removed outlier: 3.859A pdb=" N LEU E 532 " --> pdb=" O PRO E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 555 removed outlier: 3.818A pdb=" N THR E 554 " --> pdb=" O GLY E 550 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 555 " --> pdb=" O LEU E 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 550 through 555' Processing helix chain 'E' and resid 559 through 574 Processing helix chain 'E' and resid 591 through 598 Processing helix chain 'E' and resid 613 through 625 removed outlier: 3.632A pdb=" N LEU E 619 " --> pdb=" O ALA E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 635 through 646 Processing helix chain 'E' and resid 664 through 674 removed outlier: 3.524A pdb=" N ALA E 674 " --> pdb=" O ALA E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 692 removed outlier: 3.551A pdb=" N ASN E 690 " --> pdb=" O GLU E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 742 Processing helix chain 'E' and resid 749 through 761 removed outlier: 3.995A pdb=" N ILE E 753 " --> pdb=" O HIS E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 776 Processing helix chain 'E' and resid 843 through 847 removed outlier: 3.995A pdb=" N THR E 846 " --> pdb=" O THR E 843 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL E 847 " --> pdb=" O GLU E 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 843 through 847' Processing helix chain 'E' and resid 858 through 863 removed outlier: 4.382A pdb=" N THR E 863 " --> pdb=" O THR E 859 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 950 removed outlier: 3.815A pdb=" N ASP E 943 " --> pdb=" O ASP E 939 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 15 through 30 Processing helix chain 'F' and resid 44 through 48 removed outlier: 3.622A pdb=" N LEU F 47 " --> pdb=" O MET F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 90 through 95 Processing helix chain 'F' and resid 111 through 118 Processing helix chain 'F' and resid 121 through 128 removed outlier: 3.532A pdb=" N ARG F 125 " --> pdb=" O TRP F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.712A pdb=" N SER F 142 " --> pdb=" O GLU F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 163 Processing helix chain 'F' and resid 183 through 191 Processing helix chain 'F' and resid 193 through 208 removed outlier: 3.575A pdb=" N VAL F 197 " --> pdb=" O PRO F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 234 Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.627A pdb=" N GLU F 240 " --> pdb=" O PRO F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 257 Processing helix chain 'F' and resid 258 through 267 Processing helix chain 'F' and resid 284 through 288 Processing helix chain 'F' and resid 294 through 308 removed outlier: 4.001A pdb=" N VAL F 301 " --> pdb=" O SER F 297 " (cutoff:3.500A) Proline residue: F 302 - end of helix Processing helix chain 'F' and resid 308 through 313 removed outlier: 3.570A pdb=" N TYR F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 352 Processing helix chain 'F' and resid 377 through 383 removed outlier: 4.361A pdb=" N HIS F 382 " --> pdb=" O SER F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 393 Processing helix chain 'F' and resid 410 through 425 removed outlier: 3.689A pdb=" N MET F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 450 removed outlier: 3.945A pdb=" N GLY F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA F 437 " --> pdb=" O CYS F 433 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL F 438 " --> pdb=" O ARG F 434 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU F 442 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP F 445 " --> pdb=" O VAL F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 469 Processing helix chain 'F' and resid 477 through 488 removed outlier: 4.134A pdb=" N VAL F 481 " --> pdb=" O THR F 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 36 through 39 Processing helix chain 'C' and resid 40 through 48 removed outlier: 3.628A pdb=" N ALA C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 61 Processing helix chain 'C' and resid 79 through 85 Processing helix chain 'C' and resid 86 through 98 removed outlier: 4.072A pdb=" N VAL C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 removed outlier: 3.887A pdb=" N GLY C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 4.324A pdb=" N VAL H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 36 Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 removed outlier: 9.358A pdb=" N VAL A 95 " --> pdb=" O HIS A 26 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 28 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 204 Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 257 removed outlier: 3.622A pdb=" N ARG A 278 " --> pdb=" O HIS A 270 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 272 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 353 removed outlier: 5.925A pdb=" N ILE A 353 " --> pdb=" O GLN A 654 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 463 through 465 removed outlier: 6.470A pdb=" N LEU A 444 " --> pdb=" O TRP A 464 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA A 545 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ASN A 584 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE A 547 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 604 through 605 removed outlier: 3.586A pdb=" N ARG A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 706 through 709 removed outlier: 3.753A pdb=" N VAL A 778 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 827 through 828 Processing sheet with id=AB2, first strand: chain 'A' and resid 853 through 856 Processing sheet with id=AB3, first strand: chain 'B' and resid 35 through 37 removed outlier: 5.450A pdb=" N LYS B 2 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 54 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 52 " --> pdb=" O TRP B 4 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 85 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 244 through 249 removed outlier: 6.645A pdb=" N GLY B 212 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ARG B 248 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B 214 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 171 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR B 215 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS B 173 " --> pdb=" O TYR B 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 323 through 328 Processing sheet with id=AB6, first strand: chain 'B' and resid 375 through 376 removed outlier: 7.005A pdb=" N HIS B 405 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL B 366 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 403 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 111 through 112 removed outlier: 6.191A pdb=" N ILE G 74 " --> pdb=" O GLU G 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 36 removed outlier: 9.358A pdb=" N VAL E 95 " --> pdb=" O HIS E 26 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR E 28 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 175 through 177 Processing sheet with id=AC1, first strand: chain 'E' and resid 202 through 204 Processing sheet with id=AC2, first strand: chain 'E' and resid 252 through 257 removed outlier: 3.623A pdb=" N ARG E 278 " --> pdb=" O HIS E 270 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU E 272 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU E 276 " --> pdb=" O LEU E 272 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 313 through 314 Processing sheet with id=AC4, first strand: chain 'E' and resid 352 through 353 removed outlier: 5.926A pdb=" N ILE E 353 " --> pdb=" O GLN E 654 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 463 through 465 removed outlier: 6.471A pdb=" N LEU E 444 " --> pdb=" O TRP E 464 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ALA E 545 " --> pdb=" O GLY E 582 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN E 584 " --> pdb=" O ALA E 545 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE E 547 " --> pdb=" O ASN E 584 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 604 through 605 removed outlier: 3.585A pdb=" N ARG E 609 " --> pdb=" O PHE E 605 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 706 through 709 removed outlier: 3.753A pdb=" N VAL E 778 " --> pdb=" O ILE E 715 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 827 through 828 Processing sheet with id=AC9, first strand: chain 'E' and resid 853 through 856 Processing sheet with id=AD1, first strand: chain 'F' and resid 35 through 37 removed outlier: 5.451A pdb=" N LYS F 2 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 54 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU F 52 " --> pdb=" O TRP F 4 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY F 85 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 244 through 249 removed outlier: 6.645A pdb=" N GLY F 212 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ARG F 248 " --> pdb=" O GLY F 212 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL F 214 " --> pdb=" O ARG F 248 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE F 171 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N TYR F 215 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS F 173 " --> pdb=" O TYR F 215 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 323 through 328 Processing sheet with id=AD4, first strand: chain 'F' and resid 375 through 376 removed outlier: 7.005A pdb=" N HIS F 405 " --> pdb=" O LYS F 364 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL F 366 " --> pdb=" O VAL F 403 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL F 403 " --> pdb=" O VAL F 366 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 111 through 112 removed outlier: 6.191A pdb=" N ILE C 74 " --> pdb=" O GLU C 112 " (cutoff:3.500A) 958 hydrogen bonds defined for protein. 2670 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: 5.43 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 10681 1.42 - 1.64: 14919 1.64 - 1.85: 286 1.85 - 2.07: 2 2.07 - 2.28: 136 Bond restraints: 26024 Sorted by residual: bond pdb=" O3A MGD E1001 " pdb=" PA MGD E1001 " ideal model delta sigma weight residual 1.649 1.858 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" O3A MGD A1001 " pdb=" PA MGD A1001 " ideal model delta sigma weight residual 1.649 1.857 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" O3A MGD E1002 " pdb=" PA MGD E1002 " ideal model delta sigma weight residual 1.649 1.851 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O3A MGD A1002 " pdb=" PA MGD A1002 " ideal model delta sigma weight residual 1.649 1.850 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" O5' MGD E1001 " pdb=" PB MGD E1001 " ideal model delta sigma weight residual 1.646 1.830 -0.184 2.00e-02 2.50e+03 8.50e+01 ... (remaining 26019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 35160 4.18 - 8.37: 320 8.37 - 12.55: 18 12.55 - 16.74: 14 16.74 - 20.92: 8 Bond angle restraints: 35520 Sorted by residual: angle pdb=" S1 FES G 201 " pdb="FE2 FES G 201 " pdb=" S2 FES G 201 " ideal model delta sigma weight residual 104.33 83.44 20.89 1.14e+00 7.69e-01 3.36e+02 angle pdb=" S1 FES C 201 " pdb="FE2 FES C 201 " pdb=" S2 FES C 201 " ideal model delta sigma weight residual 104.33 83.46 20.87 1.14e+00 7.69e-01 3.35e+02 angle pdb=" S1 FES G 201 " pdb="FE1 FES G 201 " pdb=" S2 FES G 201 " ideal model delta sigma weight residual 104.33 83.41 20.92 1.20e+00 6.94e-01 3.04e+02 angle pdb=" S1 FES E1004 " pdb="FE2 FES E1004 " pdb=" S2 FES E1004 " ideal model delta sigma weight residual 104.33 84.46 19.87 1.14e+00 7.69e-01 3.04e+02 angle pdb=" S1 FES A1004 " pdb="FE2 FES A1004 " pdb=" S2 FES A1004 " ideal model delta sigma weight residual 104.33 84.47 19.86 1.14e+00 7.69e-01 3.03e+02 ... (remaining 35515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14029 17.99 - 35.98: 1316 35.98 - 53.97: 230 53.97 - 71.96: 61 71.96 - 89.95: 30 Dihedral angle restraints: 15666 sinusoidal: 6272 harmonic: 9394 Sorted by residual: dihedral pdb=" CA TYR A 260 " pdb=" C TYR A 260 " pdb=" N CYS A 261 " pdb=" CA CYS A 261 " ideal model delta harmonic sigma weight residual 180.00 152.28 27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA TYR E 260 " pdb=" C TYR E 260 " pdb=" N CYS E 261 " pdb=" CA CYS E 261 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA LEU F 144 " pdb=" C LEU F 144 " pdb=" N ARG F 145 " pdb=" CA ARG F 145 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 15663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3499 0.087 - 0.173: 409 0.173 - 0.260: 45 0.260 - 0.347: 11 0.347 - 0.433: 4 Chirality restraints: 3968 Sorted by residual: chirality pdb=" C14 MGD A1002 " pdb=" C13 MGD A1002 " pdb=" C23 MGD A1002 " pdb=" N15 MGD A1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.99 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C14 MGD E1002 " pdb=" C13 MGD E1002 " pdb=" C23 MGD E1002 " pdb=" N15 MGD E1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.99 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C23 MGD E1002 " pdb=" C14 MGD E1002 " pdb=" N22 MGD E1002 " pdb=" O11 MGD E1002 " both_signs ideal model delta sigma weight residual False 2.33 2.75 -0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 3965 not shown) Planarity restraints: 4612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 477 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 478 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 478 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 478 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 477 " 0.033 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO F 478 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO F 478 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 478 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 280 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 281 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.024 5.00e-02 4.00e+02 ... (remaining 4609 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 186 2.46 - 3.07: 18468 3.07 - 3.68: 38601 3.68 - 4.29: 58339 4.29 - 4.90: 101374 Nonbonded interactions: 216968 Sorted by model distance: nonbonded pdb=" OG1 THR E 882 " pdb=" O PRO E 937 " model vdw 1.847 3.040 nonbonded pdb=" OG1 THR A 882 " pdb=" O PRO A 937 " model vdw 1.848 3.040 nonbonded pdb=" OG1 THR F 357 " pdb=" O ARG F 361 " model vdw 2.015 3.040 nonbonded pdb=" OG1 THR B 357 " pdb=" O ARG B 361 " model vdw 2.016 3.040 nonbonded pdb=" O LYS E 395 " pdb=" NH2 ARG E 800 " model vdw 2.019 3.120 ... (remaining 216963 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 33.680 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.017 0.409 26080 Z= 0.838 Angle : 1.499 38.872 35658 Z= 0.890 Chirality : 0.062 0.433 3968 Planarity : 0.004 0.049 4612 Dihedral : 14.815 89.948 9658 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.78 % Favored : 91.97 % Rotamer: Outliers : 0.62 % Allowed : 5.39 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.02 (0.12), residues: 3302 helix: -2.11 (0.12), residues: 1246 sheet: -3.07 (0.23), residues: 344 loop : -3.06 (0.12), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 713 TYR 0.020 0.002 TYR A 260 PHE 0.014 0.002 PHE A 407 TRP 0.013 0.001 TRP A 11 HIS 0.010 0.002 HIS E 603 Details of bonding type rmsd covalent geometry : bond 0.01560 (26024) covalent geometry : angle 1.31737 (35520) hydrogen bonds : bond 0.15734 ( 958) hydrogen bonds : angle 7.35676 ( 2670) metal coordination : bond 0.12231 ( 56) metal coordination : angle 11.57455 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 575 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8469 (m-10) cc_final: 0.8219 (m-80) REVERT: A 209 ASP cc_start: 0.7466 (t0) cc_final: 0.7006 (t0) REVERT: A 328 THR cc_start: 0.7645 (m) cc_final: 0.7267 (m) REVERT: A 501 TRP cc_start: 0.7047 (t-100) cc_final: 0.6383 (t-100) REVERT: A 728 PHE cc_start: 0.7192 (m-80) cc_final: 0.6837 (m-10) REVERT: B 170 TYR cc_start: 0.7894 (m-80) cc_final: 0.7672 (m-80) REVERT: B 349 LEU cc_start: 0.8126 (tp) cc_final: 0.7875 (tp) REVERT: G 136 LEU cc_start: 0.7194 (mp) cc_final: 0.6994 (mt) REVERT: E 199 PHE cc_start: 0.8464 (m-10) cc_final: 0.8239 (m-10) REVERT: E 209 ASP cc_start: 0.7471 (t0) cc_final: 0.7020 (t0) REVERT: E 328 THR cc_start: 0.7658 (m) cc_final: 0.7278 (m) REVERT: E 501 TRP cc_start: 0.6979 (t-100) cc_final: 0.6349 (t-100) REVERT: E 728 PHE cc_start: 0.7221 (m-80) cc_final: 0.6840 (m-10) REVERT: F 349 LEU cc_start: 0.8116 (tp) cc_final: 0.7873 (tp) REVERT: C 115 TYR cc_start: 0.7783 (m-80) cc_final: 0.7506 (m-80) outliers start: 16 outliers final: 2 residues processed: 589 average time/residue: 0.2069 time to fit residues: 179.0721 Evaluate side-chains 364 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 362 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain E residue 12 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN A 405 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 GLN A 558 GLN A 589 GLN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 HIS E 275 GLN E 405 GLN ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 534 GLN E 558 GLN E 589 GLN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.166185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134678 restraints weight = 32288.117| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.73 r_work: 0.3239 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26080 Z= 0.163 Angle : 0.851 26.586 35658 Z= 0.334 Chirality : 0.045 0.198 3968 Planarity : 0.005 0.052 4612 Dihedral : 8.897 101.244 4016 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.12 % Favored : 95.70 % Rotamer: Outliers : 1.48 % Allowed : 11.80 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.14), residues: 3302 helix: -0.48 (0.14), residues: 1254 sheet: -2.51 (0.24), residues: 362 loop : -2.29 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 101 TYR 0.018 0.001 TYR A 260 PHE 0.014 0.001 PHE E 333 TRP 0.020 0.001 TRP A 780 HIS 0.010 0.001 HIS A 901 Details of bonding type rmsd covalent geometry : bond 0.00370 (26024) covalent geometry : angle 0.66175 (35520) hydrogen bonds : bond 0.03886 ( 958) hydrogen bonds : angle 5.16678 ( 2670) metal coordination : bond 0.01768 ( 56) metal coordination : angle 8.62247 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 424 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7982 (mmt180) cc_final: 0.7720 (mmt-90) REVERT: A 60 ASP cc_start: 0.8241 (m-30) cc_final: 0.8020 (m-30) REVERT: A 209 ASP cc_start: 0.8074 (t0) cc_final: 0.7640 (t0) REVERT: A 501 TRP cc_start: 0.7125 (t-100) cc_final: 0.6047 (t-100) REVERT: A 728 PHE cc_start: 0.7387 (m-80) cc_final: 0.7068 (m-10) REVERT: B 185 ASP cc_start: 0.7706 (m-30) cc_final: 0.7421 (m-30) REVERT: B 198 GLU cc_start: 0.7357 (tt0) cc_final: 0.6947 (pt0) REVERT: B 226 VAL cc_start: 0.8085 (t) cc_final: 0.7871 (p) REVERT: B 233 MET cc_start: 0.7576 (mtp) cc_final: 0.7196 (mtp) REVERT: B 349 LEU cc_start: 0.8446 (tp) cc_final: 0.8103 (tp) REVERT: B 381 TYR cc_start: 0.7242 (m-10) cc_final: 0.7020 (m-10) REVERT: G 3 ASP cc_start: 0.6673 (m-30) cc_final: 0.5783 (t0) REVERT: D 45 LEU cc_start: 0.7578 (mt) cc_final: 0.7363 (mt) REVERT: E 20 ARG cc_start: 0.7963 (mmt180) cc_final: 0.7693 (mmt-90) REVERT: E 209 ASP cc_start: 0.8053 (t0) cc_final: 0.7628 (t0) REVERT: E 501 TRP cc_start: 0.7123 (t-100) cc_final: 0.6051 (t-100) REVERT: E 728 PHE cc_start: 0.7351 (m-80) cc_final: 0.7047 (m-10) REVERT: F 185 ASP cc_start: 0.7705 (m-30) cc_final: 0.7438 (m-30) REVERT: F 198 GLU cc_start: 0.7378 (tt0) cc_final: 0.6953 (pt0) REVERT: F 226 VAL cc_start: 0.8083 (t) cc_final: 0.7859 (p) REVERT: F 233 MET cc_start: 0.7542 (mtp) cc_final: 0.7170 (mtp) REVERT: F 264 ASN cc_start: 0.8844 (t0) cc_final: 0.8636 (t0) REVERT: F 349 LEU cc_start: 0.8452 (tp) cc_final: 0.8124 (tp) REVERT: C 115 TYR cc_start: 0.8187 (m-80) cc_final: 0.7459 (m-80) outliers start: 38 outliers final: 15 residues processed: 447 average time/residue: 0.1910 time to fit residues: 130.2864 Evaluate side-chains 359 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 344 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain C residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 166 optimal weight: 0.9990 chunk 170 optimal weight: 0.0980 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 17 optimal weight: 0.0570 chunk 161 optimal weight: 10.0000 chunk 308 optimal weight: 0.2980 chunk 276 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 overall best weight: 0.4500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN A 794 HIS ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 GLN E 794 HIS ** E 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138454 restraints weight = 32141.586| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.77 r_work: 0.3298 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26080 Z= 0.107 Angle : 0.751 27.408 35658 Z= 0.288 Chirality : 0.042 0.151 3968 Planarity : 0.005 0.051 4612 Dihedral : 8.230 90.304 4014 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.03 % Rotamer: Outliers : 1.88 % Allowed : 12.97 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3302 helix: 0.19 (0.15), residues: 1258 sheet: -1.91 (0.26), residues: 360 loop : -1.77 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 101 TYR 0.015 0.001 TYR F 215 PHE 0.013 0.001 PHE A 333 TRP 0.019 0.001 TRP E 780 HIS 0.006 0.001 HIS E 901 Details of bonding type rmsd covalent geometry : bond 0.00241 (26024) covalent geometry : angle 0.57475 (35520) hydrogen bonds : bond 0.03189 ( 958) hydrogen bonds : angle 4.69875 ( 2670) metal coordination : bond 0.01302 ( 56) metal coordination : angle 7.78743 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 377 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7918 (mmt180) cc_final: 0.7620 (mmt-90) REVERT: A 60 ASP cc_start: 0.8133 (m-30) cc_final: 0.7893 (m-30) REVERT: A 209 ASP cc_start: 0.8034 (t0) cc_final: 0.7591 (t0) REVERT: A 501 TRP cc_start: 0.7045 (t-100) cc_final: 0.6052 (t-100) REVERT: A 873 ARG cc_start: 0.7669 (tpp80) cc_final: 0.7302 (ttp80) REVERT: B 47 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6227 (pp) REVERT: B 185 ASP cc_start: 0.7599 (m-30) cc_final: 0.7318 (m-30) REVERT: B 198 GLU cc_start: 0.7200 (tt0) cc_final: 0.6852 (pt0) REVERT: B 226 VAL cc_start: 0.8128 (t) cc_final: 0.7909 (p) REVERT: B 233 MET cc_start: 0.7537 (mtp) cc_final: 0.7194 (mtp) REVERT: D 34 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6768 (mp0) REVERT: E 20 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7613 (mmt-90) REVERT: E 209 ASP cc_start: 0.8023 (t0) cc_final: 0.7598 (t0) REVERT: E 501 TRP cc_start: 0.7062 (t-100) cc_final: 0.6057 (t-100) REVERT: F 47 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6165 (pp) REVERT: F 185 ASP cc_start: 0.7569 (m-30) cc_final: 0.7282 (m-30) REVERT: F 198 GLU cc_start: 0.7238 (tt0) cc_final: 0.6869 (pt0) REVERT: F 226 VAL cc_start: 0.8115 (t) cc_final: 0.7889 (p) REVERT: F 233 MET cc_start: 0.7507 (mtp) cc_final: 0.7186 (mtp) REVERT: C 115 TYR cc_start: 0.8065 (m-80) cc_final: 0.7386 (m-80) REVERT: H 34 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6568 (mp0) REVERT: H 45 LEU cc_start: 0.7493 (mt) cc_final: 0.7246 (mt) outliers start: 48 outliers final: 21 residues processed: 413 average time/residue: 0.1896 time to fit residues: 120.9025 Evaluate side-chains 366 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 343 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 408 ASP Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 94 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 271 optimal weight: 20.0000 chunk 175 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN A 794 HIS A 941 GLN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS E 941 GLN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.157961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127145 restraints weight = 32168.867| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.69 r_work: 0.3147 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 26080 Z= 0.238 Angle : 0.922 33.872 35658 Z= 0.342 Chirality : 0.047 0.220 3968 Planarity : 0.005 0.055 4612 Dihedral : 8.330 94.421 4014 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.39 % Favored : 94.49 % Rotamer: Outliers : 2.30 % Allowed : 14.77 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.14), residues: 3302 helix: 0.04 (0.15), residues: 1292 sheet: -1.71 (0.27), residues: 354 loop : -1.76 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 101 TYR 0.017 0.002 TYR E 260 PHE 0.016 0.002 PHE A 728 TRP 0.016 0.002 TRP A 780 HIS 0.005 0.001 HIS A 794 Details of bonding type rmsd covalent geometry : bond 0.00575 (26024) covalent geometry : angle 0.67811 (35520) hydrogen bonds : bond 0.03720 ( 958) hydrogen bonds : angle 4.79846 ( 2670) metal coordination : bond 0.02336 ( 56) metal coordination : angle 10.05887 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 350 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8135 (t0) cc_final: 0.7629 (t0) REVERT: A 866 ILE cc_start: 0.8618 (mm) cc_final: 0.8414 (mt) REVERT: A 874 LEU cc_start: 0.8123 (mp) cc_final: 0.7833 (mt) REVERT: B 47 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6339 (pp) REVERT: B 198 GLU cc_start: 0.7133 (tt0) cc_final: 0.6821 (pt0) REVERT: B 226 VAL cc_start: 0.8223 (t) cc_final: 0.8017 (p) REVERT: B 233 MET cc_start: 0.7652 (mtp) cc_final: 0.7382 (mtp) REVERT: B 262 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8365 (tp) REVERT: G 46 ASP cc_start: 0.8304 (t0) cc_final: 0.8003 (t0) REVERT: D 34 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7138 (mp0) REVERT: E 209 ASP cc_start: 0.8105 (t0) cc_final: 0.7619 (t0) REVERT: E 866 ILE cc_start: 0.8681 (mm) cc_final: 0.8478 (mt) REVERT: E 874 LEU cc_start: 0.8120 (mp) cc_final: 0.7844 (mt) REVERT: F 47 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6536 (pp) REVERT: F 198 GLU cc_start: 0.7164 (tt0) cc_final: 0.6831 (pt0) REVERT: F 226 VAL cc_start: 0.8219 (t) cc_final: 0.8008 (p) REVERT: F 233 MET cc_start: 0.7567 (mtp) cc_final: 0.7319 (mtp) REVERT: F 262 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8365 (tp) REVERT: C 115 TYR cc_start: 0.8559 (m-80) cc_final: 0.8041 (m-80) REVERT: H 34 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7059 (mp0) outliers start: 59 outliers final: 40 residues processed: 396 average time/residue: 0.1908 time to fit residues: 115.6582 Evaluate side-chains 372 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 793 MET Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 90 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 237 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 225 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS B 293 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS F 293 ASN ** C 29 GLN ** 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 = 0.3876 r_free = 0.3876 target = 0.159989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128129 restraints weight = 32104.235| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.81 r_work: 0.3151 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26080 Z= 0.151 Angle : 0.815 32.681 35658 Z= 0.298 Chirality : 0.043 0.169 3968 Planarity : 0.005 0.055 4612 Dihedral : 8.045 85.630 4014 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.66 % Favored : 95.22 % Rotamer: Outliers : 2.38 % Allowed : 15.47 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3302 helix: 0.30 (0.15), residues: 1302 sheet: -1.69 (0.26), residues: 388 loop : -1.47 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 101 TYR 0.018 0.001 TYR E 260 PHE 0.015 0.001 PHE A 333 TRP 0.018 0.001 TRP E 780 HIS 0.004 0.001 HIS B 399 Details of bonding type rmsd covalent geometry : bond 0.00364 (26024) covalent geometry : angle 0.59527 (35520) hydrogen bonds : bond 0.03217 ( 958) hydrogen bonds : angle 4.59065 ( 2670) metal coordination : bond 0.01646 ( 56) metal coordination : angle 8.97296 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 355 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8214 (t0) cc_final: 0.7721 (t0) REVERT: A 510 PHE cc_start: 0.7173 (t80) cc_final: 0.6931 (t80) REVERT: A 581 VAL cc_start: 0.8742 (m) cc_final: 0.8467 (m) REVERT: A 874 LEU cc_start: 0.8040 (mp) cc_final: 0.7836 (mt) REVERT: B 47 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6442 (pp) REVERT: B 198 GLU cc_start: 0.7284 (tt0) cc_final: 0.6920 (pt0) REVERT: B 226 VAL cc_start: 0.8209 (t) cc_final: 0.7996 (p) REVERT: B 233 MET cc_start: 0.7674 (mtp) cc_final: 0.7367 (mtp) REVERT: B 331 ASN cc_start: 0.8709 (t0) cc_final: 0.8499 (t0) REVERT: G 46 ASP cc_start: 0.8375 (t0) cc_final: 0.8085 (t0) REVERT: E 209 ASP cc_start: 0.8227 (t0) cc_final: 0.7749 (t0) REVERT: E 874 LEU cc_start: 0.8061 (mp) cc_final: 0.7852 (mt) REVERT: F 47 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6399 (pp) REVERT: F 125 ARG cc_start: 0.7392 (ptp90) cc_final: 0.6861 (mmt90) REVERT: F 198 GLU cc_start: 0.7321 (tt0) cc_final: 0.6974 (pt0) REVERT: F 226 VAL cc_start: 0.8202 (t) cc_final: 0.7987 (p) REVERT: F 233 MET cc_start: 0.7632 (mtp) cc_final: 0.7361 (mtp) REVERT: F 262 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8413 (tp) REVERT: F 331 ASN cc_start: 0.8696 (t0) cc_final: 0.8473 (t0) REVERT: C 115 TYR cc_start: 0.8431 (m-80) cc_final: 0.8198 (m-80) outliers start: 61 outliers final: 44 residues processed: 401 average time/residue: 0.1852 time to fit residues: 115.2736 Evaluate side-chains 375 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 328 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 199 PHE Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 290 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 255 optimal weight: 9.9990 chunk 133 optimal weight: 0.0040 chunk 178 optimal weight: 0.0000 chunk 41 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 ASN E 794 HIS ** C 29 GLN ** 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 = 0.3874 r_free = 0.3874 target = 0.159833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129071 restraints weight = 32368.400| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.95 r_work: 0.3152 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26080 Z= 0.144 Angle : 0.809 32.637 35658 Z= 0.295 Chirality : 0.043 0.170 3968 Planarity : 0.005 0.055 4612 Dihedral : 8.015 84.932 4014 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.88 % Favored : 95.00 % Rotamer: Outliers : 2.70 % Allowed : 16.88 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 3302 helix: 0.46 (0.15), residues: 1298 sheet: -1.56 (0.26), residues: 394 loop : -1.32 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 101 TYR 0.018 0.001 TYR B 215 PHE 0.015 0.001 PHE E 510 TRP 0.017 0.001 TRP E 780 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00345 (26024) covalent geometry : angle 0.59124 (35520) hydrogen bonds : bond 0.03132 ( 958) hydrogen bonds : angle 4.49964 ( 2670) metal coordination : bond 0.01561 ( 56) metal coordination : angle 8.89053 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 336 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8250 (t0) cc_final: 0.7744 (t0) REVERT: A 510 PHE cc_start: 0.7037 (t80) cc_final: 0.6824 (t80) REVERT: B 47 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6478 (pp) REVERT: B 125 ARG cc_start: 0.7331 (ptp90) cc_final: 0.6890 (mmt90) REVERT: B 185 ASP cc_start: 0.7668 (m-30) cc_final: 0.7274 (m-30) REVERT: B 198 GLU cc_start: 0.7244 (tt0) cc_final: 0.6927 (pt0) REVERT: B 226 VAL cc_start: 0.8217 (t) cc_final: 0.8017 (p) REVERT: B 233 MET cc_start: 0.7816 (mtp) cc_final: 0.7554 (mtp) REVERT: B 331 ASN cc_start: 0.8676 (t0) cc_final: 0.8455 (t0) REVERT: G 46 ASP cc_start: 0.8444 (t0) cc_final: 0.8157 (t0) REVERT: E 209 ASP cc_start: 0.8214 (t0) cc_final: 0.7729 (t0) REVERT: F 47 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6465 (pp) REVERT: F 125 ARG cc_start: 0.7340 (ptp90) cc_final: 0.6886 (mmt90) REVERT: F 185 ASP cc_start: 0.7623 (m-30) cc_final: 0.7242 (m-30) REVERT: F 198 GLU cc_start: 0.7298 (tt0) cc_final: 0.6978 (pt0) REVERT: F 233 MET cc_start: 0.7746 (mtp) cc_final: 0.7504 (mtp) REVERT: F 331 ASN cc_start: 0.8673 (t0) cc_final: 0.8466 (t0) REVERT: C 95 GLU cc_start: 0.7361 (pt0) cc_final: 0.7152 (mp0) outliers start: 69 outliers final: 54 residues processed: 388 average time/residue: 0.1897 time to fit residues: 114.3058 Evaluate side-chains 372 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 316 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 172 optimal weight: 0.8980 chunk 265 optimal weight: 0.0370 chunk 154 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN A 794 HIS ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN E 660 GLN E 794 HIS E 835 ASN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128938 restraints weight = 32304.230| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.89 r_work: 0.3134 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26080 Z= 0.173 Angle : 0.842 33.351 35658 Z= 0.309 Chirality : 0.044 0.192 3968 Planarity : 0.005 0.058 4612 Dihedral : 8.049 81.427 4014 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.33 % Favored : 94.55 % Rotamer: Outliers : 2.97 % Allowed : 17.03 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3302 helix: 0.45 (0.15), residues: 1302 sheet: -1.39 (0.28), residues: 380 loop : -1.26 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 101 TYR 0.018 0.002 TYR E 260 PHE 0.015 0.001 PHE E 333 TRP 0.016 0.001 TRP E 780 HIS 0.004 0.001 HIS E 794 Details of bonding type rmsd covalent geometry : bond 0.00418 (26024) covalent geometry : angle 0.61615 (35520) hydrogen bonds : bond 0.03256 ( 958) hydrogen bonds : angle 4.55034 ( 2670) metal coordination : bond 0.01820 ( 56) metal coordination : angle 9.23543 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 332 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8284 (t0) cc_final: 0.7758 (t0) REVERT: A 501 TRP cc_start: 0.7258 (t-100) cc_final: 0.7002 (t-100) REVERT: B 47 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6313 (pp) REVERT: B 125 ARG cc_start: 0.7339 (ptp90) cc_final: 0.6845 (mmt90) REVERT: B 185 ASP cc_start: 0.7704 (m-30) cc_final: 0.7325 (m-30) REVERT: B 198 GLU cc_start: 0.7259 (tt0) cc_final: 0.6947 (pt0) REVERT: B 226 VAL cc_start: 0.8234 (t) cc_final: 0.7983 (p) REVERT: B 331 ASN cc_start: 0.8720 (t0) cc_final: 0.8469 (t0) REVERT: G 46 ASP cc_start: 0.8465 (t0) cc_final: 0.8167 (t0) REVERT: E 209 ASP cc_start: 0.8212 (t0) cc_final: 0.7703 (t0) REVERT: E 501 TRP cc_start: 0.7300 (t-100) cc_final: 0.7019 (t-100) REVERT: F 47 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6422 (pp) REVERT: F 125 ARG cc_start: 0.7289 (ptp90) cc_final: 0.6852 (mmt90) REVERT: F 185 ASP cc_start: 0.7610 (m-30) cc_final: 0.7209 (m-30) REVERT: F 198 GLU cc_start: 0.7317 (tt0) cc_final: 0.6980 (pt0) REVERT: F 215 TYR cc_start: 0.8990 (t80) cc_final: 0.8782 (t80) REVERT: F 262 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8316 (tp) REVERT: F 331 ASN cc_start: 0.8707 (t0) cc_final: 0.8436 (t0) outliers start: 76 outliers final: 58 residues processed: 390 average time/residue: 0.1860 time to fit residues: 112.6668 Evaluate side-chains 381 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 320 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 199 PHE Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 935 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 32 optimal weight: 10.0000 chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 245 optimal weight: 0.5980 chunk 161 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 319 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 312 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN A 584 ASN A 794 HIS A 835 ASN ** G 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 794 HIS ** C 29 GLN ** 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 = 0.3847 r_free = 0.3847 target = 0.157520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128594 restraints weight = 32519.758| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.86 r_work: 0.3132 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26080 Z= 0.191 Angle : 0.860 33.554 35658 Z= 0.317 Chirality : 0.045 0.201 3968 Planarity : 0.005 0.057 4612 Dihedral : 8.091 79.529 4014 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.60 % Favored : 94.28 % Rotamer: Outliers : 3.09 % Allowed : 17.07 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 3302 helix: 0.50 (0.15), residues: 1288 sheet: -1.37 (0.27), residues: 380 loop : -1.24 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 622 TYR 0.019 0.002 TYR A 260 PHE 0.015 0.001 PHE E 333 TRP 0.016 0.001 TRP E 780 HIS 0.003 0.001 HIS E 291 Details of bonding type rmsd covalent geometry : bond 0.00464 (26024) covalent geometry : angle 0.63341 (35520) hydrogen bonds : bond 0.03330 ( 958) hydrogen bonds : angle 4.60884 ( 2670) metal coordination : bond 0.01968 ( 56) metal coordination : angle 9.36516 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 337 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8723 (t0) cc_final: 0.8206 (t0) REVERT: A 813 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7518 (p) REVERT: B 47 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6436 (pp) REVERT: B 125 ARG cc_start: 0.7320 (ptp90) cc_final: 0.6857 (mmt90) REVERT: B 126 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7979 (tptp) REVERT: B 198 GLU cc_start: 0.7497 (tt0) cc_final: 0.7174 (pt0) REVERT: B 215 TYR cc_start: 0.9014 (t80) cc_final: 0.8812 (t80) REVERT: B 331 ASN cc_start: 0.8812 (t0) cc_final: 0.8576 (t0) REVERT: B 434 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8467 (ttp-110) REVERT: G 46 ASP cc_start: 0.8711 (t0) cc_final: 0.8454 (t0) REVERT: E 209 ASP cc_start: 0.8676 (t0) cc_final: 0.8164 (t0) REVERT: E 813 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7540 (p) REVERT: F 47 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6451 (pp) REVERT: F 125 ARG cc_start: 0.7345 (ptp90) cc_final: 0.6859 (mmt90) REVERT: F 198 GLU cc_start: 0.7513 (tt0) cc_final: 0.7287 (pt0) REVERT: F 215 TYR cc_start: 0.9112 (t80) cc_final: 0.8906 (t80) REVERT: F 262 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8419 (tp) REVERT: F 331 ASN cc_start: 0.8813 (t0) cc_final: 0.8549 (t0) REVERT: F 434 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8471 (ttp-110) REVERT: C 95 GLU cc_start: 0.7262 (mp0) cc_final: 0.7021 (mp0) outliers start: 79 outliers final: 64 residues processed: 400 average time/residue: 0.1959 time to fit residues: 120.5438 Evaluate side-chains 392 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 320 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 935 ASN Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 199 PHE Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 813 THR Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 830 ILE Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain E residue 905 THR Chi-restraints excluded: chain E residue 935 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 163 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 243 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 252 optimal weight: 0.8980 chunk 285 optimal weight: 0.8980 chunk 114 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 HIS A 835 ASN B 168 GLN G 29 GLN E 794 HIS ** C 29 GLN ** 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 = 0.3896 r_free = 0.3896 target = 0.161760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129885 restraints weight = 32318.976| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.79 r_work: 0.3205 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26080 Z= 0.107 Angle : 0.781 31.841 35658 Z= 0.282 Chirality : 0.042 0.151 3968 Planarity : 0.004 0.057 4612 Dihedral : 7.808 72.633 4014 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 2.62 % Allowed : 18.05 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3302 helix: 0.65 (0.15), residues: 1298 sheet: -1.23 (0.28), residues: 372 loop : -1.14 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 622 TYR 0.017 0.001 TYR B 215 PHE 0.015 0.001 PHE E 333 TRP 0.020 0.001 TRP E 780 HIS 0.005 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00247 (26024) covalent geometry : angle 0.56616 (35520) hydrogen bonds : bond 0.02890 ( 958) hydrogen bonds : angle 4.39016 ( 2670) metal coordination : bond 0.01292 ( 56) metal coordination : angle 8.65591 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8244 (t0) cc_final: 0.7754 (t0) REVERT: A 501 TRP cc_start: 0.7153 (t-100) cc_final: 0.6859 (t-100) REVERT: A 610 HIS cc_start: 0.7379 (t-90) cc_final: 0.7125 (t-90) REVERT: B 47 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6351 (pp) REVERT: B 125 ARG cc_start: 0.7298 (ptp90) cc_final: 0.6860 (mmt90) REVERT: B 198 GLU cc_start: 0.7241 (tt0) cc_final: 0.6932 (pt0) REVERT: B 331 ASN cc_start: 0.8690 (t0) cc_final: 0.8358 (t0) REVERT: G 46 ASP cc_start: 0.8434 (t0) cc_final: 0.8180 (t0) REVERT: E 209 ASP cc_start: 0.8197 (t0) cc_final: 0.7729 (t0) REVERT: E 501 TRP cc_start: 0.7179 (t-100) cc_final: 0.6888 (t-100) REVERT: F 47 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6221 (pp) REVERT: F 125 ARG cc_start: 0.7279 (ptp90) cc_final: 0.6882 (mmt90) REVERT: F 198 GLU cc_start: 0.7279 (tt0) cc_final: 0.6958 (pt0) REVERT: F 303 TRP cc_start: 0.7513 (t60) cc_final: 0.7259 (t60) REVERT: F 331 ASN cc_start: 0.8699 (t0) cc_final: 0.8332 (t0) outliers start: 67 outliers final: 52 residues processed: 382 average time/residue: 0.1782 time to fit residues: 107.2197 Evaluate side-chains 367 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 313 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 830 ILE Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 41 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 13 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 263 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 HIS E 794 HIS E 835 ASN E 935 ASN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.159686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128172 restraints weight = 32359.292| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.94 r_work: 0.3144 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26080 Z= 0.146 Angle : 0.814 32.823 35658 Z= 0.300 Chirality : 0.044 0.169 3968 Planarity : 0.005 0.057 4612 Dihedral : 7.891 72.145 4014 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 2.46 % Allowed : 18.59 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.15), residues: 3302 helix: 0.65 (0.15), residues: 1288 sheet: -1.29 (0.28), residues: 380 loop : -1.11 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 622 TYR 0.020 0.001 TYR B 215 PHE 0.015 0.001 PHE E 333 TRP 0.017 0.001 TRP A 780 HIS 0.005 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00353 (26024) covalent geometry : angle 0.60119 (35520) hydrogen bonds : bond 0.03073 ( 958) hydrogen bonds : angle 4.45080 ( 2670) metal coordination : bond 0.01550 ( 56) metal coordination : angle 8.83927 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 317 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8318 (t0) cc_final: 0.7814 (t0) REVERT: A 492 LYS cc_start: 0.7664 (mmtt) cc_final: 0.7177 (mppt) REVERT: A 610 HIS cc_start: 0.7380 (t-90) cc_final: 0.7094 (t-90) REVERT: B 47 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6321 (pp) REVERT: B 125 ARG cc_start: 0.7327 (ptp90) cc_final: 0.6889 (mmt90) REVERT: B 126 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8019 (tptp) REVERT: B 198 GLU cc_start: 0.7325 (tt0) cc_final: 0.7026 (pt0) REVERT: B 331 ASN cc_start: 0.8739 (t0) cc_final: 0.8434 (t0) REVERT: G 46 ASP cc_start: 0.8476 (t0) cc_final: 0.8236 (t0) REVERT: E 209 ASP cc_start: 0.8265 (t0) cc_final: 0.7781 (t0) REVERT: F 47 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6331 (pp) REVERT: F 125 ARG cc_start: 0.7338 (ptp90) cc_final: 0.6901 (mmt90) REVERT: F 198 GLU cc_start: 0.7357 (tt0) cc_final: 0.7043 (pt0) REVERT: F 215 TYR cc_start: 0.8965 (t80) cc_final: 0.8763 (t80) REVERT: F 303 TRP cc_start: 0.7525 (t60) cc_final: 0.7281 (t60) REVERT: F 331 ASN cc_start: 0.8737 (t0) cc_final: 0.8404 (t0) outliers start: 63 outliers final: 55 residues processed: 361 average time/residue: 0.1827 time to fit residues: 104.0038 Evaluate side-chains 369 residues out of total 2560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 311 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 457 THR Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 592 VAL Chi-restraints excluded: chain E residue 601 PHE Chi-restraints excluded: chain E residue 631 GLU Chi-restraints excluded: chain E residue 658 ILE Chi-restraints excluded: chain E residue 659 LEU Chi-restraints excluded: chain E residue 678 VAL Chi-restraints excluded: chain E residue 751 SER Chi-restraints excluded: chain E residue 827 THR Chi-restraints excluded: chain E residue 898 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 424 ILE Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 34 GLU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.0060 chunk 124 optimal weight: 0.0030 chunk 291 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 237 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.1610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN A 794 HIS A 935 ASN E 794 HIS E 935 ASN ** C 29 GLN ** 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 = 0.3889 r_free = 0.3889 target = 0.161095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129361 restraints weight = 32169.164| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.88 r_work: 0.3179 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26080 Z= 0.121 Angle : 0.794 32.753 35658 Z= 0.289 Chirality : 0.042 0.154 3968 Planarity : 0.004 0.056 4612 Dihedral : 7.839 75.936 4014 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.85 % Allowed : 18.16 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 3302 helix: 0.68 (0.15), residues: 1312 sheet: -1.27 (0.28), residues: 380 loop : -1.05 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 622 TYR 0.019 0.001 TYR B 215 PHE 0.015 0.001 PHE E 333 TRP 0.019 0.001 TRP E 780 HIS 0.005 0.001 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00289 (26024) covalent geometry : angle 0.58147 (35520) hydrogen bonds : bond 0.02944 ( 958) hydrogen bonds : angle 4.39566 ( 2670) metal coordination : bond 0.01350 ( 56) metal coordination : angle 8.71507 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5556.40 seconds wall clock time: 96 minutes 18.86 seconds (5778.86 seconds total)