Starting phenix.real_space_refine on Mon Sep 14 03:54:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6q9d_4480/09_2026/6q9d_4480.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q9d_4480/09_2026/6q9d_4480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6q9d_4480/09_2026/6q9d_4480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q9d_4480/09_2026/6q9d_4480.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6q9d_4480/09_2026/6q9d_4480.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6q9d_4480/09_2026/6q9d_4480.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6q9d_4480/09_2026/6q9d_4480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q9d_4480/09_2026/6q9d_4480.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 Fe 28 7.16 5 Zn 1 6.06 5 P 5 5.49 5 S 186 5.16 5 C 17481 2.51 5 N 4860 2.21 5 O 5101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27662 Number of models: 1 Model: "" Number of chains: 26 Chain: "V1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 21, 'TRANS': 408} Chain: "V2" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1647 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 189} Chain: "S1" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "S2" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3071 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 361} Chain breaks: 1 Chain: "S3" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "S7" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "S8" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain: "V3" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 345 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "S6" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S4" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "A9" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2402 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 15, 'TRANS': 287} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A2" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 665 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "A5" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 901 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "A6" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "A7" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 766 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Chain: "AL" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1160 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain: "AA" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 645 Classifications: {'peptide': 80} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain: "AM" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 186 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 4, 'TRANS': 18} Chain: "V1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "S1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S7" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "S8" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A9" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYSV1 365 45.061 101.575 107.156 1.00 50.56 S ATOM 3039 SG CYSV1 405 47.158 103.730 112.929 1.00 34.82 S ATOM 2695 SG CYSV1 362 50.989 101.924 108.047 1.00 34.91 S ATOM 2676 SG CYSV1 359 47.643 107.690 107.772 1.00 39.68 S ATOM 4116 SG CYSV2 103 27.537 111.722 113.489 1.00 70.84 S ATOM 4150 SG CYSV2 108 24.797 109.674 115.838 1.00 54.73 S ATOM 4430 SG CYSV2 144 31.519 110.460 116.823 1.00 57.06 S ATOM 4453 SG CYSV2 148 29.138 108.946 119.280 1.00 58.53 S ATOM 5785 SG CYSS1 114 56.836 95.028 89.116 1.00 37.24 S ATOM 5724 SG CYSS1 105 52.106 91.870 85.861 1.00 37.49 S ATOM 5745 SG CYSS1 108 54.395 97.647 83.813 1.00 36.75 S ATOM 6117 SG CYSS1 156 57.253 103.845 96.269 1.00 30.33 S ATOM 6094 SG CYSS1 153 51.418 105.155 93.342 1.00 24.01 S ATOM 6141 SG CYSS1 159 56.181 109.633 93.549 1.00 39.39 S ATOM 6471 SG CYSS1 203 56.919 104.300 89.962 1.00 38.16 S ATOM 5230 SG CYSS1 41 58.888 102.303 102.429 1.00 41.51 S ATOM 5316 SG CYSS1 52 58.034 98.510 102.027 1.00 34.47 S ATOM 5341 SG CYSS1 55 60.631 97.385 106.673 1.00 34.04 S ATOM 5442 SG CYSS1 69 61.603 101.208 107.087 1.00 50.05 S ATOM 15784 SG CYSS7 119 66.199 68.233 63.042 1.00 43.50 S ATOM 16014 SG CYSS7 149 60.405 68.501 64.942 1.00 38.51 S ATOM 15286 SG CYSS7 55 61.667 64.666 59.661 1.00 46.73 S ATOM 15280 SG CYSS7 54 63.344 62.558 65.166 1.00 53.30 S ATOM 17206 SG CYSS8 116 57.189 76.273 64.601 1.00 30.26 S ATOM 17253 SG CYSS8 122 53.964 79.528 69.081 1.00 30.07 S ATOM 16980 SG CYSS8 87 60.476 80.149 68.961 1.00 25.40 S ATOM 17282 SG CYSS8 126 49.068 85.450 72.802 1.00 28.22 S ATOM 16953 SG CYSS8 83 55.282 85.674 70.650 1.00 23.92 S ATOM 16911 SG CYSS8 77 51.341 90.644 69.412 1.00 26.28 S ATOM 16930 SG CYSS8 80 53.224 89.233 75.620 1.00 24.55 S ATOM 18503 SG CYSS6 59 37.448 95.469 77.969 1.00 55.95 S ATOM 18681 SG CYSS6 84 41.225 97.115 77.201 1.00 48.25 S ATOM 18703 SG CYSS6 87 38.732 95.216 75.423 1.00 46.35 S Time building chain proxies: 5.53, per 1000 atoms: 0.20 Number of scatterers: 27662 At special positions: 0 Unit cell: (145.6, 158.2, 162.4, 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) Zn 1 29.99 Fe 28 26.01 S 186 16.00 P 5 15.00 O 5101 8.00 N 4860 7.00 C 17481 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESS1 803 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 52 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 55 " pdb="FE1 FESS1 803 " - pdb=" SG CYSS1 41 " pdb="FE2 FESS1 803 " - pdb=" SG CYSS1 69 " pdb=" FESV2 300 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 148 " pdb="FE2 FESV2 300 " - pdb=" SG CYSV2 144 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 108 " pdb="FE1 FESV2 300 " - pdb=" SG CYSV2 103 " pdb=" SF4S1 801 " pdb="FE3 SF4S1 801 " - pdb=" NE2 HISS1 101 " pdb="FE4 SF4S1 801 " - pdb=" SG CYSS1 108 " pdb="FE1 SF4S1 801 " - pdb=" SG CYSS1 114 " pdb="FE2 SF4S1 801 " - pdb=" SG CYSS1 105 " pdb=" SF4S1 802 " pdb="FE4 SF4S1 802 " - pdb=" SG CYSS1 203 " pdb="FE2 SF4S1 802 " - pdb=" SG CYSS1 153 " pdb="FE1 SF4S1 802 " - pdb=" SG CYSS1 156 " pdb="FE3 SF4S1 802 " - pdb=" SG CYSS1 159 " pdb=" SF4S7 300 " pdb="FE4 SF4S7 300 " - pdb=" SG CYSS7 54 " pdb="FE1 SF4S7 300 " - pdb=" SG CYSS7 119 " pdb="FE3 SF4S7 300 " - pdb=" SG CYSS7 55 " pdb="FE2 SF4S7 300 " - pdb=" SG CYSS7 149 " pdb=" SF4S8 201 " pdb="FE3 SF4S8 201 " - pdb=" SG CYSS8 122 " pdb="FE2 SF4S8 201 " - pdb=" SG CYSS8 116 " pdb="FE4 SF4S8 201 " - pdb=" SG CYSS8 87 " pdb="FE1 SF4S8 201 " - pdb=" SG CYSS8 119 " pdb=" SF4S8 202 " pdb="FE1 SF4S8 202 " - pdb=" SG CYSS8 126 " pdb="FE4 SF4S8 202 " - pdb=" SG CYSS8 80 " pdb="FE2 SF4S8 202 " - pdb=" SG CYSS8 83 " pdb="FE3 SF4S8 202 " - pdb=" SG CYSS8 77 " pdb=" SF4V1 500 " pdb="FE1 SF4V1 500 " - pdb=" SG CYSV1 365 " pdb="FE3 SF4V1 500 " - pdb=" SG CYSV1 362 " pdb="FE2 SF4V1 500 " - pdb=" SG CYSV1 405 " pdb="FE4 SF4V1 500 " - pdb=" SG CYSV1 359 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZNS6 300 " pdb="ZN ZNS6 300 " - pdb=" NE2 HISS6 68 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 87 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 59 " pdb="ZN ZNS6 300 " - pdb=" SG CYSS6 84 " Number of angles added : 3 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6434 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 29 sheets defined 40.9% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'V1' and resid 32 through 40 Processing helix chain 'V1' and resid 45 through 50 Processing helix chain 'V1' and resid 52 through 64 removed outlier: 3.537A pdb=" N ILEV1 56 " --> pdb=" O GLYV1 52 " (cutoff:3.500A) Processing helix chain 'V1' and resid 74 through 82 removed outlier: 3.614A pdb=" N LYSV1 78 " --> pdb=" O PROV1 74 " (cutoff:3.500A) Processing helix chain 'V1' and resid 106 through 114 removed outlier: 4.298A pdb=" N ILEV1 110 " --> pdb=" O LYSV1 106 " (cutoff:3.500A) Processing helix chain 'V1' and resid 114 through 129 removed outlier: 3.870A pdb=" N LEUV1 118 " --> pdb=" O ASPV1 114 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N METV1 129 " --> pdb=" O GLYV1 125 " (cutoff:3.500A) Processing helix chain 'V1' and resid 142 through 159 Processing helix chain 'V1' and resid 165 through 169 Processing helix chain 'V1' and resid 184 through 188 Processing helix chain 'V1' and resid 190 through 197 Processing helix chain 'V1' and resid 225 through 237 Proline residue: V1 232 - end of helix removed outlier: 3.799A pdb=" N CYSV1 235 " --> pdb=" O SERV1 231 " (cutoff:3.500A) Processing helix chain 'V1' and resid 241 through 245 removed outlier: 3.851A pdb=" N PHEV1 245 " --> pdb=" O PHEV1 242 " (cutoff:3.500A) Processing helix chain 'V1' and resid 275 through 282 Processing helix chain 'V1' and resid 290 through 292 No H-bonds generated for 'chain 'V1' and resid 290 through 292' Processing helix chain 'V1' and resid 318 through 325 Processing helix chain 'V1' and resid 342 through 357 Processing helix chain 'V1' and resid 362 through 381 removed outlier: 3.561A pdb=" N ARGV1 366 " --> pdb=" O CYSV1 362 " (cutoff:3.500A) Processing helix chain 'V1' and resid 385 through 400 removed outlier: 3.865A pdb=" N ILEV1 389 " --> pdb=" O ARGV1 385 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLUV1 400 " --> pdb=" O SERV1 396 " (cutoff:3.500A) Processing helix chain 'V1' and resid 405 through 422 removed outlier: 4.537A pdb=" N ASPV1 409 " --> pdb=" O CYSV1 405 " (cutoff:3.500A) Proline residue: V1 414 - end of helix Processing helix chain 'V1' and resid 422 through 438 removed outlier: 3.564A pdb=" N LEUV1 426 " --> pdb=" O PHEV1 422 " (cutoff:3.500A) Processing helix chain 'V2' and resid 24 through 38 removed outlier: 3.939A pdb=" N TYRV2 38 " --> pdb=" O ILEV2 34 " (cutoff:3.500A) Processing helix chain 'V2' and resid 42 through 45 Processing helix chain 'V2' and resid 46 through 58 Processing helix chain 'V2' and resid 62 through 73 removed outlier: 3.588A pdb=" N METV2 66 " --> pdb=" O PROV2 62 " (cutoff:3.500A) Processing helix chain 'V2' and resid 76 through 87 removed outlier: 4.008A pdb=" N VALV2 80 " --> pdb=" O PROV2 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYRV2 87 " --> pdb=" O VALV2 83 " (cutoff:3.500A) Processing helix chain 'V2' and resid 108 through 111 Processing helix chain 'V2' and resid 112 through 125 removed outlier: 4.265A pdb=" N ILEV2 116 " --> pdb=" O ASNV2 112 " (cutoff:3.500A) Processing helix chain 'V2' and resid 165 through 179 Processing helix chain 'S1' and resid 25 through 33 Processing helix chain 'S1' and resid 83 through 98 removed outlier: 3.596A pdb=" N LYSS1 87 " --> pdb=" O SERS1 83 " (cutoff:3.500A) Processing helix chain 'S1' and resid 115 through 123 Processing helix chain 'S1' and resid 158 through 166 Processing helix chain 'S1' and resid 198 through 203 removed outlier: 3.534A pdb=" N ILES1 202 " --> pdb=" O ASNS1 198 " (cutoff:3.500A) Processing helix chain 'S1' and resid 264 through 269 Processing helix chain 'S1' and resid 272 through 276 removed outlier: 3.660A pdb=" N ARGS1 276 " --> pdb=" O GLYS1 273 " (cutoff:3.500A) Processing helix chain 'S1' and resid 295 through 309 removed outlier: 3.810A pdb=" N ALAS1 299 " --> pdb=" O THRS1 295 " (cutoff:3.500A) Processing helix chain 'S1' and resid 325 through 339 removed outlier: 3.944A pdb=" N ASPS1 339 " --> pdb=" O LEUS1 335 " (cutoff:3.500A) Processing helix chain 'S1' and resid 358 through 362 removed outlier: 3.549A pdb=" N TYRS1 362 " --> pdb=" O ARGS1 359 " (cutoff:3.500A) Processing helix chain 'S1' and resid 368 through 374 removed outlier: 3.617A pdb=" N VALS1 371 " --> pdb=" O ILES1 368 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLUS1 373 " --> pdb=" O GLYS1 370 " (cutoff:3.500A) Processing helix chain 'S1' and resid 388 through 402 removed outlier: 3.540A pdb=" N ASNS1 392 " --> pdb=" O ALAS1 388 " (cutoff:3.500A) Processing helix chain 'S1' and resid 425 through 435 removed outlier: 3.744A pdb=" N LEUS1 429 " --> pdb=" O SERS1 425 " (cutoff:3.500A) Processing helix chain 'S1' and resid 439 through 445 Processing helix chain 'S1' and resid 462 through 480 Processing helix chain 'S1' and resid 496 through 505 removed outlier: 4.011A pdb=" N VALS1 500 " --> pdb=" O ILES1 496 " (cutoff:3.500A) Processing helix chain 'S1' and resid 511 through 517 Processing helix chain 'S1' and resid 595 through 607 Processing helix chain 'S1' and resid 615 through 625 Processing helix chain 'S1' and resid 627 through 631 removed outlier: 3.673A pdb=" N LEUS1 630 " --> pdb=" O SERS1 627 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VALS1 631 " --> pdb=" O PROS1 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'S1' and resid 627 through 631' Processing helix chain 'S1' and resid 641 through 649 Processing helix chain 'S1' and resid 667 through 674 removed outlier: 3.953A pdb=" N THRS1 674 " --> pdb=" O ASPS1 670 " (cutoff:3.500A) Processing helix chain 'S1' and resid 675 through 681 removed outlier: 3.501A pdb=" N SERS1 681 " --> pdb=" O ILES1 677 " (cutoff:3.500A) Processing helix chain 'S1' and resid 682 through 693 Processing helix chain 'S2' and resid 86 through 93 Processing helix chain 'S2' and resid 99 through 106 removed outlier: 3.813A pdb=" N PHES2 103 " --> pdb=" O ALAS2 99 " (cutoff:3.500A) Processing helix chain 'S2' and resid 112 through 126 Processing helix chain 'S2' and resid 131 through 162 Processing helix chain 'S2' and resid 164 through 185 removed outlier: 3.992A pdb=" N PHES2 168 " --> pdb=" O METS2 164 " (cutoff:3.500A) Processing helix chain 'S2' and resid 207 through 229 Processing helix chain 'S2' and resid 232 through 239 Processing helix chain 'S2' and resid 246 through 253 Processing helix chain 'S2' and resid 257 through 263 Processing helix chain 'S2' and resid 268 through 273 Processing helix chain 'S2' and resid 276 through 280 removed outlier: 3.859A pdb=" N ASPS2 279 " --> pdb=" O ASPS2 276 " (cutoff:3.500A) Processing helix chain 'S2' and resid 292 through 317 Processing helix chain 'S2' and resid 334 through 340 Processing helix chain 'S2' and resid 341 through 354 removed outlier: 3.518A pdb=" N LEUS2 345 " --> pdb=" O SERS2 341 " (cutoff:3.500A) Processing helix chain 'S2' and resid 393 through 400 Processing helix chain 'S2' and resid 401 through 406 Processing helix chain 'S2' and resid 410 through 421 removed outlier: 3.687A pdb=" N GLNS2 421 " --> pdb=" O ILES2 417 " (cutoff:3.500A) Processing helix chain 'S3' and resid 16 through 33 Processing helix chain 'S3' and resid 56 through 66 removed outlier: 3.756A pdb=" N ASPS3 66 " --> pdb=" O THRS3 62 " (cutoff:3.500A) Processing helix chain 'S3' and resid 119 through 123 removed outlier: 4.061A pdb=" N SERS3 122 " --> pdb=" O SERS3 119 " (cutoff:3.500A) Processing helix chain 'S3' and resid 124 through 125 No H-bonds generated for 'chain 'S3' and resid 124 through 125' Processing helix chain 'S3' and resid 126 through 138 removed outlier: 4.171A pdb=" N TYRS3 130 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) Processing helix chain 'S3' and resid 206 through 210 removed outlier: 3.766A pdb=" N TYRS3 209 " --> pdb=" O PHES3 206 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARGS3 210 " --> pdb=" O PROS3 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'S3' and resid 206 through 210' Processing helix chain 'S7' and resid 25 through 45 removed outlier: 4.092A pdb=" N SERS7 44 " --> pdb=" O ALAS7 40 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEUS7 45 " --> pdb=" O ARGS7 41 " (cutoff:3.500A) Processing helix chain 'S7' and resid 54 through 62 Processing helix chain 'S7' and resid 79 through 83 removed outlier: 3.688A pdb=" N GLNS7 82 " --> pdb=" O SERS7 79 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SERS7 83 " --> pdb=" O PROS7 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'S7' and resid 79 through 83' Processing helix chain 'S7' and resid 96 through 106 removed outlier: 4.080A pdb=" N GLNS7 106 " --> pdb=" O LYSS7 102 " (cutoff:3.500A) Processing helix chain 'S7' and resid 123 through 127 removed outlier: 3.908A pdb=" N TYRS7 126 " --> pdb=" O GLYS7 123 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HISS7 127 " --> pdb=" O GLYS7 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'S7' and resid 123 through 127' Processing helix chain 'S7' and resid 152 through 169 Processing helix chain 'S7' and resid 171 through 178 Processing helix chain 'S8' and resid 13 through 27 removed outlier: 3.848A pdb=" N TRPS8 27 " --> pdb=" O GLNS8 23 " (cutoff:3.500A) Processing helix chain 'S8' and resid 27 through 42 removed outlier: 3.879A pdb=" N ILES8 31 " --> pdb=" O TRPS8 27 " (cutoff:3.500A) Processing helix chain 'S8' and resid 81 through 87 Processing helix chain 'S8' and resid 120 through 126 removed outlier: 3.889A pdb=" N CYSS8 126 " --> pdb=" O CYSS8 122 " (cutoff:3.500A) Processing helix chain 'S8' and resid 150 through 161 removed outlier: 4.005A pdb=" N TRPS8 161 " --> pdb=" O ASNS8 157 " (cutoff:3.500A) Processing helix chain 'S8' and resid 162 through 172 Processing helix chain 'V3' and resid 49 through 58 Processing helix chain 'S6' and resid 23 through 28 Processing helix chain 'S4' and resid 18 through 22 removed outlier: 3.694A pdb=" N THRS4 21 " --> pdb=" O ASPS4 18 " (cutoff:3.500A) Processing helix chain 'S4' and resid 26 through 32 Processing helix chain 'S4' and resid 48 through 52 removed outlier: 4.231A pdb=" N ASNS4 51 " --> pdb=" O GLYS4 48 " (cutoff:3.500A) Processing helix chain 'S4' and resid 78 through 82 removed outlier: 4.074A pdb=" N ASNS4 81 " --> pdb=" O PROS4 78 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEUS4 82 " --> pdb=" O LEUS4 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'S4' and resid 78 through 82' Processing helix chain 'S4' and resid 88 through 99 Processing helix chain 'S4' and resid 117 through 122 Processing helix chain 'A9' and resid 29 through 42 Processing helix chain 'A9' and resid 52 through 59 removed outlier: 4.184A pdb=" N THRA9 56 " --> pdb=" O GLUA9 52 " (cutoff:3.500A) Processing helix chain 'A9' and resid 60 through 63 removed outlier: 3.918A pdb=" N GLYA9 63 " --> pdb=" O ARGA9 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'A9' and resid 60 through 63' Processing helix chain 'A9' and resid 77 through 85 removed outlier: 3.902A pdb=" N ILEA9 81 " --> pdb=" O ASPA9 77 " (cutoff:3.500A) Processing helix chain 'A9' and resid 108 through 125 Proline residue: A9 114 - end of helix Processing helix chain 'A9' and resid 143 through 159 Processing helix chain 'A9' and resid 177 through 184 Processing helix chain 'A9' and resid 207 through 220 Processing helix chain 'A9' and resid 238 through 249 Processing helix chain 'A9' and resid 280 through 288 Processing helix chain 'A9' and resid 309 through 318 removed outlier: 4.760A pdb=" N LYSA9 313 " --> pdb=" O PROA9 309 " (cutoff:3.500A) Processing helix chain 'A2' and resid 26 through 39 Processing helix chain 'A2' and resid 40 through 47 Processing helix chain 'A2' and resid 82 through 94 Processing helix chain 'A5' and resid 18 through 36 removed outlier: 3.797A pdb=" N ARGA5 22 " --> pdb=" O THRA5 18 " (cutoff:3.500A) Processing helix chain 'A5' and resid 41 through 59 removed outlier: 4.061A pdb=" N LYSA5 45 " --> pdb=" O ALAA5 41 " (cutoff:3.500A) Processing helix chain 'A5' and resid 64 through 71 Processing helix chain 'A5' and resid 75 through 95 removed outlier: 3.740A pdb=" N ILEA5 80 " --> pdb=" O ILEA5 76 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLNA5 95 " --> pdb=" O ARGA5 91 " (cutoff:3.500A) Processing helix chain 'A6' and resid 23 through 49 removed outlier: 3.812A pdb=" N ALAA6 27 " --> pdb=" O ASPA6 23 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VALA6 42 " --> pdb=" O TRPA6 38 " (cutoff:3.500A) Proline residue: A6 43 - end of helix Processing helix chain 'A6' and resid 54 through 69 removed outlier: 4.212A pdb=" N ASNA6 69 " --> pdb=" O META6 65 " (cutoff:3.500A) Processing helix chain 'A6' and resid 74 through 94 Processing helix chain 'A6' and resid 98 through 106 removed outlier: 3.614A pdb=" N VALA6 102 " --> pdb=" O GLNA6 98 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHEA6 106 " --> pdb=" O VALA6 102 " (cutoff:3.500A) Processing helix chain 'A6' and resid 116 through 123 removed outlier: 3.539A pdb=" N VALA6 123 " --> pdb=" O SERA6 119 " (cutoff:3.500A) Processing helix chain 'A7' and resid 4 through 15 Processing helix chain 'AL' and resid 8 through 18 removed outlier: 3.785A pdb=" N GLNAL 12 " --> pdb=" O LYSAL 8 " (cutoff:3.500A) Processing helix chain 'AL' and resid 19 through 26 removed outlier: 3.775A pdb=" N TYRAL 23 " --> pdb=" O GLYAL 19 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEUAL 24 " --> pdb=" O LEUAL 20 " (cutoff:3.500A) Processing helix chain 'AL' and resid 83 through 91 removed outlier: 3.758A pdb=" N HISAL 91 " --> pdb=" O HISAL 87 " (cutoff:3.500A) Processing helix chain 'AA' and resid 7 through 22 Processing helix chain 'AA' and resid 43 through 58 Processing helix chain 'AA' and resid 63 through 69 Processing helix chain 'AA' and resid 72 through 84 Processing sheet with id=AA1, first strand: chain 'V1' and resid 174 through 179 Processing sheet with id=AA2, first strand: chain 'V1' and resid 253 through 258 Processing sheet with id=AA3, first strand: chain 'V1' and resid 307 through 308 removed outlier: 6.683A pdb=" N METV1 337 " --> pdb=" O LEUV1 295 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VALV1 297 " --> pdb=" O ILEV1 335 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILEV1 335 " --> pdb=" O VALV1 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'V2' and resid 138 through 142 removed outlier: 6.162A pdb=" N ILEV2 100 " --> pdb=" O ILEV2 140 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VALV2 142 " --> pdb=" O ILEV2 100 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VALV2 102 " --> pdb=" O VALV2 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S1' and resid 16 through 20 removed outlier: 7.017A pdb=" N GLUS1 10 " --> pdb=" O TRPS1 77 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILES1 79 " --> pdb=" O GLUS1 10 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHES1 12 " --> pdb=" O ILES1 79 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLUS1 58 " --> pdb=" O LEUS1 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S1' and resid 146 through 148 Processing sheet with id=AA7, first strand: chain 'S1' and resid 173 through 177 Processing sheet with id=AA8, first strand: chain 'S1' and resid 223 through 228 Processing sheet with id=AA9, first strand: chain 'S1' and resid 291 through 293 removed outlier: 6.631A pdb=" N LEUS1 522 " --> pdb=" O VALS1 544 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLNS1 546 " --> pdb=" O LEUS1 522 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEUS1 524 " --> pdb=" O GLNS1 546 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S1' and resid 420 through 423 removed outlier: 6.598A pdb=" N VALS1 406 " --> pdb=" O ASPS1 420 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEUS1 422 " --> pdb=" O VALS1 406 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEUS1 408 " --> pdb=" O LEUS1 422 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VALS1 377 " --> pdb=" O ALAS1 407 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILES1 409 " --> pdb=" O VALS1 377 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEUS1 379 " --> pdb=" O ILES1 409 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VALS1 376 " --> pdb=" O METS1 450 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VALS1 452 " --> pdb=" O VALS1 376 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEUS1 378 " --> pdb=" O VALS1 452 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLYS1 454 " --> pdb=" O LEUS1 378 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VALS1 380 " --> pdb=" O GLYS1 454 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASNS1 491 " --> pdb=" O PROS1 449 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VALS1 451 " --> pdb=" O ASNS1 491 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEUS1 493 " --> pdb=" O VALS1 451 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEUS1 453 " --> pdb=" O LEUS1 493 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'S1' and resid 573 through 574 Processing sheet with id=AB3, first strand: chain 'S2' and resid 47 through 51 Processing sheet with id=AB4, first strand: chain 'S2' and resid 194 through 195 Processing sheet with id=AB5, first strand: chain 'S2' and resid 361 through 369 Processing sheet with id=AB6, first strand: chain 'S3' and resid 74 through 76 Processing sheet with id=AB7, first strand: chain 'S3' and resid 172 through 177 Processing sheet with id=AB8, first strand: chain 'S7' and resid 48 through 49 removed outlier: 3.840A pdb=" N ILES7 87 " --> pdb=" O METS7 48 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N METS7 86 " --> pdb=" O VALS7 114 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N METS7 116 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VALS7 88 " --> pdb=" O METS7 116 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VALS7 113 " --> pdb=" O ILES7 144 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VALS7 146 " --> pdb=" O VALS7 113 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SERS7 115 " --> pdb=" O VALS7 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S8' and resid 66 through 67 Processing sheet with id=AC1, first strand: chain 'S8' and resid 92 through 95 Processing sheet with id=AC2, first strand: chain 'S6' and resid 50 through 52 removed outlier: 3.960A pdb=" N SERS6 50 " --> pdb=" O GLNS6 90 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLYS6 82 " --> pdb=" O PHES6 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S6' and resid 56 through 59 Processing sheet with id=AC4, first strand: chain 'S4' and resid 11 through 12 Processing sheet with id=AC5, first strand: chain 'S4' and resid 84 through 86 Processing sheet with id=AC6, first strand: chain 'S4' and resid 64 through 66 Processing sheet with id=AC7, first strand: chain 'A9' and resid 69 through 72 removed outlier: 6.360A pdb=" N VALA9 45 " --> pdb=" O ILEA9 69 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N META9 71 " --> pdb=" O VALA9 45 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VALA9 47 " --> pdb=" O META9 71 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALAA9 21 " --> pdb=" O ILEA9 46 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VALA9 23 " --> pdb=" O PROA9 48 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VALA9 20 " --> pdb=" O VALA9 90 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILEA9 92 " --> pdb=" O VALA9 20 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THRA9 22 " --> pdb=" O ILEA9 92 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHEA9 129 " --> pdb=" O THRA9 164 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILEA9 166 " --> pdb=" O PHEA9 129 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HISA9 131 " --> pdb=" O ILEA9 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A9' and resid 171 through 172 Processing sheet with id=AC9, first strand: chain 'A9' and resid 201 through 202 Processing sheet with id=AD1, first strand: chain 'A2' and resid 53 through 56 Processing sheet with id=AD2, first strand: chain 'AL' and resid 40 through 41 1042 hydrogen bonds defined for protein. 2952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 11932 1.43 - 1.65: 16039 1.65 - 1.87: 251 1.87 - 2.09: 0 2.09 - 2.30: 80 Bond restraints: 28302 Sorted by residual: bond pdb=" O5 ZMPAA 101 " pdb=" P1 ZMPAA 101 " ideal model delta sigma weight residual 1.715 1.603 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" O2B NDPA9 401 " pdb=" P2B NDPA9 401 " ideal model delta sigma weight residual 1.833 1.621 0.212 3.80e-02 6.93e+02 3.12e+01 bond pdb=" O5D NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 1.757 1.581 0.176 3.50e-02 8.16e+02 2.52e+01 bond pdb=" C4A FMNV1 501 " pdb=" N5 FMNV1 501 " ideal model delta sigma weight residual 1.380 1.300 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C2B NDPA9 401 " pdb=" O2B NDPA9 401 " ideal model delta sigma weight residual 1.330 1.445 -0.115 2.90e-02 1.19e+03 1.57e+01 ... (remaining 28297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.53: 38001 4.53 - 9.07: 311 9.07 - 13.60: 36 13.60 - 18.13: 5 18.13 - 22.67: 3 Bond angle restraints: 38356 Sorted by residual: angle pdb=" PA NDPA9 401 " pdb=" O3 NDPA9 401 " pdb=" PN NDPA9 401 " ideal model delta sigma weight residual 107.74 130.41 -22.67 1.95e+00 2.62e-01 1.35e+02 angle pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 91.40 12.93 1.14e+00 7.69e-01 1.29e+02 angle pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " pdb="FE2 FESV2 300 " ideal model delta sigma weight residual 75.66 88.59 -12.93 1.14e+00 7.69e-01 1.29e+02 angle pdb=" S1 FESV2 300 " pdb="FE1 FESV2 300 " pdb=" S2 FESV2 300 " ideal model delta sigma weight residual 104.33 91.33 13.00 1.20e+00 6.94e-01 1.17e+02 angle pdb="FE1 FESV2 300 " pdb=" S1 FESV2 300 " pdb="FE2 FESV2 300 " ideal model delta sigma weight residual 75.66 88.51 -12.85 1.20e+00 6.94e-01 1.15e+02 ... (remaining 38351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.44: 16796 27.44 - 54.89: 299 54.89 - 82.33: 16 82.33 - 109.77: 4 109.77 - 137.21: 2 Dihedral angle restraints: 17117 sinusoidal: 7118 harmonic: 9999 Sorted by residual: dihedral pdb=" CA ILEA7 67 " pdb=" C ILEA7 67 " pdb=" N VALA7 68 " pdb=" CA VALA7 68 " ideal model delta harmonic sigma weight residual 180.00 126.70 53.30 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA META7 69 " pdb=" C META7 69 " pdb=" N SERA7 70 " pdb=" CA SERA7 70 " ideal model delta harmonic sigma weight residual -180.00 -132.53 -47.47 0 5.00e+00 4.00e-02 9.01e+01 dihedral pdb=" CA VALA7 68 " pdb=" C VALA7 68 " pdb=" N META7 69 " pdb=" CA META7 69 " ideal model delta harmonic sigma weight residual -180.00 -133.57 -46.43 0 5.00e+00 4.00e-02 8.62e+01 ... (remaining 17114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.227: 4153 4.227 - 8.453: 0 8.453 - 12.680: 0 12.680 - 16.906: 0 16.906 - 21.133: 24 Chirality restraints: 4177 Sorted by residual: chirality pdb="FE4 SF4S8 202 " pdb=" S1 SF4S8 202 " pdb=" S2 SF4S8 202 " pdb=" S3 SF4S8 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.58 21.13 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4V1 500 " pdb=" S1 SF4V1 500 " pdb=" S2 SF4V1 500 " pdb=" S3 SF4V1 500 " both_signs ideal model delta sigma weight residual False 10.55 -10.55 21.11 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE1 SF4S1 802 " pdb=" S2 SF4S1 802 " pdb=" S3 SF4S1 802 " pdb=" S4 SF4S1 802 " both_signs ideal model delta sigma weight residual False -10.55 10.55 -21.10 2.00e-01 2.50e+01 1.11e+04 ... (remaining 4174 not shown) Planarity restraints: 4957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMNV1 501 " 0.145 2.00e-02 2.50e+03 9.84e-02 4.60e+02 pdb=" C10 FMNV1 501 " -0.085 2.00e-02 2.50e+03 pdb=" C2 FMNV1 501 " 0.047 2.00e-02 2.50e+03 pdb=" C4 FMNV1 501 " -0.036 2.00e-02 2.50e+03 pdb=" C4A FMNV1 501 " -0.083 2.00e-02 2.50e+03 pdb=" C5A FMNV1 501 " -0.047 2.00e-02 2.50e+03 pdb=" C6 FMNV1 501 " 0.039 2.00e-02 2.50e+03 pdb=" C7 FMNV1 501 " 0.075 2.00e-02 2.50e+03 pdb=" C7M FMNV1 501 " 0.252 2.00e-02 2.50e+03 pdb=" C8 FMNV1 501 " -0.015 2.00e-02 2.50e+03 pdb=" C8M FMNV1 501 " -0.125 2.00e-02 2.50e+03 pdb=" C9 FMNV1 501 " -0.078 2.00e-02 2.50e+03 pdb=" C9A FMNV1 501 " -0.078 2.00e-02 2.50e+03 pdb=" N1 FMNV1 501 " -0.028 2.00e-02 2.50e+03 pdb=" N10 FMNV1 501 " -0.071 2.00e-02 2.50e+03 pdb=" N3 FMNV1 501 " 0.030 2.00e-02 2.50e+03 pdb=" N5 FMNV1 501 " -0.061 2.00e-02 2.50e+03 pdb=" O2 FMNV1 501 " 0.175 2.00e-02 2.50e+03 pdb=" O4 FMNV1 501 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALA7 68 " -0.032 2.00e-02 2.50e+03 6.45e-02 4.16e+01 pdb=" C VALA7 68 " 0.112 2.00e-02 2.50e+03 pdb=" O VALA7 68 " -0.042 2.00e-02 2.50e+03 pdb=" N META7 69 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALS2 73 " -0.029 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" C VALS2 73 " 0.098 2.00e-02 2.50e+03 pdb=" O VALS2 73 " -0.036 2.00e-02 2.50e+03 pdb=" N ARGS2 74 " -0.033 2.00e-02 2.50e+03 ... (remaining 4954 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 492 2.67 - 3.22: 25007 3.22 - 3.78: 42560 3.78 - 4.34: 55673 4.34 - 4.90: 91113 Nonbonded interactions: 214845 Sorted by model distance: nonbonded pdb=" CA ALAS3 80 " pdb=" O GLUS3 91 " model vdw 2.107 3.470 nonbonded pdb=" O GLNS3 38 " pdb=" CA SERA7 70 " model vdw 2.164 3.470 nonbonded pdb=" O ARGS1 243 " pdb=" O GLUS1 246 " model vdw 2.209 3.040 nonbonded pdb=" O SERS2 69 " pdb=" O METS2 72 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THRS6 12 " pdb=" O THRS6 14 " model vdw 2.231 3.040 ... (remaining 214840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 30.180 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.009 0.785 28339 Z= 0.335 Angle : 1.178 34.691 38440 Z= 0.630 Chirality : 1.597 21.133 4177 Planarity : 0.008 0.098 4957 Dihedral : 10.661 137.214 10683 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.77 % Favored : 89.03 % Rotamer: Outliers : 0.24 % Allowed : 4.24 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.49 % Twisted General : 0.31 % 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: -4.23 (0.11), residues: 3417 helix: -2.38 (0.10), residues: 1321 sheet: -1.91 (0.26), residues: 321 loop : -3.40 (0.12), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGS2 174 TYR 0.039 0.003 TYRS7 125 PHE 0.033 0.003 PHEV1 81 TRP 0.054 0.004 TRPV1 413 HIS 0.019 0.002 HISA9 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.30 (28302) covalent geometry : angle 1.14627 / 0.63 (38356) hydrogen bonds : bond 0.12068 / 8.06 ( 1042) hydrogen bonds : angle 6.64507 / 4.67 ( 2952) metal coordination : bond 0.14046 / 7.06 ( 36) metal coordination : angle 5.92054 / 3.86 ( 84) Misc. bond : bond 0.05483 / 2.89 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1145 time to evaluate : 1.197 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: 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: V1 21 ILE cc_start: 0.8226 (mm) cc_final: 0.7862 (mm) REVERT: V1 114 ASP cc_start: 0.8472 (t0) cc_final: 0.8240 (t0) REVERT: V1 120 GLU cc_start: 0.7769 (mm-30) cc_final: 0.6955 (mt-10) REVERT: V1 302 SER cc_start: 0.8497 (m) cc_final: 0.7954 (t) REVERT: V1 313 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7615 (tm-30) REVERT: V2 52 ASP cc_start: 0.8828 (t0) cc_final: 0.8585 (t0) REVERT: V2 159 ASN cc_start: 0.7481 (m-40) cc_final: 0.7240 (m110) REVERT: V2 168 ASP cc_start: 0.8205 (m-30) cc_final: 0.7959 (t0) REVERT: S1 71 MET cc_start: 0.8491 (tpp) cc_final: 0.8276 (tpp) REVERT: S1 187 ILE cc_start: 0.8948 (pt) cc_final: 0.8694 (mp) REVERT: S1 328 LEU cc_start: 0.9036 (mt) cc_final: 0.8801 (mt) REVERT: S1 356 THR cc_start: 0.8567 (p) cc_final: 0.8195 (t) REVERT: S1 373 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7790 (tp30) REVERT: S1 635 ASP cc_start: 0.8240 (m-30) cc_final: 0.7940 (m-30) REVERT: S2 92 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7899 (mt-10) REVERT: S2 112 MET cc_start: 0.8358 (mmm) cc_final: 0.8141 (mmt) REVERT: S2 149 ASN cc_start: 0.9303 (t0) cc_final: 0.9075 (t0) REVERT: S2 151 ILE cc_start: 0.8663 (tp) cc_final: 0.8383 (tp) REVERT: S2 199 VAL cc_start: 0.8787 (t) cc_final: 0.8547 (t) REVERT: S2 268 ASP cc_start: 0.7285 (t0) cc_final: 0.6961 (t0) REVERT: S2 285 VAL cc_start: 0.9383 (p) cc_final: 0.9074 (m) REVERT: S2 402 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8012 (tm) REVERT: S2 417 ILE cc_start: 0.9331 (mm) cc_final: 0.9130 (mm) REVERT: S3 68 SER cc_start: 0.8275 (m) cc_final: 0.7645 (p) REVERT: S3 137 MET cc_start: 0.8667 (mmm) cc_final: 0.8448 (mmm) REVERT: S3 192 GLN cc_start: 0.8030 (tt0) cc_final: 0.7712 (tt0) REVERT: S7 48 MET cc_start: 0.7957 (ptm) cc_final: 0.7739 (ptp) REVERT: S7 71 ARG cc_start: 0.7236 (mtm110) cc_final: 0.5680 (tpm170) REVERT: S7 92 LEU cc_start: 0.9432 (tp) cc_final: 0.9207 (tt) REVERT: S7 105 ASP cc_start: 0.8318 (m-30) cc_final: 0.7896 (m-30) REVERT: S7 112 TYR cc_start: 0.8139 (m-80) cc_final: 0.7599 (m-80) REVERT: S7 125 TYR cc_start: 0.9194 (t80) cc_final: 0.8593 (t80) REVERT: S7 143 ASP cc_start: 0.8360 (m-30) cc_final: 0.7975 (m-30) REVERT: S7 164 GLN cc_start: 0.9079 (mt0) cc_final: 0.8644 (mt0) REVERT: S8 6 ASN cc_start: 0.7184 (m-40) cc_final: 0.6907 (m-40) REVERT: S8 32 ARG cc_start: 0.7692 (ttm170) cc_final: 0.6922 (mmp-170) REVERT: S8 110 ASP cc_start: 0.7615 (m-30) cc_final: 0.6807 (m-30) REVERT: S8 140 SER cc_start: 0.9057 (m) cc_final: 0.8406 (t) REVERT: S8 149 TYR cc_start: 0.9160 (m-10) cc_final: 0.8908 (m-80) REVERT: S8 153 LYS cc_start: 0.9221 (tptp) cc_final: 0.8659 (tptt) REVERT: V3 56 LEU cc_start: 0.9151 (tp) cc_final: 0.8886 (tt) REVERT: S6 17 VAL cc_start: 0.8870 (p) cc_final: 0.8451 (p) REVERT: S4 59 PHE cc_start: 0.9100 (m-10) cc_final: 0.8660 (m-80) REVERT: S4 67 ASN cc_start: 0.8862 (t0) cc_final: 0.8551 (t0) REVERT: S4 70 MET cc_start: 0.7905 (mmm) cc_final: 0.7477 (mmm) REVERT: S4 104 ASP cc_start: 0.8488 (m-30) cc_final: 0.8243 (m-30) REVERT: A9 41 MET cc_start: 0.7800 (ttt) cc_final: 0.7542 (ttm) REVERT: A9 89 ASN cc_start: 0.8703 (t0) cc_final: 0.8469 (t0) REVERT: A9 90 VAL cc_start: 0.8516 (m) cc_final: 0.8212 (m) REVERT: A9 92 ILE cc_start: 0.8902 (pt) cc_final: 0.8689 (mt) REVERT: A9 206 TYR cc_start: 0.9070 (t80) cc_final: 0.8698 (t80) REVERT: A9 216 ASN cc_start: 0.9358 (m-40) cc_final: 0.8760 (m110) REVERT: A5 46 TYR cc_start: 0.7856 (m-80) cc_final: 0.7457 (m-80) REVERT: A5 50 ILE cc_start: 0.9262 (tt) cc_final: 0.8792 (tp) REVERT: A5 64 VAL cc_start: 0.8820 (t) cc_final: 0.8469 (p) REVERT: A5 91 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7833 (tpp80) REVERT: A6 73 THR cc_start: 0.8968 (p) cc_final: 0.8681 (t) REVERT: A7 8 GLN cc_start: 0.9017 (tt0) cc_final: 0.8643 (tt0) REVERT: A7 51 ASN cc_start: 0.8239 (p0) cc_final: 0.7715 (p0) REVERT: A7 52 TYR cc_start: 0.8465 (m-10) cc_final: 0.6910 (m-10) REVERT: A7 57 ASP cc_start: 0.8564 (t0) cc_final: 0.7580 (t70) REVERT: A7 100 ILE cc_start: 0.8723 (mm) cc_final: 0.8447 (mm) REVERT: AL 55 PHE cc_start: 0.9067 (p90) cc_final: 0.8843 (p90) REVERT: AL 56 PHE cc_start: 0.8542 (t80) cc_final: 0.8292 (t80) REVERT: AL 118 SER cc_start: 0.8779 (t) cc_final: 0.8493 (m) REVERT: AA 12 LYS cc_start: 0.8287 (ttpt) cc_final: 0.8065 (tmtt) REVERT: AA 13 ASP cc_start: 0.8619 (m-30) cc_final: 0.8214 (m-30) REVERT: AA 21 LEU cc_start: 0.9253 (tp) cc_final: 0.8956 (mt) REVERT: AA 52 MET cc_start: 0.8730 (ppp) cc_final: 0.8528 (ppp) REVERT: AA 64 ASP cc_start: 0.8211 (p0) cc_final: 0.7958 (p0) REVERT: AA 68 GLU cc_start: 0.8632 (tt0) cc_final: 0.8112 (mt-10) REVERT: AM 23 ASN cc_start: 0.8749 (t0) cc_final: 0.8178 (m-40) outliers start: 7 outliers final: 2 residues processed: 1151 average time/residue: 0.2141 time to fit residues: 373.2354 Evaluate side-chains 669 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 666 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 365 CYS Chi-restraints excluded: chain S2 residue 402 LEU Chi-restraints excluded: chain S3 residue 78 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V1 150 GLN V1 373 ASN V2 37 ASN V2 99 HIS S1 36 GLN S1 182 GLN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 365 ASN ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1 582 GLN S1 665 GLN S2 55 HIS S2 306 GLN S2 347 HIS ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S3 88 ASN S3 192 GLN S7 61 HIS ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 6 ASN S8 65 HIS S8 123 GLN S8 157 ASN V3 75 HIS S6 16 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 46 GLN S4 50 ASN ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 37 HIS A9 89 ASN A9 288 HIS ** A2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 49 GLN A5 72 GLN A5 82 GLN A6 125 HIS A7 20 GLN A7 50 ASN AL 72 ASN AA 35 HIS AA 47 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.088214 restraints weight = 60718.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.090658 restraints weight = 37186.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092379 restraints weight = 25987.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093599 restraints weight = 19810.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094539 restraints weight = 16091.860| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.263 28339 Z= 0.439 Angle : 2.768 61.914 38440 Z= 1.575 Chirality : 0.484 6.547 4177 Planarity : 0.006 0.073 4957 Dihedral : 8.052 144.120 3870 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.66 % Favored : 90.31 % Rotamer: Outliers : 3.43 % Allowed : 14.16 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.93 (0.13), residues: 3417 helix: -0.74 (0.13), residues: 1355 sheet: -1.68 (0.27), residues: 307 loop : -3.10 (0.13), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGS3 150 TYR 0.032 0.002 TYRAA 17 PHE 0.025 0.002 PHES2 214 TRP 0.019 0.002 TRPS4 124 HIS 0.011 0.001 HISS1 549 Details of bonding type rmsd/Z covalent geometry : bond 0.01245 / 0.44 (28302) covalent geometry : angle 2.41278 / 1.57 (38356) hydrogen bonds : bond 0.05612 / 3.76 ( 1042) hydrogen bonds : angle 5.48136 / 3.82 ( 2952) metal coordination : bond 0.03065 / 2.00 ( 36) metal coordination : angle 29.13178 / 17.99 ( 84) Misc. bond : bond 0.00100 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 732 time to evaluate : 1.055 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V1 82 MET cc_start: 0.8881 (tpp) cc_final: 0.8283 (tpp) REVERT: V2 163 ASP cc_start: 0.7610 (m-30) cc_final: 0.7171 (m-30) REVERT: S1 45 ARG cc_start: 0.8384 (mmt-90) cc_final: 0.8137 (mpt180) REVERT: S1 52 CYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8980 (p) REVERT: S1 150 MET cc_start: 0.8888 (mmt) cc_final: 0.8665 (mmt) REVERT: S1 356 THR cc_start: 0.8591 (p) cc_final: 0.8196 (t) REVERT: S2 82 LEU cc_start: 0.8634 (mp) cc_final: 0.8375 (tp) REVERT: S2 92 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7316 (mt-10) REVERT: S2 149 ASN cc_start: 0.9231 (t0) cc_final: 0.8910 (t0) REVERT: S2 151 ILE cc_start: 0.8682 (tp) cc_final: 0.8433 (tp) REVERT: S2 174 ARG cc_start: 0.7712 (ttt180) cc_final: 0.7406 (ttt180) REVERT: S2 261 ARG cc_start: 0.8028 (mpt-90) cc_final: 0.7426 (mmt90) REVERT: S2 338 MET cc_start: 0.9162 (tmm) cc_final: 0.8951 (tmm) REVERT: S3 62 THR cc_start: 0.9382 (m) cc_final: 0.9171 (t) REVERT: S3 105 ILE cc_start: 0.8774 (pt) cc_final: 0.8488 (mt) REVERT: S3 153 THR cc_start: 0.9102 (p) cc_final: 0.8601 (p) REVERT: S3 192 GLN cc_start: 0.7875 (tt0) cc_final: 0.7549 (tt0) REVERT: S7 58 GLU cc_start: 0.7947 (tp30) cc_final: 0.7386 (tp30) REVERT: S7 62 MET cc_start: 0.7718 (ttp) cc_final: 0.7019 (ttt) REVERT: S7 69 MET cc_start: 0.8650 (mmm) cc_final: 0.8242 (mmm) REVERT: S7 71 ARG cc_start: 0.7661 (mtm110) cc_final: 0.5389 (mmp-170) REVERT: S7 95 LYS cc_start: 0.8992 (tttt) cc_final: 0.8630 (ttmm) REVERT: S7 105 ASP cc_start: 0.8159 (m-30) cc_final: 0.7761 (m-30) REVERT: S7 112 TYR cc_start: 0.8277 (m-80) cc_final: 0.7561 (m-80) REVERT: S7 125 TYR cc_start: 0.9353 (t80) cc_final: 0.8963 (t80) REVERT: S7 130 TYR cc_start: 0.8262 (p90) cc_final: 0.7852 (p90) REVERT: S7 152 THR cc_start: 0.8639 (m) cc_final: 0.8237 (p) REVERT: S7 164 GLN cc_start: 0.9088 (mt0) cc_final: 0.8714 (mt0) REVERT: S8 4 TYR cc_start: 0.7647 (p90) cc_final: 0.7366 (p90) REVERT: S8 32 ARG cc_start: 0.7670 (ttm170) cc_final: 0.7149 (mmp-170) REVERT: S8 110 ASP cc_start: 0.7091 (m-30) cc_final: 0.6186 (m-30) REVERT: S8 149 TYR cc_start: 0.9143 (m-10) cc_final: 0.8902 (m-80) REVERT: S8 153 LYS cc_start: 0.9089 (tptp) cc_final: 0.8792 (tptt) REVERT: V3 63 MET cc_start: 0.6788 (mmm) cc_final: 0.6549 (mmm) REVERT: S6 23 TYR cc_start: 0.7565 (p90) cc_final: 0.7343 (p90) REVERT: S6 32 GLN cc_start: 0.8890 (pp30) cc_final: 0.8160 (pp30) REVERT: S6 38 ASN cc_start: 0.8080 (t0) cc_final: 0.7725 (t0) REVERT: S4 44 ASN cc_start: 0.7830 (t0) cc_final: 0.7545 (t0) REVERT: S4 46 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: S4 67 ASN cc_start: 0.9105 (t0) cc_final: 0.8661 (t0) REVERT: S4 70 MET cc_start: 0.8138 (mmm) cc_final: 0.7300 (mmm) REVERT: A9 89 ASN cc_start: 0.8729 (t0) cc_final: 0.8427 (t0) REVERT: A9 92 ILE cc_start: 0.8747 (pt) cc_final: 0.8442 (mt) REVERT: A9 171 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9054 (pp) REVERT: A9 176 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.5990 (t0) REVERT: A9 203 GLN cc_start: 0.8014 (pt0) cc_final: 0.7782 (pt0) REVERT: A9 244 TYR cc_start: 0.8926 (t80) cc_final: 0.8718 (t80) REVERT: A5 53 GLU cc_start: 0.7737 (pt0) cc_final: 0.7498 (pt0) REVERT: A6 73 THR cc_start: 0.8781 (p) cc_final: 0.8527 (t) REVERT: A6 113 ARG cc_start: 0.7594 (mtm180) cc_final: 0.7345 (mtp-110) REVERT: A7 51 ASN cc_start: 0.8018 (p0) cc_final: 0.7486 (p0) REVERT: A7 57 ASP cc_start: 0.8369 (t0) cc_final: 0.7733 (t70) REVERT: A7 111 TYR cc_start: 0.7925 (m-80) cc_final: 0.7665 (m-80) REVERT: AL 124 TYR cc_start: 0.8591 (t80) cc_final: 0.8302 (t80) REVERT: AA 12 LYS cc_start: 0.8343 (ttpt) cc_final: 0.7901 (tmtt) REVERT: AA 13 ASP cc_start: 0.8409 (m-30) cc_final: 0.8104 (m-30) REVERT: AA 22 TYR cc_start: 0.7368 (t80) cc_final: 0.7118 (t80) REVERT: AA 52 MET cc_start: 0.8585 (ppp) cc_final: 0.8161 (ppp) REVERT: AA 64 ASP cc_start: 0.8418 (p0) cc_final: 0.8079 (p0) REVERT: AA 66 ASP cc_start: 0.7881 (m-30) cc_final: 0.7572 (m-30) REVERT: AA 79 TYR cc_start: 0.8836 (t80) cc_final: 0.8474 (t80) REVERT: AA 83 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6693 (ttpp) outliers start: 102 outliers final: 54 residues processed: 799 average time/residue: 0.1891 time to fit residues: 238.0979 Evaluate side-chains 670 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 611 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 185 ILE Chi-restraints excluded: chain V1 residue 267 THR Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 306 LEU Chi-restraints excluded: chain V1 residue 356 HIS Chi-restraints excluded: chain V1 residue 362 CYS Chi-restraints excluded: chain V2 residue 113 SER Chi-restraints excluded: chain S1 residue 33 VAL Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 145 LEU Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 236 SER Chi-restraints excluded: chain S1 residue 253 ARG Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S2 residue 323 ILE Chi-restraints excluded: chain S2 residue 414 VAL Chi-restraints excluded: chain S2 residue 418 ILE Chi-restraints excluded: chain S3 residue 78 LEU Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S3 residue 196 LYS Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 87 ILE Chi-restraints excluded: chain S7 residue 140 VAL Chi-restraints excluded: chain S7 residue 161 LEU Chi-restraints excluded: chain S8 residue 40 TYR Chi-restraints excluded: chain S8 residue 75 GLU Chi-restraints excluded: chain S8 residue 83 CYS Chi-restraints excluded: chain S8 residue 119 CYS Chi-restraints excluded: chain S8 residue 162 GLU Chi-restraints excluded: chain S6 residue 4 THR Chi-restraints excluded: chain S6 residue 26 VAL Chi-restraints excluded: chain S6 residue 44 ILE Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 25 VAL Chi-restraints excluded: chain S4 residue 46 GLN Chi-restraints excluded: chain S4 residue 105 VAL Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 111 VAL Chi-restraints excluded: chain A9 residue 171 ILE Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 323 THR Chi-restraints excluded: chain A2 residue 15 LEU Chi-restraints excluded: chain A2 residue 52 ILE Chi-restraints excluded: chain A2 residue 56 GLU Chi-restraints excluded: chain A5 residue 26 LEU Chi-restraints excluded: chain A5 residue 58 VAL Chi-restraints excluded: chain A5 residue 112 LYS Chi-restraints excluded: chain A6 residue 45 THR Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A6 residue 116 ASP Chi-restraints excluded: chain A6 residue 119 SER Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 34 THR Chi-restraints excluded: chain AL residue 14 VAL Chi-restraints excluded: chain AL residue 120 THR Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 83 LYS Chi-restraints excluded: chain AM residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 180 optimal weight: 1.9990 chunk 281 optimal weight: 0.7980 chunk 262 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 279 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 chunk 314 optimal weight: 0.7980 chunk 198 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... V1 113 HIS V2 37 ASN V2 101 GLN S1 179 ASN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 53 HIS ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 6 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 29 HIS ** S4 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 82 GLN A6 25 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.087951 restraints weight = 60297.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.090456 restraints weight = 36240.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092215 restraints weight = 25026.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.093495 restraints weight = 18947.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.094419 restraints weight = 15259.168| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 28339 Z= 0.425 Angle : 2.752 56.342 38440 Z= 1.567 Chirality : 0.481 6.429 4177 Planarity : 0.005 0.077 4957 Dihedral : 7.622 142.928 3867 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.51 % Favored : 90.46 % Rotamer: Outliers : 3.97 % Allowed : 17.25 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.29 (0.14), residues: 3417 helix: 0.04 (0.14), residues: 1351 sheet: -1.62 (0.28), residues: 313 loop : -2.90 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGA9 40 TYR 0.030 0.002 TYRAA 17 PHE 0.023 0.002 PHES2 214 TRP 0.019 0.001 TRPS8 161 HIS 0.012 0.001 HISS1 549 Details of bonding type rmsd/Z covalent geometry : bond 0.01229 / 0.42 (28302) covalent geometry : angle 2.39531 / 1.56 (38356) hydrogen bonds : bond 0.05036 / 3.37 ( 1042) hydrogen bonds : angle 5.25162 / 3.66 ( 2952) metal coordination : bond 0.02388 / 1.66 ( 36) metal coordination : angle 29.08343 / 18.04 ( 84) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 664 time to evaluate : 1.090 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: V1 82 MET cc_start: 0.8952 (tpp) cc_final: 0.8378 (tpp) REVERT: V1 101 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7451 (tp30) REVERT: V1 120 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6925 (mt-10) REVERT: V1 189 GLU cc_start: 0.8158 (mp0) cc_final: 0.7814 (mp0) REVERT: V1 272 MET cc_start: 0.8332 (tpp) cc_final: 0.7648 (tpp) REVERT: V1 302 SER cc_start: 0.8802 (m) cc_final: 0.8123 (p) REVERT: V1 363 THR cc_start: 0.9351 (p) cc_final: 0.9131 (t) REVERT: V2 163 ASP cc_start: 0.7665 (m-30) cc_final: 0.7202 (m-30) REVERT: V2 190 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7229 (ptt-90) REVERT: S1 52 CYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8902 (p) REVERT: S1 356 THR cc_start: 0.8451 (p) cc_final: 0.8082 (t) REVERT: S1 450 MET cc_start: 0.7981 (ttp) cc_final: 0.7744 (ttp) REVERT: S1 490 MET cc_start: 0.8507 (tmm) cc_final: 0.8130 (tmm) REVERT: S2 92 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7402 (mt-10) REVERT: S2 149 ASN cc_start: 0.9315 (t0) cc_final: 0.8891 (t0) REVERT: S2 151 ILE cc_start: 0.8823 (tp) cc_final: 0.8591 (tp) REVERT: S2 164 MET cc_start: 0.6128 (tmm) cc_final: 0.5914 (tmm) REVERT: S2 228 MET cc_start: 0.8832 (tmm) cc_final: 0.8271 (tmm) REVERT: S2 268 ASP cc_start: 0.7346 (t0) cc_final: 0.6900 (t0) REVERT: S2 270 ARG cc_start: 0.7335 (mtt180) cc_final: 0.7131 (mtt180) REVERT: S2 338 MET cc_start: 0.9247 (tmm) cc_final: 0.8989 (tmm) REVERT: S3 105 ILE cc_start: 0.8822 (pt) cc_final: 0.8601 (mt) REVERT: S3 147 ASP cc_start: 0.7628 (m-30) cc_final: 0.7363 (m-30) REVERT: S3 174 LEU cc_start: 0.8996 (mp) cc_final: 0.8716 (pt) REVERT: S3 200 ASN cc_start: 0.8122 (p0) cc_final: 0.7920 (p0) REVERT: S7 71 ARG cc_start: 0.7714 (mtm110) cc_final: 0.5313 (mmp-170) REVERT: S7 95 LYS cc_start: 0.9040 (tttt) cc_final: 0.8794 (ttmm) REVERT: S7 105 ASP cc_start: 0.8087 (m-30) cc_final: 0.7700 (m-30) REVERT: S7 112 TYR cc_start: 0.8275 (m-80) cc_final: 0.7482 (m-80) REVERT: S7 130 TYR cc_start: 0.8377 (p90) cc_final: 0.7809 (p90) REVERT: S7 164 GLN cc_start: 0.9109 (mt0) cc_final: 0.8749 (mt0) REVERT: S8 32 ARG cc_start: 0.7437 (ttm170) cc_final: 0.7114 (mmp-170) REVERT: S8 110 ASP cc_start: 0.7150 (m-30) cc_final: 0.6113 (m-30) REVERT: S8 153 LYS cc_start: 0.9010 (tptp) cc_final: 0.8701 (tptt) REVERT: S8 160 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8777 (ttpp) REVERT: S6 9 GLU cc_start: 0.6887 (pm20) cc_final: 0.6568 (pm20) REVERT: S6 32 GLN cc_start: 0.8919 (pp30) cc_final: 0.8341 (pp30) REVERT: S4 46 GLN cc_start: 0.8465 (mt0) cc_final: 0.7941 (mt0) REVERT: S4 67 ASN cc_start: 0.9097 (t0) cc_final: 0.8882 (t0) REVERT: S4 70 MET cc_start: 0.7923 (mmm) cc_final: 0.7416 (mmm) REVERT: A9 74 ASN cc_start: 0.8386 (p0) cc_final: 0.7838 (p0) REVERT: A9 89 ASN cc_start: 0.8940 (t0) cc_final: 0.8441 (t0) REVERT: A9 92 ILE cc_start: 0.8829 (pt) cc_final: 0.8493 (mt) REVERT: A9 176 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.5858 (t0) REVERT: A9 206 TYR cc_start: 0.8757 (t80) cc_final: 0.8206 (t80) REVERT: A2 67 ARG cc_start: 0.8548 (ttp80) cc_final: 0.7930 (tmm160) REVERT: A5 46 TYR cc_start: 0.8250 (m-80) cc_final: 0.7856 (m-80) REVERT: A5 53 GLU cc_start: 0.7808 (pt0) cc_final: 0.7545 (pt0) REVERT: A6 39 TYR cc_start: 0.8842 (t80) cc_final: 0.8395 (t80) REVERT: A6 41 GLU cc_start: 0.8812 (tp30) cc_final: 0.8420 (tp30) REVERT: A6 73 THR cc_start: 0.8788 (p) cc_final: 0.8518 (t) REVERT: A7 51 ASN cc_start: 0.7851 (p0) cc_final: 0.7447 (p0) REVERT: A7 57 ASP cc_start: 0.8340 (t0) cc_final: 0.7585 (t70) REVERT: AL 43 LYS cc_start: 0.8166 (tmmt) cc_final: 0.7503 (tppt) REVERT: AL 61 TRP cc_start: 0.8863 (p90) cc_final: 0.8112 (p90) REVERT: AL 123 GLN cc_start: 0.8350 (pm20) cc_final: 0.8110 (pt0) REVERT: AL 124 TYR cc_start: 0.8639 (t80) cc_final: 0.8382 (t80) REVERT: AL 134 ILE cc_start: 0.8874 (pt) cc_final: 0.8626 (mp) REVERT: AA 7 THR cc_start: 0.7350 (p) cc_final: 0.7147 (p) REVERT: AA 12 LYS cc_start: 0.8250 (ttpt) cc_final: 0.8013 (tmtt) REVERT: AA 13 ASP cc_start: 0.8450 (m-30) cc_final: 0.8058 (m-30) REVERT: AA 47 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8634 (tp40) REVERT: AA 52 MET cc_start: 0.8755 (ppp) cc_final: 0.8306 (ppp) REVERT: AA 66 ASP cc_start: 0.7872 (m-30) cc_final: 0.7569 (m-30) REVERT: AA 83 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6958 (ttpp) outliers start: 118 outliers final: 71 residues processed: 738 average time/residue: 0.1862 time to fit residues: 218.8042 Evaluate side-chains 675 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 599 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 185 ILE Chi-restraints excluded: chain V1 residue 267 THR Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 306 LEU Chi-restraints excluded: chain V1 residue 356 HIS Chi-restraints excluded: chain V1 residue 362 CYS Chi-restraints excluded: chain V1 residue 389 ILE Chi-restraints excluded: chain V2 residue 14 LYS Chi-restraints excluded: chain V2 residue 113 SER Chi-restraints excluded: chain V2 residue 190 ARG Chi-restraints excluded: chain S1 residue 30 CYS Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 107 ILE Chi-restraints excluded: chain S1 residue 145 LEU Chi-restraints excluded: chain S1 residue 199 ILE Chi-restraints excluded: chain S1 residue 202 ILE Chi-restraints excluded: chain S1 residue 216 THR Chi-restraints excluded: chain S1 residue 236 SER Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 199 VAL Chi-restraints excluded: chain S2 residue 203 LEU Chi-restraints excluded: chain S2 residue 340 THR Chi-restraints excluded: chain S2 residue 354 GLU Chi-restraints excluded: chain S2 residue 414 VAL Chi-restraints excluded: chain S2 residue 418 ILE Chi-restraints excluded: chain S3 residue 78 LEU Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 87 ILE Chi-restraints excluded: chain S7 residue 109 GLU Chi-restraints excluded: chain S7 residue 118 SER Chi-restraints excluded: chain S7 residue 140 VAL Chi-restraints excluded: chain S7 residue 161 LEU Chi-restraints excluded: chain S7 residue 175 ILE Chi-restraints excluded: chain S8 residue 40 TYR Chi-restraints excluded: chain S8 residue 75 GLU Chi-restraints excluded: chain S8 residue 119 CYS Chi-restraints excluded: chain V3 residue 52 LEU Chi-restraints excluded: chain S6 residue 4 THR Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 26 VAL Chi-restraints excluded: chain S6 residue 43 LEU Chi-restraints excluded: chain S6 residue 89 LEU Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 25 VAL Chi-restraints excluded: chain S4 residue 105 VAL Chi-restraints excluded: chain A9 residue 58 HIS Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 90 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 323 THR Chi-restraints excluded: chain A2 residue 15 LEU Chi-restraints excluded: chain A2 residue 52 ILE Chi-restraints excluded: chain A2 residue 56 GLU Chi-restraints excluded: chain A5 residue 11 VAL Chi-restraints excluded: chain A5 residue 26 LEU Chi-restraints excluded: chain A5 residue 58 VAL Chi-restraints excluded: chain A5 residue 64 VAL Chi-restraints excluded: chain A6 residue 45 THR Chi-restraints excluded: chain A6 residue 64 GLU Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A6 residue 116 ASP Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 34 THR Chi-restraints excluded: chain AL residue 37 THR Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 47 GLN Chi-restraints excluded: chain AA residue 83 LYS Chi-restraints excluded: chain AM residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 43 optimal weight: 6.9990 chunk 254 optimal weight: 0.9990 chunk 255 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 290 optimal weight: 0.7980 chunk 307 optimal weight: 9.9990 chunk 279 optimal weight: 0.6980 chunk 236 optimal weight: 0.0770 chunk 66 optimal weight: 3.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 306 GLN ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V3 42 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN S4 46 GLN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 24 GLN A5 82 GLN A6 25 ASN A6 107 HIS AL 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.103917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.088768 restraints weight = 60870.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.091256 restraints weight = 36767.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093006 restraints weight = 25489.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094258 restraints weight = 19323.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095158 restraints weight = 15619.762| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 28339 Z= 0.418 Angle : 2.747 56.622 38440 Z= 1.562 Chirality : 0.480 6.364 4177 Planarity : 0.005 0.075 4957 Dihedral : 7.265 143.322 3867 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.13 % Favored : 90.84 % Rotamer: Outliers : 3.60 % Allowed : 18.86 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.89 (0.14), residues: 3417 helix: 0.42 (0.14), residues: 1364 sheet: -1.44 (0.28), residues: 308 loop : -2.73 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGS2 174 TYR 0.029 0.002 TYRS7 28 PHE 0.022 0.001 PHEV3 61 TRP 0.013 0.001 TRPS7 46 HIS 0.009 0.001 HISS1 549 Details of bonding type rmsd/Z covalent geometry : bond 0.01221 / 0.42 (28302) covalent geometry : angle 2.38317 / 1.56 (38356) hydrogen bonds : bond 0.04478 / 3.01 ( 1042) hydrogen bonds : angle 5.01450 / 3.48 ( 2952) metal coordination : bond 0.01541 / 1.01 ( 36) metal coordination : angle 29.32483 / 18.17 ( 84) Misc. bond : bond 0.00069 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 629 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V1 82 MET cc_start: 0.8963 (tpp) cc_final: 0.8397 (tpp) REVERT: V1 101 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7395 (tp30) REVERT: V1 120 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6946 (mt-10) REVERT: V1 189 GLU cc_start: 0.8071 (mp0) cc_final: 0.7810 (mp0) REVERT: V1 302 SER cc_start: 0.8766 (m) cc_final: 0.8150 (p) REVERT: V2 163 ASP cc_start: 0.7683 (m-30) cc_final: 0.7203 (m-30) REVERT: V2 190 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7155 (ptt-90) REVERT: S1 52 CYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8889 (p) REVERT: S1 119 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: S1 248 MET cc_start: 0.7838 (mmm) cc_final: 0.7610 (mmm) REVERT: S1 450 MET cc_start: 0.8036 (ttp) cc_final: 0.7748 (ttp) REVERT: S1 490 MET cc_start: 0.8543 (tmm) cc_final: 0.8147 (tmm) REVERT: S2 67 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7614 (tm-30) REVERT: S2 83 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9236 (tt) REVERT: S2 92 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7403 (mt-10) REVERT: S2 103 PHE cc_start: 0.8558 (m-80) cc_final: 0.8295 (m-10) REVERT: S2 115 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7723 (tp30) REVERT: S2 127 ASN cc_start: 0.9008 (t0) cc_final: 0.8250 (t0) REVERT: S2 149 ASN cc_start: 0.9163 (t0) cc_final: 0.8887 (t0) REVERT: S2 228 MET cc_start: 0.8899 (tmm) cc_final: 0.8176 (tmm) REVERT: S2 268 ASP cc_start: 0.7428 (t0) cc_final: 0.7064 (t0) REVERT: S2 338 MET cc_start: 0.9221 (tmm) cc_final: 0.8978 (tmm) REVERT: S3 39 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7892 (tt0) REVERT: S3 91 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7369 (mm-30) REVERT: S3 174 LEU cc_start: 0.8981 (mp) cc_final: 0.8748 (mp) REVERT: S7 58 GLU cc_start: 0.8023 (tp30) cc_final: 0.7728 (tp30) REVERT: S7 71 ARG cc_start: 0.7616 (mtm110) cc_final: 0.5099 (mmp-170) REVERT: S7 94 ASN cc_start: 0.8942 (m-40) cc_final: 0.8551 (t0) REVERT: S7 105 ASP cc_start: 0.8091 (m-30) cc_final: 0.7682 (m-30) REVERT: S7 130 TYR cc_start: 0.8182 (p90) cc_final: 0.7736 (p90) REVERT: S7 168 LYS cc_start: 0.8052 (tttt) cc_final: 0.7837 (tttt) REVERT: S8 54 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8650 (mtmm) REVERT: S8 110 ASP cc_start: 0.7362 (m-30) cc_final: 0.6336 (m-30) REVERT: S8 113 MET cc_start: 0.9006 (mmm) cc_final: 0.8573 (mmm) REVERT: S8 160 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8856 (ttpp) REVERT: V3 63 MET cc_start: 0.7175 (mmm) cc_final: 0.6839 (mmm) REVERT: S6 32 GLN cc_start: 0.8861 (pp30) cc_final: 0.8164 (pp30) REVERT: S6 89 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8928 (pp) REVERT: S4 46 GLN cc_start: 0.8218 (mt0) cc_final: 0.7707 (mt0) REVERT: S4 70 MET cc_start: 0.7814 (mmm) cc_final: 0.7327 (mmm) REVERT: A9 92 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8463 (mt) REVERT: A9 176 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.5823 (t0) REVERT: A9 287 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8670 (mp) REVERT: A2 17 GLU cc_start: 0.7567 (pt0) cc_final: 0.6964 (pt0) REVERT: A5 46 TYR cc_start: 0.8011 (m-80) cc_final: 0.7777 (m-80) REVERT: A5 53 GLU cc_start: 0.7784 (pt0) cc_final: 0.7370 (pt0) REVERT: A5 104 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6597 (mt-10) REVERT: A6 39 TYR cc_start: 0.8783 (t80) cc_final: 0.8353 (t80) REVERT: A6 41 GLU cc_start: 0.8894 (tp30) cc_final: 0.8485 (tp30) REVERT: A6 73 THR cc_start: 0.8682 (p) cc_final: 0.8416 (t) REVERT: A7 51 ASN cc_start: 0.7825 (p0) cc_final: 0.7480 (p0) REVERT: AL 27 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8121 (tt) REVERT: AL 43 LYS cc_start: 0.8069 (tmmt) cc_final: 0.7400 (tppt) REVERT: AL 120 THR cc_start: 0.7612 (t) cc_final: 0.7361 (m) REVERT: AL 123 GLN cc_start: 0.8383 (pm20) cc_final: 0.8142 (pt0) REVERT: AA 12 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7989 (tmtt) REVERT: AA 13 ASP cc_start: 0.8428 (m-30) cc_final: 0.8007 (m-30) REVERT: AA 52 MET cc_start: 0.8731 (ppp) cc_final: 0.8231 (ppp) outliers start: 107 outliers final: 66 residues processed: 696 average time/residue: 0.1849 time to fit residues: 205.0534 Evaluate side-chains 633 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 558 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 107 ASP Chi-restraints excluded: chain V1 residue 185 ILE Chi-restraints excluded: chain V1 residue 267 THR Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 306 LEU Chi-restraints excluded: chain V1 residue 389 ILE Chi-restraints excluded: chain V2 residue 14 LYS Chi-restraints excluded: chain V2 residue 113 SER Chi-restraints excluded: chain V2 residue 169 ILE Chi-restraints excluded: chain V2 residue 190 ARG Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 119 GLN Chi-restraints excluded: chain S1 residue 145 LEU Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 202 ILE Chi-restraints excluded: chain S1 residue 216 THR Chi-restraints excluded: chain S1 residue 236 SER Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S2 residue 83 LEU Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 199 VAL Chi-restraints excluded: chain S2 residue 340 THR Chi-restraints excluded: chain S2 residue 414 VAL Chi-restraints excluded: chain S3 residue 78 LEU Chi-restraints excluded: chain S3 residue 79 THR Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 48 MET Chi-restraints excluded: chain S7 residue 107 MET Chi-restraints excluded: chain S7 residue 109 GLU Chi-restraints excluded: chain S7 residue 140 VAL Chi-restraints excluded: chain S7 residue 175 ILE Chi-restraints excluded: chain S8 residue 40 TYR Chi-restraints excluded: chain S8 residue 75 GLU Chi-restraints excluded: chain S8 residue 83 CYS Chi-restraints excluded: chain S8 residue 119 CYS Chi-restraints excluded: chain S8 residue 161 TRP Chi-restraints excluded: chain V3 residue 42 GLN Chi-restraints excluded: chain V3 residue 52 LEU Chi-restraints excluded: chain V3 residue 58 LEU Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 26 VAL Chi-restraints excluded: chain S6 residue 89 LEU Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 25 VAL Chi-restraints excluded: chain S4 residue 45 MET Chi-restraints excluded: chain S4 residue 105 VAL Chi-restraints excluded: chain A9 residue 58 HIS Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 92 ILE Chi-restraints excluded: chain A9 residue 111 VAL Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 243 GLN Chi-restraints excluded: chain A9 residue 287 ILE Chi-restraints excluded: chain A9 residue 323 THR Chi-restraints excluded: chain A2 residue 15 LEU Chi-restraints excluded: chain A2 residue 52 ILE Chi-restraints excluded: chain A2 residue 56 GLU Chi-restraints excluded: chain A5 residue 26 LEU Chi-restraints excluded: chain A5 residue 58 VAL Chi-restraints excluded: chain A6 residue 64 GLU Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A6 residue 107 HIS Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 34 THR Chi-restraints excluded: chain A7 residue 40 LEU Chi-restraints excluded: chain AL residue 27 LEU Chi-restraints excluded: chain AL residue 37 THR Chi-restraints excluded: chain AL residue 39 VAL Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AA residue 32 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 149 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 279 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 255 HIS ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 46 ASN S2 116 GLN S2 190 HIS ** S2 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 61 HIS ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 70 GLN A5 82 GLN AA 47 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.103128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087957 restraints weight = 60799.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.090388 restraints weight = 37020.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.092120 restraints weight = 25743.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.093373 restraints weight = 19580.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094286 restraints weight = 15822.744| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 28339 Z= 0.419 Angle : 2.750 54.687 38440 Z= 1.563 Chirality : 0.479 6.371 4177 Planarity : 0.005 0.073 4957 Dihedral : 7.070 140.123 3867 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.66 % Favored : 90.31 % Rotamer: Outliers : 3.87 % Allowed : 20.48 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.71 (0.14), residues: 3417 helix: 0.63 (0.14), residues: 1366 sheet: -1.48 (0.28), residues: 317 loop : -2.66 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGS8 105 TYR 0.028 0.002 TYRS8 149 PHE 0.022 0.001 PHEV3 61 TRP 0.013 0.001 TRPS7 46 HIS 0.017 0.001 HISA6 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01222 / 0.42 (28302) covalent geometry : angle 2.38400 / 1.56 (38356) hydrogen bonds : bond 0.04422 / 2.97 ( 1042) hydrogen bonds : angle 4.91338 / 3.42 ( 2952) metal coordination : bond 0.01551 / 1.09 ( 36) metal coordination : angle 29.41009 / 18.25 ( 84) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 592 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: symmetry clash REVERT: V1 82 MET cc_start: 0.9116 (tpp) cc_final: 0.8512 (tpp) REVERT: V1 101 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7430 (tp30) REVERT: V1 189 GLU cc_start: 0.8182 (mp0) cc_final: 0.7874 (mp0) REVERT: V1 213 VAL cc_start: 0.9457 (t) cc_final: 0.9159 (m) REVERT: V1 302 SER cc_start: 0.8827 (m) cc_final: 0.8186 (p) REVERT: V2 163 ASP cc_start: 0.7725 (m-30) cc_final: 0.7256 (m-30) REVERT: V2 190 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7163 (ptt-90) REVERT: S1 52 CYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8966 (p) REVERT: S1 119 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: S1 450 MET cc_start: 0.8002 (ttp) cc_final: 0.7770 (ttp) REVERT: S2 82 LEU cc_start: 0.8441 (mp) cc_final: 0.8170 (tp) REVERT: S2 83 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9117 (tt) REVERT: S2 92 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7470 (mt-10) REVERT: S2 103 PHE cc_start: 0.8538 (m-80) cc_final: 0.8307 (m-10) REVERT: S2 127 ASN cc_start: 0.8988 (t0) cc_final: 0.8331 (t0) REVERT: S2 149 ASN cc_start: 0.9191 (t0) cc_final: 0.8913 (t0) REVERT: S2 228 MET cc_start: 0.8792 (tmm) cc_final: 0.8065 (tmm) REVERT: S2 231 ASN cc_start: 0.7848 (m110) cc_final: 0.7576 (m110) REVERT: S2 338 MET cc_start: 0.9251 (tmm) cc_final: 0.8994 (tmm) REVERT: S3 39 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7825 (tt0) REVERT: S3 174 LEU cc_start: 0.9041 (mp) cc_final: 0.8629 (mp) REVERT: S3 176 TYR cc_start: 0.8750 (t80) cc_final: 0.8347 (t80) REVERT: S3 192 GLN cc_start: 0.8209 (tt0) cc_final: 0.7693 (tt0) REVERT: S7 58 GLU cc_start: 0.7968 (tp30) cc_final: 0.7613 (tp30) REVERT: S7 94 ASN cc_start: 0.9032 (m-40) cc_final: 0.8563 (t0) REVERT: S7 105 ASP cc_start: 0.8117 (m-30) cc_final: 0.7726 (m-30) REVERT: S7 130 TYR cc_start: 0.8225 (p90) cc_final: 0.7761 (p90) REVERT: S7 152 THR cc_start: 0.8769 (m) cc_final: 0.8376 (p) REVERT: S8 54 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8619 (mtmm) REVERT: S8 110 ASP cc_start: 0.7474 (m-30) cc_final: 0.6843 (m-30) REVERT: S8 160 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8775 (ttpp) REVERT: S8 170 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8483 (tp-100) REVERT: V3 63 MET cc_start: 0.7245 (mmm) cc_final: 0.6856 (mmp) REVERT: S6 32 GLN cc_start: 0.8862 (pp30) cc_final: 0.8391 (pp30) REVERT: S4 70 MET cc_start: 0.7792 (mmm) cc_final: 0.6940 (mmt) REVERT: A9 92 ILE cc_start: 0.8824 (pt) cc_final: 0.8526 (mt) REVERT: A9 111 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.7971 (p) REVERT: A9 176 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.5704 (t0) REVERT: A2 25 ARG cc_start: 0.8223 (mpp-170) cc_final: 0.7827 (mpp80) REVERT: A5 46 TYR cc_start: 0.8001 (m-80) cc_final: 0.7623 (m-80) REVERT: A5 53 GLU cc_start: 0.7791 (pt0) cc_final: 0.7388 (pt0) REVERT: A5 104 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6571 (mt-10) REVERT: A6 39 TYR cc_start: 0.8753 (t80) cc_final: 0.8453 (t80) REVERT: A6 41 GLU cc_start: 0.8930 (tp30) cc_final: 0.8480 (tp30) REVERT: A6 73 THR cc_start: 0.8711 (p) cc_final: 0.8420 (t) REVERT: A6 89 LEU cc_start: 0.8653 (tt) cc_final: 0.8425 (tp) REVERT: A7 51 ASN cc_start: 0.7838 (p0) cc_final: 0.7488 (p0) REVERT: A7 57 ASP cc_start: 0.8304 (t0) cc_final: 0.7775 (t70) REVERT: AL 61 TRP cc_start: 0.8920 (p90) cc_final: 0.7931 (p90) REVERT: AL 135 GLN cc_start: 0.8407 (tp40) cc_final: 0.8038 (tm-30) REVERT: AA 12 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7994 (tmtt) REVERT: AA 52 MET cc_start: 0.8793 (ppp) cc_final: 0.8219 (ppp) REVERT: AA 79 TYR cc_start: 0.8659 (t80) cc_final: 0.8396 (t80) outliers start: 115 outliers final: 77 residues processed: 668 average time/residue: 0.1786 time to fit residues: 191.2797 Evaluate side-chains 629 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 546 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 185 ILE Chi-restraints excluded: chain V1 residue 267 THR Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 306 LEU Chi-restraints excluded: chain V1 residue 341 THR Chi-restraints excluded: chain V1 residue 356 HIS Chi-restraints excluded: chain V1 residue 362 CYS Chi-restraints excluded: chain V1 residue 389 ILE Chi-restraints excluded: chain V2 residue 14 LYS Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 113 SER Chi-restraints excluded: chain V2 residue 169 ILE Chi-restraints excluded: chain V2 residue 190 ARG Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 77 TRP Chi-restraints excluded: chain S1 residue 119 GLN Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 187 ILE Chi-restraints excluded: chain S1 residue 199 ILE Chi-restraints excluded: chain S1 residue 202 ILE Chi-restraints excluded: chain S1 residue 205 VAL Chi-restraints excluded: chain S1 residue 216 THR Chi-restraints excluded: chain S1 residue 236 SER Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S2 residue 83 LEU Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 199 VAL Chi-restraints excluded: chain S2 residue 203 LEU Chi-restraints excluded: chain S2 residue 229 LEU Chi-restraints excluded: chain S2 residue 323 ILE Chi-restraints excluded: chain S2 residue 340 THR Chi-restraints excluded: chain S2 residue 414 VAL Chi-restraints excluded: chain S3 residue 78 LEU Chi-restraints excluded: chain S3 residue 79 THR Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 134 ILE Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 48 MET Chi-restraints excluded: chain S7 residue 61 HIS Chi-restraints excluded: chain S7 residue 109 GLU Chi-restraints excluded: chain S7 residue 116 MET Chi-restraints excluded: chain S7 residue 118 SER Chi-restraints excluded: chain S7 residue 140 VAL Chi-restraints excluded: chain S7 residue 146 VAL Chi-restraints excluded: chain S7 residue 175 ILE Chi-restraints excluded: chain S8 residue 12 MET Chi-restraints excluded: chain S8 residue 40 TYR Chi-restraints excluded: chain S8 residue 75 GLU Chi-restraints excluded: chain S8 residue 83 CYS Chi-restraints excluded: chain S8 residue 119 CYS Chi-restraints excluded: chain S8 residue 161 TRP Chi-restraints excluded: chain V3 residue 52 LEU Chi-restraints excluded: chain V3 residue 58 LEU Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 26 VAL Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 25 VAL Chi-restraints excluded: chain S4 residue 105 VAL Chi-restraints excluded: chain S4 residue 130 VAL Chi-restraints excluded: chain A9 residue 58 HIS Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 90 VAL Chi-restraints excluded: chain A9 residue 111 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 323 THR Chi-restraints excluded: chain A2 residue 15 LEU Chi-restraints excluded: chain A2 residue 52 ILE Chi-restraints excluded: chain A2 residue 56 GLU Chi-restraints excluded: chain A5 residue 26 LEU Chi-restraints excluded: chain A5 residue 58 VAL Chi-restraints excluded: chain A5 residue 112 LYS Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 40 LEU Chi-restraints excluded: chain AL residue 39 VAL Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 47 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 258 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 330 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 149 ASN ** S2 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 157 ASN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 70 GLN A5 82 GLN A5 95 GLN A6 107 HIS AA 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.087626 restraints weight = 60828.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.090063 restraints weight = 36943.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.091783 restraints weight = 25736.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093014 restraints weight = 19606.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.093926 restraints weight = 15895.366| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 28339 Z= 0.419 Angle : 2.750 55.758 38440 Z= 1.562 Chirality : 0.479 6.366 4177 Planarity : 0.005 0.072 4957 Dihedral : 6.866 137.877 3867 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.63 % Favored : 90.34 % Rotamer: Outliers : 4.17 % Allowed : 20.58 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.60 (0.14), residues: 3417 helix: 0.78 (0.14), residues: 1365 sheet: -1.41 (0.28), residues: 311 loop : -2.64 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAL 131 TYR 0.028 0.002 TYRS7 28 PHE 0.024 0.001 PHEA9 29 TRP 0.014 0.001 TRPS7 46 HIS 0.012 0.001 HISS7 61 Details of bonding type rmsd/Z covalent geometry : bond 0.01222 / 0.42 (28302) covalent geometry : angle 2.38297 / 1.56 (38356) hydrogen bonds : bond 0.04339 / 2.90 ( 1042) hydrogen bonds : angle 4.85966 / 3.38 ( 2952) metal coordination : bond 0.01767 / 1.18 ( 36) metal coordination : angle 29.47194 / 18.34 ( 84) Misc. bond : bond 0.00117 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 565 time to evaluate : 1.125 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: V1 82 MET cc_start: 0.9137 (tpp) cc_final: 0.8558 (tpp) REVERT: V1 101 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7369 (tp30) REVERT: V1 185 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8278 (tp) REVERT: V1 213 VAL cc_start: 0.9439 (t) cc_final: 0.9213 (m) REVERT: V1 302 SER cc_start: 0.8870 (m) cc_final: 0.8224 (p) REVERT: V2 28 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.7877 (m-10) REVERT: V2 74 GLN cc_start: 0.8503 (pm20) cc_final: 0.8294 (pm20) REVERT: V2 163 ASP cc_start: 0.7614 (m-30) cc_final: 0.7124 (m-30) REVERT: V2 190 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7179 (ptt-90) REVERT: S1 52 CYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8975 (p) REVERT: S1 119 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: S1 450 MET cc_start: 0.8048 (ttp) cc_final: 0.7774 (ttp) REVERT: S2 83 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9026 (tt) REVERT: S2 92 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7520 (mt-10) REVERT: S2 103 PHE cc_start: 0.8534 (m-80) cc_final: 0.8304 (m-10) REVERT: S2 127 ASN cc_start: 0.9019 (t0) cc_final: 0.8349 (t0) REVERT: S2 149 ASN cc_start: 0.9283 (t160) cc_final: 0.8988 (t0) REVERT: S2 228 MET cc_start: 0.8902 (tmm) cc_final: 0.8255 (tmm) REVERT: S2 338 MET cc_start: 0.9272 (tmm) cc_final: 0.9000 (tmm) REVERT: S3 39 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7799 (tt0) REVERT: S3 176 TYR cc_start: 0.8798 (t80) cc_final: 0.8315 (t80) REVERT: S3 192 GLN cc_start: 0.8252 (tt0) cc_final: 0.7717 (tt0) REVERT: S7 58 GLU cc_start: 0.7997 (tp30) cc_final: 0.7649 (tp30) REVERT: S7 69 MET cc_start: 0.8257 (mmm) cc_final: 0.7774 (mmp) REVERT: S7 105 ASP cc_start: 0.8125 (m-30) cc_final: 0.7722 (m-30) REVERT: S7 112 TYR cc_start: 0.7959 (m-80) cc_final: 0.7327 (m-80) REVERT: S7 130 TYR cc_start: 0.8300 (p90) cc_final: 0.7822 (p90) REVERT: S7 152 THR cc_start: 0.8826 (m) cc_final: 0.8419 (p) REVERT: S8 54 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8597 (mtmm) REVERT: S8 110 ASP cc_start: 0.7489 (m-30) cc_final: 0.6845 (m-30) REVERT: S8 160 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8816 (ttpp) REVERT: S8 170 GLN cc_start: 0.8690 (tp-100) cc_final: 0.8469 (tp-100) REVERT: V3 63 MET cc_start: 0.7360 (mmm) cc_final: 0.6961 (mmp) REVERT: S6 32 GLN cc_start: 0.8842 (pp30) cc_final: 0.8411 (pp30) REVERT: S4 9 GLN cc_start: 0.5955 (pm20) cc_final: 0.5721 (pm20) REVERT: S4 70 MET cc_start: 0.7815 (mmm) cc_final: 0.6910 (mmt) REVERT: A9 92 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8580 (mt) REVERT: A9 111 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8051 (p) REVERT: A9 176 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.5992 (t0) REVERT: A2 67 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7966 (ttp80) REVERT: A5 46 TYR cc_start: 0.8008 (m-80) cc_final: 0.7633 (m-80) REVERT: A5 53 GLU cc_start: 0.7796 (pt0) cc_final: 0.7373 (pt0) REVERT: A5 104 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6536 (mt-10) REVERT: A6 39 TYR cc_start: 0.8704 (t80) cc_final: 0.8409 (t80) REVERT: A6 41 GLU cc_start: 0.8935 (tp30) cc_final: 0.8511 (tp30) REVERT: A6 73 THR cc_start: 0.8728 (p) cc_final: 0.8426 (t) REVERT: A6 89 LEU cc_start: 0.8641 (tt) cc_final: 0.8435 (tp) REVERT: A7 51 ASN cc_start: 0.7864 (p0) cc_final: 0.7510 (p0) REVERT: A7 57 ASP cc_start: 0.8328 (t0) cc_final: 0.7696 (t70) REVERT: AL 27 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7992 (tt) REVERT: AL 53 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7785 (tppt) REVERT: AL 135 GLN cc_start: 0.8453 (tp40) cc_final: 0.8059 (tm-30) REVERT: AA 12 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8060 (tmtt) REVERT: AA 13 ASP cc_start: 0.8237 (m-30) cc_final: 0.7925 (m-30) REVERT: AA 51 ILE cc_start: 0.9139 (mm) cc_final: 0.8928 (mm) REVERT: AA 52 MET cc_start: 0.8746 (ppp) cc_final: 0.8189 (ppp) outliers start: 124 outliers final: 93 residues processed: 646 average time/residue: 0.1778 time to fit residues: 185.6137 Evaluate side-chains 646 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 543 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 185 ILE Chi-restraints excluded: chain V1 residue 267 THR Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 306 LEU Chi-restraints excluded: chain V1 residue 341 THR Chi-restraints excluded: chain V1 residue 356 HIS Chi-restraints excluded: chain V1 residue 362 CYS Chi-restraints excluded: chain V1 residue 389 ILE Chi-restraints excluded: chain V2 residue 14 LYS Chi-restraints excluded: chain V2 residue 28 TYR Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 110 LEU Chi-restraints excluded: chain V2 residue 113 SER Chi-restraints excluded: chain V2 residue 132 THR Chi-restraints excluded: chain V2 residue 169 ILE Chi-restraints excluded: chain V2 residue 190 ARG Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 77 TRP Chi-restraints excluded: chain S1 residue 119 GLN Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 187 ILE Chi-restraints excluded: chain S1 residue 199 ILE Chi-restraints excluded: chain S1 residue 202 ILE Chi-restraints excluded: chain S1 residue 205 VAL Chi-restraints excluded: chain S1 residue 216 THR Chi-restraints excluded: chain S1 residue 231 MET Chi-restraints excluded: chain S1 residue 236 SER Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 636 VAL Chi-restraints excluded: chain S1 residue 661 LEU Chi-restraints excluded: chain S2 residue 83 LEU Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 199 VAL Chi-restraints excluded: chain S2 residue 203 LEU Chi-restraints excluded: chain S2 residue 229 LEU Chi-restraints excluded: chain S2 residue 340 THR Chi-restraints excluded: chain S2 residue 354 GLU Chi-restraints excluded: chain S2 residue 414 VAL Chi-restraints excluded: chain S3 residue 78 LEU Chi-restraints excluded: chain S3 residue 79 THR Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 117 VAL Chi-restraints excluded: chain S3 residue 134 ILE Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 48 MET Chi-restraints excluded: chain S7 residue 109 GLU Chi-restraints excluded: chain S7 residue 116 MET Chi-restraints excluded: chain S7 residue 118 SER Chi-restraints excluded: chain S7 residue 140 VAL Chi-restraints excluded: chain S7 residue 146 VAL Chi-restraints excluded: chain S7 residue 161 LEU Chi-restraints excluded: chain S7 residue 175 ILE Chi-restraints excluded: chain S8 residue 12 MET Chi-restraints excluded: chain S8 residue 40 TYR Chi-restraints excluded: chain S8 residue 75 GLU Chi-restraints excluded: chain S8 residue 83 CYS Chi-restraints excluded: chain S8 residue 119 CYS Chi-restraints excluded: chain S8 residue 161 TRP Chi-restraints excluded: chain V3 residue 52 LEU Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 26 VAL Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 25 VAL Chi-restraints excluded: chain S4 residue 45 MET Chi-restraints excluded: chain S4 residue 79 LEU Chi-restraints excluded: chain S4 residue 105 VAL Chi-restraints excluded: chain S4 residue 130 VAL Chi-restraints excluded: chain A9 residue 58 HIS Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 90 VAL Chi-restraints excluded: chain A9 residue 92 ILE Chi-restraints excluded: chain A9 residue 111 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 179 LEU Chi-restraints excluded: chain A9 residue 218 ILE Chi-restraints excluded: chain A9 residue 243 GLN Chi-restraints excluded: chain A9 residue 290 THR Chi-restraints excluded: chain A9 residue 323 THR Chi-restraints excluded: chain A2 residue 15 LEU Chi-restraints excluded: chain A2 residue 52 ILE Chi-restraints excluded: chain A2 residue 53 LEU Chi-restraints excluded: chain A2 residue 56 GLU Chi-restraints excluded: chain A5 residue 26 LEU Chi-restraints excluded: chain A5 residue 58 VAL Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A6 residue 107 HIS Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 34 THR Chi-restraints excluded: chain A7 residue 40 LEU Chi-restraints excluded: chain A7 residue 101 LYS Chi-restraints excluded: chain AL residue 27 LEU Chi-restraints excluded: chain AL residue 37 THR Chi-restraints excluded: chain AL residue 39 VAL Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AL residue 138 VAL Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 47 GLN Chi-restraints excluded: chain AM residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 160 optimal weight: 0.5980 chunk 162 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V3 42 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN A9 3 HIS ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 70 GLN A5 82 GLN A6 107 HIS AL 123 GLN AA 47 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.102450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087274 restraints weight = 60844.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.089705 restraints weight = 37042.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.091372 restraints weight = 25821.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.092623 restraints weight = 19740.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.093526 restraints weight = 16020.902| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 28339 Z= 0.420 Angle : 2.755 56.729 38440 Z= 1.563 Chirality : 0.479 6.369 4177 Planarity : 0.005 0.071 4957 Dihedral : 6.757 135.990 3867 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.75 % Favored : 90.23 % Rotamer: Outliers : 4.57 % Allowed : 20.51 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 3417 helix: 0.84 (0.14), residues: 1371 sheet: -1.36 (0.28), residues: 314 loop : -2.62 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGS7 42 TYR 0.027 0.002 TYRS7 28 PHE 0.031 0.001 PHEA9 29 TRP 0.014 0.001 TRPS7 46 HIS 0.022 0.001 HISA6 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01223 / 0.42 (28302) covalent geometry : angle 2.38638 / 1.56 (38356) hydrogen bonds : bond 0.04352 / 2.91 ( 1042) hydrogen bonds : angle 4.84920 / 3.38 ( 2952) metal coordination : bond 0.01755 / 1.20 ( 36) metal coordination : angle 29.52753 / 18.38 ( 84) Misc. bond : bond 0.00116 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 550 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V1 82 MET cc_start: 0.9134 (tpp) cc_final: 0.8583 (tpp) REVERT: V1 101 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7685 (tp30) REVERT: V1 185 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8320 (tp) REVERT: V1 213 VAL cc_start: 0.9437 (t) cc_final: 0.9226 (m) REVERT: V2 28 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7815 (m-10) REVERT: V2 163 ASP cc_start: 0.7628 (m-30) cc_final: 0.7143 (m-30) REVERT: V2 190 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7247 (ptt-90) REVERT: S1 52 CYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8995 (p) REVERT: S1 450 MET cc_start: 0.8126 (ttp) cc_final: 0.7797 (ttp) REVERT: S1 490 MET cc_start: 0.8597 (tmm) cc_final: 0.8092 (tmm) REVERT: S2 83 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9305 (tt) REVERT: S2 92 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7591 (mt-10) REVERT: S2 103 PHE cc_start: 0.8501 (m-80) cc_final: 0.8283 (m-10) REVERT: S2 127 ASN cc_start: 0.9067 (t0) cc_final: 0.8294 (t0) REVERT: S2 149 ASN cc_start: 0.9269 (t0) cc_final: 0.8952 (t0) REVERT: S2 164 MET cc_start: 0.6144 (tmm) cc_final: 0.5943 (tmm) REVERT: S2 261 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6466 (mpt-90) REVERT: S2 268 ASP cc_start: 0.8005 (t0) cc_final: 0.7801 (t0) REVERT: S2 371 LYS cc_start: 0.9172 (mmtm) cc_final: 0.8359 (mmtm) REVERT: S2 422 ASP cc_start: 0.7768 (p0) cc_final: 0.6628 (p0) REVERT: S3 39 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7806 (tt0) REVERT: S7 69 MET cc_start: 0.7930 (mmm) cc_final: 0.7664 (mmp) REVERT: S7 96 MET cc_start: 0.8514 (tpp) cc_final: 0.8082 (tpp) REVERT: S7 105 ASP cc_start: 0.8204 (m-30) cc_final: 0.7772 (m-30) REVERT: S7 112 TYR cc_start: 0.7937 (m-80) cc_final: 0.7264 (m-80) REVERT: S7 130 TYR cc_start: 0.8317 (p90) cc_final: 0.7813 (p90) REVERT: S8 54 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8626 (mtmm) REVERT: S8 110 ASP cc_start: 0.7481 (m-30) cc_final: 0.6861 (m-30) REVERT: S8 160 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8881 (ttpp) REVERT: S8 170 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8439 (tp-100) REVERT: V3 63 MET cc_start: 0.7155 (mmm) cc_final: 0.6861 (mmp) REVERT: S6 32 GLN cc_start: 0.8821 (pp30) cc_final: 0.8421 (pp30) REVERT: S6 54 SER cc_start: 0.7848 (t) cc_final: 0.7552 (m) REVERT: S4 9 GLN cc_start: 0.6004 (pm20) cc_final: 0.5770 (pm20) REVERT: S4 70 MET cc_start: 0.7807 (mmm) cc_final: 0.6917 (mmt) REVERT: S4 106 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A9 62 MET cc_start: 0.8160 (tpp) cc_final: 0.7845 (tpp) REVERT: A9 92 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8629 (mt) REVERT: A9 111 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.7966 (p) REVERT: A9 176 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6066 (t0) REVERT: A2 17 GLU cc_start: 0.7402 (pt0) cc_final: 0.6937 (pt0) REVERT: A2 67 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7741 (ttp80) REVERT: A5 46 TYR cc_start: 0.8105 (m-80) cc_final: 0.7649 (m-80) REVERT: A5 53 GLU cc_start: 0.7789 (pt0) cc_final: 0.7357 (pt0) REVERT: A5 104 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6525 (mt-10) REVERT: A6 39 TYR cc_start: 0.8703 (t80) cc_final: 0.8311 (t80) REVERT: A6 41 GLU cc_start: 0.8944 (tp30) cc_final: 0.8536 (tp30) REVERT: A6 73 THR cc_start: 0.8707 (p) cc_final: 0.8394 (t) REVERT: A6 89 LEU cc_start: 0.8651 (tt) cc_final: 0.8440 (tp) REVERT: A7 51 ASN cc_start: 0.7842 (p0) cc_final: 0.7544 (p0) REVERT: A7 57 ASP cc_start: 0.8040 (t0) cc_final: 0.7362 (t70) REVERT: A7 108 ASP cc_start: 0.6733 (t0) cc_final: 0.6477 (t0) REVERT: AL 27 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8035 (tt) REVERT: AL 53 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7818 (tppt) REVERT: AL 61 TRP cc_start: 0.8934 (p90) cc_final: 0.8037 (p90) REVERT: AL 135 GLN cc_start: 0.8442 (tp40) cc_final: 0.8049 (tm-30) REVERT: AA 12 LYS cc_start: 0.8345 (ttpt) cc_final: 0.8010 (tmtt) REVERT: AA 13 ASP cc_start: 0.8246 (m-30) cc_final: 0.7866 (m-30) REVERT: AA 51 ILE cc_start: 0.9120 (mm) cc_final: 0.8882 (mm) REVERT: AA 52 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7648 (ppp) outliers start: 136 outliers final: 105 residues processed: 633 average time/residue: 0.1841 time to fit residues: 188.5519 Evaluate side-chains 652 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 536 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 185 ILE Chi-restraints excluded: chain V1 residue 267 THR Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 306 LEU Chi-restraints excluded: chain V1 residue 341 THR Chi-restraints excluded: chain V1 residue 356 HIS Chi-restraints excluded: chain V1 residue 362 CYS Chi-restraints excluded: chain V1 residue 389 ILE Chi-restraints excluded: chain V2 residue 14 LYS Chi-restraints excluded: chain V2 residue 28 TYR Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 110 LEU Chi-restraints excluded: chain V2 residue 113 SER Chi-restraints excluded: chain V2 residue 132 THR Chi-restraints excluded: chain V2 residue 169 ILE Chi-restraints excluded: chain V2 residue 190 ARG Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 77 TRP Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 187 ILE Chi-restraints excluded: chain S1 residue 199 ILE Chi-restraints excluded: chain S1 residue 202 ILE Chi-restraints excluded: chain S1 residue 205 VAL Chi-restraints excluded: chain S1 residue 216 THR Chi-restraints excluded: chain S1 residue 231 MET Chi-restraints excluded: chain S1 residue 236 SER Chi-restraints excluded: chain S1 residue 242 THR Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 636 VAL Chi-restraints excluded: chain S1 residue 661 LEU Chi-restraints excluded: chain S2 residue 83 LEU Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 199 VAL Chi-restraints excluded: chain S2 residue 203 LEU Chi-restraints excluded: chain S2 residue 229 LEU Chi-restraints excluded: chain S2 residue 261 ARG Chi-restraints excluded: chain S2 residue 340 THR Chi-restraints excluded: chain S2 residue 354 GLU Chi-restraints excluded: chain S2 residue 414 VAL Chi-restraints excluded: chain S3 residue 78 LEU Chi-restraints excluded: chain S3 residue 79 THR Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 117 VAL Chi-restraints excluded: chain S3 residue 134 ILE Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S3 residue 147 ASP Chi-restraints excluded: chain S3 residue 200 ASN Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 48 MET Chi-restraints excluded: chain S7 residue 107 MET Chi-restraints excluded: chain S7 residue 109 GLU Chi-restraints excluded: chain S7 residue 118 SER Chi-restraints excluded: chain S7 residue 140 VAL Chi-restraints excluded: chain S7 residue 146 VAL Chi-restraints excluded: chain S7 residue 161 LEU Chi-restraints excluded: chain S8 residue 40 TYR Chi-restraints excluded: chain S8 residue 75 GLU Chi-restraints excluded: chain S8 residue 83 CYS Chi-restraints excluded: chain S8 residue 119 CYS Chi-restraints excluded: chain S8 residue 161 TRP Chi-restraints excluded: chain V3 residue 42 GLN Chi-restraints excluded: chain V3 residue 52 LEU Chi-restraints excluded: chain V3 residue 58 LEU Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 26 VAL Chi-restraints excluded: chain S6 residue 44 ILE Chi-restraints excluded: chain S6 residue 66 LEU Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 25 VAL Chi-restraints excluded: chain S4 residue 30 ILE Chi-restraints excluded: chain S4 residue 45 MET Chi-restraints excluded: chain S4 residue 79 LEU Chi-restraints excluded: chain S4 residue 105 VAL Chi-restraints excluded: chain S4 residue 130 VAL Chi-restraints excluded: chain A9 residue 58 HIS Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 90 VAL Chi-restraints excluded: chain A9 residue 92 ILE Chi-restraints excluded: chain A9 residue 111 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 179 LEU Chi-restraints excluded: chain A9 residue 218 ILE Chi-restraints excluded: chain A9 residue 243 GLN Chi-restraints excluded: chain A9 residue 290 THR Chi-restraints excluded: chain A9 residue 323 THR Chi-restraints excluded: chain A2 residue 15 LEU Chi-restraints excluded: chain A2 residue 52 ILE Chi-restraints excluded: chain A2 residue 53 LEU Chi-restraints excluded: chain A2 residue 56 GLU Chi-restraints excluded: chain A5 residue 13 LEU Chi-restraints excluded: chain A5 residue 26 LEU Chi-restraints excluded: chain A5 residue 58 VAL Chi-restraints excluded: chain A5 residue 103 VAL Chi-restraints excluded: chain A5 residue 112 LYS Chi-restraints excluded: chain A6 residue 45 THR Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A6 residue 107 HIS Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 34 THR Chi-restraints excluded: chain A7 residue 40 LEU Chi-restraints excluded: chain A7 residue 101 LYS Chi-restraints excluded: chain AL residue 27 LEU Chi-restraints excluded: chain AL residue 37 THR Chi-restraints excluded: chain AL residue 39 VAL Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AL residue 138 VAL Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 52 MET Chi-restraints excluded: chain AA residue 54 MET Chi-restraints excluded: chain AA residue 65 ILE Chi-restraints excluded: chain AA residue 66 ASP Chi-restraints excluded: chain AM residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 279 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 290 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 284 optimal weight: 0.9990 chunk 259 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 240 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V3 42 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 203 GLN A5 70 GLN A5 82 GLN A6 107 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.102697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087498 restraints weight = 61383.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.089928 restraints weight = 37114.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.091639 restraints weight = 25833.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092880 restraints weight = 19700.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093793 restraints weight = 15964.824| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 28339 Z= 0.419 Angle : 2.758 56.762 38440 Z= 1.564 Chirality : 0.479 6.364 4177 Planarity : 0.005 0.071 4957 Dihedral : 6.701 134.546 3867 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.72 % Favored : 90.23 % Rotamer: Outliers : 4.27 % Allowed : 20.98 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.47 (0.14), residues: 3417 helix: 0.87 (0.14), residues: 1369 sheet: -1.25 (0.28), residues: 333 loop : -2.61 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGS7 42 TYR 0.028 0.002 TYRS7 28 PHE 0.024 0.001 PHEA9 29 TRP 0.014 0.001 TRPS7 46 HIS 0.011 0.001 HISA6 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01223 / 0.42 (28302) covalent geometry : angle 2.39004 / 1.56 (38356) hydrogen bonds : bond 0.04330 / 2.92 ( 1042) hydrogen bonds : angle 4.81254 / 3.36 ( 2952) metal coordination : bond 0.01609 / 1.10 ( 36) metal coordination : angle 29.52321 / 18.37 ( 84) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 558 time to evaluate : 1.060 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: V1 82 MET cc_start: 0.9133 (tpp) cc_final: 0.8564 (tpp) REVERT: V1 101 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7694 (tp30) REVERT: V1 185 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8372 (tp) REVERT: V1 213 VAL cc_start: 0.9420 (t) cc_final: 0.9219 (m) REVERT: V2 28 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7761 (m-10) REVERT: V2 82 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6487 (mt-10) REVERT: V2 163 ASP cc_start: 0.7634 (m-30) cc_final: 0.6986 (m-30) REVERT: S1 52 CYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8991 (p) REVERT: S1 69 CYS cc_start: 0.7996 (p) cc_final: 0.7767 (p) REVERT: S1 450 MET cc_start: 0.8117 (ttp) cc_final: 0.7777 (ttp) REVERT: S1 490 MET cc_start: 0.8617 (tmm) cc_final: 0.8085 (tmm) REVERT: S2 71 GLU cc_start: 0.8105 (tp30) cc_final: 0.7847 (tp30) REVERT: S2 92 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7591 (mt-10) REVERT: S2 127 ASN cc_start: 0.9067 (t0) cc_final: 0.8275 (t0) REVERT: S2 149 ASN cc_start: 0.9230 (t0) cc_final: 0.8907 (t0) REVERT: S2 157 HIS cc_start: 0.8102 (t-170) cc_final: 0.7893 (t70) REVERT: S2 164 MET cc_start: 0.6144 (tmm) cc_final: 0.5887 (tmm) REVERT: S2 261 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6414 (mpt-90) REVERT: S2 422 ASP cc_start: 0.7749 (p0) cc_final: 0.6850 (p0) REVERT: S3 39 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7790 (tt0) REVERT: S3 131 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7913 (mt-10) REVERT: S3 211 GLN cc_start: 0.8483 (pm20) cc_final: 0.8240 (pm20) REVERT: S7 58 GLU cc_start: 0.8292 (tp30) cc_final: 0.7950 (tp30) REVERT: S7 105 ASP cc_start: 0.8199 (m-30) cc_final: 0.7765 (m-30) REVERT: S7 112 TYR cc_start: 0.7885 (m-80) cc_final: 0.7253 (m-80) REVERT: S7 130 TYR cc_start: 0.8301 (p90) cc_final: 0.7807 (p90) REVERT: S8 54 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8625 (mtmm) REVERT: S8 110 ASP cc_start: 0.7474 (m-30) cc_final: 0.6848 (m-30) REVERT: S8 160 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8913 (ttpp) REVERT: S8 170 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8418 (tp-100) REVERT: V3 63 MET cc_start: 0.7115 (mmm) cc_final: 0.6913 (mmp) REVERT: S6 32 GLN cc_start: 0.8829 (pp30) cc_final: 0.8415 (pp30) REVERT: S6 54 SER cc_start: 0.7885 (t) cc_final: 0.7563 (m) REVERT: S4 9 GLN cc_start: 0.6001 (pm20) cc_final: 0.5771 (pm20) REVERT: S4 70 MET cc_start: 0.7852 (mmm) cc_final: 0.6953 (mmt) REVERT: S4 106 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7434 (mt-10) REVERT: A9 62 MET cc_start: 0.8113 (tpp) cc_final: 0.7841 (tpp) REVERT: A9 92 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8689 (mt) REVERT: A9 111 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.7990 (p) REVERT: A9 176 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6023 (t0) REVERT: A9 206 TYR cc_start: 0.8527 (t80) cc_final: 0.8146 (t80) REVERT: A2 17 GLU cc_start: 0.7389 (pt0) cc_final: 0.6896 (pt0) REVERT: A2 67 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7762 (ttp80) REVERT: A5 46 TYR cc_start: 0.8140 (m-80) cc_final: 0.7689 (m-80) REVERT: A5 53 GLU cc_start: 0.7781 (pt0) cc_final: 0.7350 (pt0) REVERT: A5 104 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6488 (mt-10) REVERT: A6 41 GLU cc_start: 0.8938 (tp30) cc_final: 0.8537 (tp30) REVERT: A6 73 THR cc_start: 0.8728 (p) cc_final: 0.8405 (t) REVERT: A6 89 LEU cc_start: 0.8753 (tt) cc_final: 0.8542 (tp) REVERT: A7 51 ASN cc_start: 0.7808 (p0) cc_final: 0.7497 (p0) REVERT: A7 57 ASP cc_start: 0.8060 (t0) cc_final: 0.7360 (t70) REVERT: A7 108 ASP cc_start: 0.6749 (t0) cc_final: 0.6511 (t0) REVERT: AL 27 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7963 (tt) REVERT: AL 53 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7803 (tppt) REVERT: AL 135 GLN cc_start: 0.8454 (tp40) cc_final: 0.8129 (tm-30) REVERT: AA 12 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8001 (tmtt) REVERT: AA 13 ASP cc_start: 0.8240 (m-30) cc_final: 0.7869 (m-30) REVERT: AA 52 MET cc_start: 0.8717 (ppp) cc_final: 0.7999 (tmm) outliers start: 127 outliers final: 99 residues processed: 633 average time/residue: 0.1862 time to fit residues: 189.8802 Evaluate side-chains 653 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 546 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 185 ILE Chi-restraints excluded: chain V1 residue 188 GLU Chi-restraints excluded: chain V1 residue 267 THR Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 306 LEU Chi-restraints excluded: chain V1 residue 341 THR Chi-restraints excluded: chain V1 residue 356 HIS Chi-restraints excluded: chain V1 residue 362 CYS Chi-restraints excluded: chain V1 residue 389 ILE Chi-restraints excluded: chain V2 residue 14 LYS Chi-restraints excluded: chain V2 residue 28 TYR Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 110 LEU Chi-restraints excluded: chain V2 residue 113 SER Chi-restraints excluded: chain V2 residue 132 THR Chi-restraints excluded: chain V2 residue 169 ILE Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 77 TRP Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 187 ILE Chi-restraints excluded: chain S1 residue 199 ILE Chi-restraints excluded: chain S1 residue 205 VAL Chi-restraints excluded: chain S1 residue 216 THR Chi-restraints excluded: chain S1 residue 231 MET Chi-restraints excluded: chain S1 residue 236 SER Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 636 VAL Chi-restraints excluded: chain S1 residue 661 LEU Chi-restraints excluded: chain S2 residue 72 MET Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 199 VAL Chi-restraints excluded: chain S2 residue 203 LEU Chi-restraints excluded: chain S2 residue 229 LEU Chi-restraints excluded: chain S2 residue 261 ARG Chi-restraints excluded: chain S2 residue 340 THR Chi-restraints excluded: chain S2 residue 354 GLU Chi-restraints excluded: chain S2 residue 414 VAL Chi-restraints excluded: chain S3 residue 78 LEU Chi-restraints excluded: chain S3 residue 79 THR Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 103 SER Chi-restraints excluded: chain S3 residue 117 VAL Chi-restraints excluded: chain S3 residue 134 ILE Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S3 residue 147 ASP Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 48 MET Chi-restraints excluded: chain S7 residue 107 MET Chi-restraints excluded: chain S7 residue 109 GLU Chi-restraints excluded: chain S7 residue 118 SER Chi-restraints excluded: chain S7 residue 140 VAL Chi-restraints excluded: chain S7 residue 146 VAL Chi-restraints excluded: chain S7 residue 161 LEU Chi-restraints excluded: chain S7 residue 175 ILE Chi-restraints excluded: chain S8 residue 40 TYR Chi-restraints excluded: chain S8 residue 75 GLU Chi-restraints excluded: chain S8 residue 83 CYS Chi-restraints excluded: chain S8 residue 119 CYS Chi-restraints excluded: chain S8 residue 161 TRP Chi-restraints excluded: chain V3 residue 42 GLN Chi-restraints excluded: chain V3 residue 52 LEU Chi-restraints excluded: chain V3 residue 58 LEU Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 26 VAL Chi-restraints excluded: chain S6 residue 66 LEU Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 30 ILE Chi-restraints excluded: chain S4 residue 105 VAL Chi-restraints excluded: chain S4 residue 130 VAL Chi-restraints excluded: chain A9 residue 57 MET Chi-restraints excluded: chain A9 residue 58 HIS Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 90 VAL Chi-restraints excluded: chain A9 residue 92 ILE Chi-restraints excluded: chain A9 residue 111 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 179 LEU Chi-restraints excluded: chain A9 residue 218 ILE Chi-restraints excluded: chain A9 residue 290 THR Chi-restraints excluded: chain A9 residue 323 THR Chi-restraints excluded: chain A2 residue 15 LEU Chi-restraints excluded: chain A2 residue 52 ILE Chi-restraints excluded: chain A2 residue 53 LEU Chi-restraints excluded: chain A2 residue 56 GLU Chi-restraints excluded: chain A5 residue 13 LEU Chi-restraints excluded: chain A5 residue 26 LEU Chi-restraints excluded: chain A5 residue 58 VAL Chi-restraints excluded: chain A5 residue 103 VAL Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A6 residue 107 HIS Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 40 LEU Chi-restraints excluded: chain AL residue 27 LEU Chi-restraints excluded: chain AL residue 37 THR Chi-restraints excluded: chain AL residue 39 VAL Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AL residue 111 THR Chi-restraints excluded: chain AL residue 138 VAL Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 54 MET Chi-restraints excluded: chain AA residue 65 ILE Chi-restraints excluded: chain AA residue 66 ASP Chi-restraints excluded: chain AM residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 317 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 302 optimal weight: 0.6980 chunk 260 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 333 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V3 44 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN A5 70 GLN A5 82 GLN A6 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.102641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087934 restraints weight = 61338.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.090342 restraints weight = 36456.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092479 restraints weight = 23952.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093361 restraints weight = 17051.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.094089 restraints weight = 14123.627| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 28339 Z= 0.420 Angle : 2.763 57.462 38440 Z= 1.565 Chirality : 0.479 6.364 4177 Planarity : 0.005 0.070 4957 Dihedral : 6.671 132.885 3867 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.77 % Favored : 90.17 % Rotamer: Outliers : 4.20 % Allowed : 21.45 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.41 (0.14), residues: 3417 helix: 0.92 (0.14), residues: 1357 sheet: -1.16 (0.28), residues: 331 loop : -2.55 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAL 131 TYR 0.026 0.002 TYRAA 17 PHE 0.023 0.001 PHEA9 29 TRP 0.014 0.001 TRPV1 31 HIS 0.021 0.001 HISA6 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01224 / 0.42 (28302) covalent geometry : angle 2.39558 / 1.56 (38356) hydrogen bonds : bond 0.04286 / 2.87 ( 1042) hydrogen bonds : angle 4.80049 / 3.35 ( 2952) metal coordination : bond 0.01601 / 1.09 ( 36) metal coordination : angle 29.53203 / 18.38 ( 84) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 577 time to evaluate : 1.176 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: V1 82 MET cc_start: 0.9135 (tpp) cc_final: 0.8561 (tpp) REVERT: V1 101 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7719 (tp30) REVERT: V1 185 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8419 (tp) REVERT: V2 28 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7753 (m-10) REVERT: V2 82 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6471 (mt-10) REVERT: S1 52 CYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8972 (p) REVERT: S1 69 CYS cc_start: 0.7958 (p) cc_final: 0.7726 (p) REVERT: S2 92 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7605 (mt-10) REVERT: S2 127 ASN cc_start: 0.9068 (t0) cc_final: 0.8329 (t0) REVERT: S2 149 ASN cc_start: 0.9236 (t0) cc_final: 0.8852 (t0) REVERT: S2 157 HIS cc_start: 0.8123 (t-170) cc_final: 0.7870 (t70) REVERT: S2 164 MET cc_start: 0.6121 (tmm) cc_final: 0.5842 (tmm) REVERT: S2 261 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6344 (mpt-90) REVERT: S2 371 LYS cc_start: 0.9209 (mmtm) cc_final: 0.8721 (mmtm) REVERT: S2 422 ASP cc_start: 0.7522 (p0) cc_final: 0.6722 (p0) REVERT: S3 39 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7745 (tt0) REVERT: S3 95 ASN cc_start: 0.8457 (m-40) cc_final: 0.8022 (m-40) REVERT: S7 58 GLU cc_start: 0.8189 (tp30) cc_final: 0.7842 (tp30) REVERT: S7 105 ASP cc_start: 0.8220 (m-30) cc_final: 0.7825 (m-30) REVERT: S7 112 TYR cc_start: 0.7788 (m-80) cc_final: 0.7116 (m-80) REVERT: S7 130 TYR cc_start: 0.8149 (p90) cc_final: 0.7663 (p90) REVERT: S8 54 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8627 (mtmm) REVERT: S8 110 ASP cc_start: 0.7398 (m-30) cc_final: 0.6797 (m-30) REVERT: S8 160 LYS cc_start: 0.9175 (ttmt) cc_final: 0.8895 (ttpp) REVERT: S8 170 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8470 (tp-100) REVERT: V3 63 MET cc_start: 0.7184 (mmm) cc_final: 0.6969 (mmp) REVERT: S6 32 GLN cc_start: 0.8812 (pp30) cc_final: 0.8406 (pp30) REVERT: S6 86 TYR cc_start: 0.9055 (m-80) cc_final: 0.8850 (m-80) REVERT: S4 9 GLN cc_start: 0.6060 (pm20) cc_final: 0.5842 (pm20) REVERT: S4 70 MET cc_start: 0.7822 (mmm) cc_final: 0.6933 (mmt) REVERT: A9 62 MET cc_start: 0.7953 (tpp) cc_final: 0.7642 (tpp) REVERT: A9 92 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8748 (mt) REVERT: A9 111 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7864 (p) REVERT: A9 176 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.5998 (t0) REVERT: A5 46 TYR cc_start: 0.8162 (m-80) cc_final: 0.7720 (m-80) REVERT: A5 53 GLU cc_start: 0.7817 (pt0) cc_final: 0.7372 (pt0) REVERT: A5 104 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6462 (mt-10) REVERT: A6 41 GLU cc_start: 0.8943 (tp30) cc_final: 0.8542 (tp30) REVERT: A6 73 THR cc_start: 0.8729 (p) cc_final: 0.8414 (t) REVERT: A6 89 LEU cc_start: 0.8753 (tt) cc_final: 0.8544 (tp) REVERT: A7 51 ASN cc_start: 0.7823 (p0) cc_final: 0.7519 (p0) REVERT: A7 57 ASP cc_start: 0.8094 (t0) cc_final: 0.7354 (t70) REVERT: AL 27 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8068 (tt) REVERT: AL 53 LYS cc_start: 0.8292 (mmmt) cc_final: 0.7835 (tppt) REVERT: AL 61 TRP cc_start: 0.8922 (p90) cc_final: 0.8093 (p90) REVERT: AL 135 GLN cc_start: 0.8475 (tp40) cc_final: 0.8138 (tm-30) REVERT: AA 12 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8016 (tmtt) REVERT: AA 13 ASP cc_start: 0.8241 (m-30) cc_final: 0.7894 (m-30) REVERT: AA 24 LYS cc_start: 0.7752 (tptt) cc_final: 0.7463 (tttp) REVERT: AA 46 ASP cc_start: 0.8805 (m-30) cc_final: 0.8533 (m-30) REVERT: AA 52 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8269 (ppp) outliers start: 125 outliers final: 104 residues processed: 650 average time/residue: 0.1851 time to fit residues: 194.0602 Evaluate side-chains 670 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 557 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 185 ILE Chi-restraints excluded: chain V1 residue 188 GLU Chi-restraints excluded: chain V1 residue 267 THR Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 341 THR Chi-restraints excluded: chain V1 residue 356 HIS Chi-restraints excluded: chain V1 residue 362 CYS Chi-restraints excluded: chain V1 residue 389 ILE Chi-restraints excluded: chain V2 residue 14 LYS Chi-restraints excluded: chain V2 residue 28 TYR Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 110 LEU Chi-restraints excluded: chain V2 residue 113 SER Chi-restraints excluded: chain V2 residue 132 THR Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 77 TRP Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 187 ILE Chi-restraints excluded: chain S1 residue 202 ILE Chi-restraints excluded: chain S1 residue 205 VAL Chi-restraints excluded: chain S1 residue 216 THR Chi-restraints excluded: chain S1 residue 231 MET Chi-restraints excluded: chain S1 residue 236 SER Chi-restraints excluded: chain S1 residue 242 THR Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 636 VAL Chi-restraints excluded: chain S1 residue 661 LEU Chi-restraints excluded: chain S2 residue 72 MET Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 199 VAL Chi-restraints excluded: chain S2 residue 203 LEU Chi-restraints excluded: chain S2 residue 229 LEU Chi-restraints excluded: chain S2 residue 261 ARG Chi-restraints excluded: chain S2 residue 340 THR Chi-restraints excluded: chain S2 residue 414 VAL Chi-restraints excluded: chain S3 residue 78 LEU Chi-restraints excluded: chain S3 residue 79 THR Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 103 SER Chi-restraints excluded: chain S3 residue 117 VAL Chi-restraints excluded: chain S3 residue 134 ILE Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S3 residue 147 ASP Chi-restraints excluded: chain S3 residue 200 ASN Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 48 MET Chi-restraints excluded: chain S7 residue 107 MET Chi-restraints excluded: chain S7 residue 109 GLU Chi-restraints excluded: chain S7 residue 140 VAL Chi-restraints excluded: chain S7 residue 146 VAL Chi-restraints excluded: chain S7 residue 175 ILE Chi-restraints excluded: chain S8 residue 40 TYR Chi-restraints excluded: chain S8 residue 75 GLU Chi-restraints excluded: chain S8 residue 83 CYS Chi-restraints excluded: chain S8 residue 119 CYS Chi-restraints excluded: chain S8 residue 161 TRP Chi-restraints excluded: chain V3 residue 52 LEU Chi-restraints excluded: chain V3 residue 58 LEU Chi-restraints excluded: chain V3 residue 75 HIS Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 26 VAL Chi-restraints excluded: chain S6 residue 44 ILE Chi-restraints excluded: chain S6 residue 66 LEU Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 30 ILE Chi-restraints excluded: chain S4 residue 79 LEU Chi-restraints excluded: chain S4 residue 105 VAL Chi-restraints excluded: chain S4 residue 115 SER Chi-restraints excluded: chain S4 residue 130 VAL Chi-restraints excluded: chain A9 residue 57 MET Chi-restraints excluded: chain A9 residue 58 HIS Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 90 VAL Chi-restraints excluded: chain A9 residue 92 ILE Chi-restraints excluded: chain A9 residue 111 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 179 LEU Chi-restraints excluded: chain A9 residue 218 ILE Chi-restraints excluded: chain A9 residue 243 GLN Chi-restraints excluded: chain A9 residue 290 THR Chi-restraints excluded: chain A9 residue 323 THR Chi-restraints excluded: chain A2 residue 15 LEU Chi-restraints excluded: chain A2 residue 52 ILE Chi-restraints excluded: chain A2 residue 53 LEU Chi-restraints excluded: chain A2 residue 56 GLU Chi-restraints excluded: chain A5 residue 13 LEU Chi-restraints excluded: chain A5 residue 26 LEU Chi-restraints excluded: chain A5 residue 58 VAL Chi-restraints excluded: chain A5 residue 103 VAL Chi-restraints excluded: chain A5 residue 112 LYS Chi-restraints excluded: chain A6 residue 45 THR Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A6 residue 107 HIS Chi-restraints excluded: chain A7 residue 10 LEU Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 34 THR Chi-restraints excluded: chain A7 residue 40 LEU Chi-restraints excluded: chain A7 residue 101 LYS Chi-restraints excluded: chain AL residue 27 LEU Chi-restraints excluded: chain AL residue 37 THR Chi-restraints excluded: chain AL residue 39 VAL Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AL residue 111 THR Chi-restraints excluded: chain AL residue 138 VAL Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 52 MET Chi-restraints excluded: chain AA residue 54 MET Chi-restraints excluded: chain AA residue 65 ILE Chi-restraints excluded: chain AM residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 213 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 226 optimal weight: 3.9990 chunk 253 optimal weight: 0.0980 chunk 310 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 192 GLN S3 200 ASN ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V3 42 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A5 70 GLN A5 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.102124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087384 restraints weight = 61388.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.089676 restraints weight = 36577.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.091938 restraints weight = 24377.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092800 restraints weight = 17088.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.093564 restraints weight = 14165.516| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.241 28339 Z= 0.424 Angle : 2.773 57.689 38440 Z= 1.569 Chirality : 0.479 6.369 4177 Planarity : 0.005 0.081 4957 Dihedral : 6.678 131.689 3867 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.13 % Favored : 89.82 % Rotamer: Outliers : 3.97 % Allowed : 22.09 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.43 (0.14), residues: 3417 helix: 0.90 (0.14), residues: 1357 sheet: -1.25 (0.29), residues: 328 loop : -2.54 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAL 131 TYR 0.026 0.002 TYRAA 17 PHE 0.026 0.001 PHEV3 61 TRP 0.015 0.001 TRPV1 31 HIS 0.021 0.001 HISA6 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01230 / 0.42 (28302) covalent geometry : angle 2.40569 / 1.57 (38356) hydrogen bonds : bond 0.04414 / 2.96 ( 1042) hydrogen bonds : angle 4.81940 / 3.36 ( 2952) metal coordination : bond 0.01726 / 1.16 ( 36) metal coordination : angle 29.59184 / 18.40 ( 84) Misc. bond : bond 0.00031 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6834 Ramachandran restraints generated. 3417 Oldfield, 0 Emsley, 3417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 563 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V1 82 MET cc_start: 0.8967 (tpp) cc_final: 0.8748 (tpp) REVERT: V1 101 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7736 (tp30) REVERT: V1 185 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8503 (tp) REVERT: V2 28 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.7843 (m-10) REVERT: V2 82 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6382 (mt-10) REVERT: S1 52 CYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8976 (p) REVERT: S1 69 CYS cc_start: 0.8013 (p) cc_final: 0.7783 (p) REVERT: S2 127 ASN cc_start: 0.9062 (t0) cc_final: 0.8304 (t0) REVERT: S2 149 ASN cc_start: 0.9242 (t0) cc_final: 0.8844 (t0) REVERT: S2 157 HIS cc_start: 0.8139 (t-170) cc_final: 0.7893 (t70) REVERT: S2 164 MET cc_start: 0.6126 (tmm) cc_final: 0.5861 (tmm) REVERT: S2 228 MET cc_start: 0.8924 (tmm) cc_final: 0.8693 (tmm) REVERT: S2 261 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6407 (mpt-90) REVERT: S2 391 ILE cc_start: 0.9109 (mp) cc_final: 0.8899 (mm) REVERT: S3 39 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7760 (tt0) REVERT: S3 95 ASN cc_start: 0.8453 (m-40) cc_final: 0.8075 (m-40) REVERT: S7 58 GLU cc_start: 0.8297 (tp30) cc_final: 0.7989 (tm-30) REVERT: S7 105 ASP cc_start: 0.8261 (m-30) cc_final: 0.7876 (m-30) REVERT: S7 112 TYR cc_start: 0.7778 (m-80) cc_final: 0.7132 (m-80) REVERT: S7 130 TYR cc_start: 0.8297 (p90) cc_final: 0.7756 (p90) REVERT: S8 54 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8752 (mtpt) REVERT: S8 110 ASP cc_start: 0.7409 (m-30) cc_final: 0.6380 (m-30) REVERT: S8 160 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8930 (ttpp) REVERT: S8 170 GLN cc_start: 0.8795 (tp-100) cc_final: 0.8561 (tp-100) REVERT: V3 63 MET cc_start: 0.7184 (mmm) cc_final: 0.6956 (mmp) REVERT: S6 32 GLN cc_start: 0.8835 (pp30) cc_final: 0.8430 (pp30) REVERT: S6 86 TYR cc_start: 0.9061 (m-80) cc_final: 0.8840 (m-80) REVERT: S4 9 GLN cc_start: 0.6117 (pm20) cc_final: 0.5902 (pm20) REVERT: S4 70 MET cc_start: 0.7822 (mmm) cc_final: 0.7584 (mmm) REVERT: A9 62 MET cc_start: 0.7967 (tpp) cc_final: 0.7717 (tpp) REVERT: A9 92 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8777 (mt) REVERT: A9 111 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.7872 (p) REVERT: A9 176 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6086 (t0) REVERT: A9 206 TYR cc_start: 0.8505 (t80) cc_final: 0.8143 (t80) REVERT: A2 67 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7763 (ttp80) REVERT: A5 46 TYR cc_start: 0.8104 (m-80) cc_final: 0.7673 (m-80) REVERT: A5 104 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6471 (mt-10) REVERT: A6 41 GLU cc_start: 0.8960 (tp30) cc_final: 0.8570 (tp30) REVERT: A6 73 THR cc_start: 0.8758 (p) cc_final: 0.8453 (t) REVERT: A6 89 LEU cc_start: 0.8769 (tt) cc_final: 0.8564 (tp) REVERT: A7 51 ASN cc_start: 0.7831 (p0) cc_final: 0.7573 (p0) REVERT: A7 57 ASP cc_start: 0.8171 (t0) cc_final: 0.7449 (t70) REVERT: AL 27 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8085 (tt) REVERT: AL 53 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7827 (tppt) REVERT: AL 61 TRP cc_start: 0.8928 (p90) cc_final: 0.8555 (p90) REVERT: AL 135 GLN cc_start: 0.8563 (tp40) cc_final: 0.8137 (tm-30) REVERT: AA 12 LYS cc_start: 0.8365 (ttpt) cc_final: 0.8029 (tmtt) REVERT: AA 13 ASP cc_start: 0.8244 (m-30) cc_final: 0.7907 (m-30) REVERT: AA 24 LYS cc_start: 0.7793 (tptt) cc_final: 0.7513 (tttp) REVERT: AA 46 ASP cc_start: 0.8767 (m-30) cc_final: 0.8451 (m-30) REVERT: AA 52 MET cc_start: 0.8651 (ppp) cc_final: 0.7911 (tmm) outliers start: 118 outliers final: 100 residues processed: 631 average time/residue: 0.1839 time to fit residues: 188.3782 Evaluate side-chains 656 residues out of total 2983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 548 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 185 ILE Chi-restraints excluded: chain V1 residue 267 THR Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 341 THR Chi-restraints excluded: chain V1 residue 356 HIS Chi-restraints excluded: chain V1 residue 362 CYS Chi-restraints excluded: chain V1 residue 389 ILE Chi-restraints excluded: chain V2 residue 14 LYS Chi-restraints excluded: chain V2 residue 28 TYR Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 110 LEU Chi-restraints excluded: chain V2 residue 113 SER Chi-restraints excluded: chain V2 residue 132 THR Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 77 TRP Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 187 ILE Chi-restraints excluded: chain S1 residue 202 ILE Chi-restraints excluded: chain S1 residue 205 VAL Chi-restraints excluded: chain S1 residue 216 THR Chi-restraints excluded: chain S1 residue 231 MET Chi-restraints excluded: chain S1 residue 236 SER Chi-restraints excluded: chain S1 residue 242 THR Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 636 VAL Chi-restraints excluded: chain S1 residue 661 LEU Chi-restraints excluded: chain S2 residue 72 MET Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 199 VAL Chi-restraints excluded: chain S2 residue 203 LEU Chi-restraints excluded: chain S2 residue 261 ARG Chi-restraints excluded: chain S2 residue 340 THR Chi-restraints excluded: chain S2 residue 414 VAL Chi-restraints excluded: chain S3 residue 78 LEU Chi-restraints excluded: chain S3 residue 79 THR Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 103 SER Chi-restraints excluded: chain S3 residue 117 VAL Chi-restraints excluded: chain S3 residue 134 ILE Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S3 residue 147 ASP Chi-restraints excluded: chain S3 residue 200 ASN Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 48 MET Chi-restraints excluded: chain S7 residue 107 MET Chi-restraints excluded: chain S7 residue 109 GLU Chi-restraints excluded: chain S7 residue 140 VAL Chi-restraints excluded: chain S7 residue 146 VAL Chi-restraints excluded: chain S8 residue 40 TYR Chi-restraints excluded: chain S8 residue 75 GLU Chi-restraints excluded: chain S8 residue 83 CYS Chi-restraints excluded: chain S8 residue 119 CYS Chi-restraints excluded: chain S8 residue 161 TRP Chi-restraints excluded: chain V3 residue 42 GLN Chi-restraints excluded: chain V3 residue 52 LEU Chi-restraints excluded: chain V3 residue 58 LEU Chi-restraints excluded: chain V3 residue 75 HIS Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 26 VAL Chi-restraints excluded: chain S6 residue 44 ILE Chi-restraints excluded: chain S6 residue 66 LEU Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 105 VAL Chi-restraints excluded: chain S4 residue 115 SER Chi-restraints excluded: chain S4 residue 130 VAL Chi-restraints excluded: chain A9 residue 57 MET Chi-restraints excluded: chain A9 residue 58 HIS Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 90 VAL Chi-restraints excluded: chain A9 residue 92 ILE Chi-restraints excluded: chain A9 residue 111 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 179 LEU Chi-restraints excluded: chain A9 residue 218 ILE Chi-restraints excluded: chain A9 residue 290 THR Chi-restraints excluded: chain A2 residue 15 LEU Chi-restraints excluded: chain A2 residue 52 ILE Chi-restraints excluded: chain A2 residue 53 LEU Chi-restraints excluded: chain A2 residue 56 GLU Chi-restraints excluded: chain A5 residue 13 LEU Chi-restraints excluded: chain A5 residue 26 LEU Chi-restraints excluded: chain A5 residue 58 VAL Chi-restraints excluded: chain A5 residue 103 VAL Chi-restraints excluded: chain A5 residue 112 LYS Chi-restraints excluded: chain A6 residue 45 THR Chi-restraints excluded: chain A6 residue 64 GLU Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A6 residue 107 HIS Chi-restraints excluded: chain A7 residue 5 ARG Chi-restraints excluded: chain A7 residue 10 LEU Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 40 LEU Chi-restraints excluded: chain A7 residue 101 LYS Chi-restraints excluded: chain AL residue 27 LEU Chi-restraints excluded: chain AL residue 37 THR Chi-restraints excluded: chain AL residue 39 VAL Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AL residue 111 THR Chi-restraints excluded: chain AL residue 120 THR Chi-restraints excluded: chain AL residue 138 VAL Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 54 MET Chi-restraints excluded: chain AA residue 65 ILE Chi-restraints excluded: chain AM residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 319 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 315 optimal weight: 0.0570 chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S7 164 GLN V3 42 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S4 44 ASN A2 61 GLN A5 70 GLN A5 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092001 restraints weight = 59946.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.094726 restraints weight = 34040.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096605 restraints weight = 22980.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.097961 restraints weight = 17240.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098928 restraints weight = 13836.824| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.251 28339 Z= 0.451 Angle : 2.822 59.200 38440 Z= 1.601 Chirality : 0.479 6.362 4177 Planarity : 0.006 0.151 4957 Dihedral : 6.702 131.654 3867 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.95 % Favored : 89.99 % Rotamer: Outliers : 3.87 % Allowed : 22.26 % Favored : 73.87 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.43 (0.14), residues: 3417 helix: 0.90 (0.14), residues: 1357 sheet: -1.25 (0.29), residues: 328 loop : -2.53 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARGS4 129 TYR 0.056 0.002 TYRA9 236 PHE 0.026 0.001 PHEV3 61 TRP 0.014 0.001 TRPV1 31 HIS 0.019 0.001 HISA6 107 Details of bonding type rmsd/Z covalent geometry : bond 0.01286 / 0.45 (28302) covalent geometry : angle 2.46268 / 1.60 (38356) hydrogen bonds : bond 0.04398 / 2.95 ( 1042) hydrogen bonds : angle 4.82169 / 3.36 ( 2952) metal coordination : bond 0.01680 / 1.13 ( 36) metal coordination : angle 29.58798 / 18.39 ( 84) Misc. bond : bond 0.00030 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5357.75 seconds wall clock time: 93 minutes 22.93 seconds (5602.93 seconds total)