Starting phenix.real_space_refine on Tue Feb 20 10:56:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2024/6q9d_4480_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2024/6q9d_4480.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2024/6q9d_4480_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2024/6q9d_4480_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2024/6q9d_4480_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2024/6q9d_4480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2024/6q9d_4480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2024/6q9d_4480_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9d_4480/02_2024/6q9d_4480_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 Residue "V1 ARG 32": "NH1" <-> "NH2" Residue "V1 ARG 237": "NH1" <-> "NH2" Residue "V1 ARG 423": "NH1" <-> "NH2" Residue "V2 ARG 187": "NH1" <-> "NH2" Residue "V2 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S1 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 ARG 74": "NH1" <-> "NH2" Residue "S2 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 ARG 290": "NH1" <-> "NH2" Residue "S3 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S7 ARG 174": "NH1" <-> "NH2" Residue "S7 ARG 178": "NH1" <-> "NH2" Residue "S8 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V3 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S6 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S4 ARG 64": "NH1" <-> "NH2" Residue "A9 ARG 97": "NH1" <-> "NH2" Residue "A9 ARG 186": "NH1" <-> "NH2" Residue "A9 ARG 292": "NH1" <-> "NH2" Residue "A2 ARG 33": "NH1" <-> "NH2" Residue "A6 ARG 22": "NH1" <-> "NH2" Residue "AL ARG 106": "NH1" <-> "NH2" Residue "AL PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ARG 26": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 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: 14.85, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.94 Conformation dependent library (CDL) restraints added in 5.3 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... running ksdssp... Secondary structure from input PDB file: 127 helices and 25 sheets defined 34.7% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.03 Creating SS restraints... Processing helix chain 'V1' and resid 33 through 39 Processing helix chain 'V1' and resid 45 through 49 Processing helix chain 'V1' and resid 53 through 63 Processing helix chain 'V1' and resid 75 through 81 Processing helix chain 'V1' and resid 107 through 113 Processing helix chain 'V1' and resid 115 through 129 removed outlier: 3.614A pdb=" N METV1 129 " --> pdb=" O GLYV1 125 " (cutoff:3.500A) Processing helix chain 'V1' and resid 143 through 158 Processing helix chain 'V1' and resid 166 through 168 No H-bonds generated for 'chain 'V1' and resid 166 through 168' Processing helix chain 'V1' and resid 185 through 187 No H-bonds generated for 'chain 'V1' and resid 185 through 187' Processing helix chain 'V1' and resid 191 through 196 Processing helix chain 'V1' and resid 225 through 236 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 242 through 244 No H-bonds generated for 'chain 'V1' and resid 242 through 244' Processing helix chain 'V1' and resid 276 through 281 Processing helix chain 'V1' and resid 291 through 293 No H-bonds generated for 'chain 'V1' and resid 291 through 293' Processing helix chain 'V1' and resid 309 through 312 No H-bonds generated for 'chain 'V1' and resid 309 through 312' Processing helix chain 'V1' and resid 319 through 324 Processing helix chain 'V1' and resid 343 through 356 Processing helix chain 'V1' and resid 363 through 381 Processing helix chain 'V1' and resid 386 through 399 Processing helix chain 'V1' and resid 406 through 421 Proline residue: V1 414 - end of helix Processing helix chain 'V1' and resid 423 through 437 Processing helix chain 'V2' and resid 25 through 37 Processing helix chain 'V2' and resid 43 through 57 removed outlier: 3.538A pdb=" N ALAV2 46 " --> pdb=" O LYSV2 43 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VALV2 47 " --> pdb=" O ALAV2 44 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEUV2 48 " --> pdb=" O ALAV2 45 " (cutoff:3.500A) Proline residue: V2 49 - end of helix Processing helix chain 'V2' and resid 63 through 72 Processing helix chain 'V2' and resid 77 through 86 Processing helix chain 'V2' and resid 107 through 111 Processing helix chain 'V2' and resid 113 through 124 Processing helix chain 'V2' and resid 166 through 178 Processing helix chain 'S1' and resid 13 through 15 No H-bonds generated for 'chain 'S1' and resid 13 through 15' Processing helix chain 'S1' and resid 26 through 32 Processing helix chain 'S1' and resid 84 through 97 Processing helix chain 'S1' and resid 116 through 122 Processing helix chain 'S1' and resid 159 through 165 Processing helix chain 'S1' and resid 197 through 202 removed outlier: 3.503A pdb=" N ILES1 200 " --> pdb=" O GLYS1 197 " (cutoff:3.500A) Processing helix chain 'S1' and resid 265 through 268 No H-bonds generated for 'chain 'S1' and resid 265 through 268' Processing helix chain 'S1' and resid 273 through 275 No H-bonds generated for 'chain 'S1' and resid 273 through 275' Processing helix chain 'S1' and resid 296 through 308 Processing helix chain 'S1' and resid 326 through 338 Processing helix chain 'S1' and resid 359 through 361 No H-bonds generated for 'chain 'S1' and resid 359 through 361' Processing helix chain 'S1' and resid 369 through 373 removed outlier: 3.695A pdb=" N GLUS1 373 " --> pdb=" O GLYS1 370 " (cutoff:3.500A) Processing helix chain 'S1' and resid 389 through 401 Processing helix chain 'S1' and resid 426 through 434 Processing helix chain 'S1' and resid 440 through 444 Processing helix chain 'S1' and resid 463 through 479 Processing helix chain 'S1' and resid 497 through 504 Processing helix chain 'S1' and resid 512 through 516 Processing helix chain 'S1' and resid 596 through 606 Processing helix chain 'S1' and resid 616 through 624 Processing helix chain 'S1' and resid 628 through 630 No H-bonds generated for 'chain 'S1' and resid 628 through 630' Processing helix chain 'S1' and resid 642 through 648 Processing helix chain 'S1' and resid 668 through 673 Processing helix chain 'S1' and resid 676 through 680 Processing helix chain 'S1' and resid 683 through 692 Processing helix chain 'S2' and resid 87 through 92 Processing helix chain 'S2' and resid 96 through 105 Proline residue: S2 101 - end of helix Processing helix chain 'S2' and resid 113 through 125 Processing helix chain 'S2' and resid 132 through 161 Processing helix chain 'S2' and resid 165 through 184 Processing helix chain 'S2' and resid 208 through 228 Processing helix chain 'S2' and resid 233 through 238 Processing helix chain 'S2' and resid 247 through 252 Processing helix chain 'S2' and resid 257 through 262 Processing helix chain 'S2' and resid 269 through 272 No H-bonds generated for 'chain 'S2' and resid 269 through 272' Processing helix chain 'S2' and resid 277 through 279 No H-bonds generated for 'chain 'S2' and resid 277 through 279' Processing helix chain 'S2' and resid 293 through 316 Processing helix chain 'S2' and resid 335 through 339 Processing helix chain 'S2' and resid 342 through 353 Processing helix chain 'S2' and resid 394 through 405 removed outlier: 4.039A pdb=" N GLYS2 401 " --> pdb=" O ALAS2 397 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEUS2 402 " --> pdb=" O HISS2 398 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASPS2 403 " --> pdb=" O LEUS2 399 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYSS2 404 " --> pdb=" O ALAS2 400 " (cutoff:3.500A) Processing helix chain 'S2' and resid 411 through 420 Processing helix chain 'S3' and resid 17 through 32 Processing helix chain 'S3' and resid 57 through 64 Processing helix chain 'S3' and resid 120 through 122 No H-bonds generated for 'chain 'S3' and resid 120 through 122' Processing helix chain 'S3' and resid 125 through 137 removed outlier: 3.631A pdb=" N ASNS3 128 " --> pdb=" O LYSS3 125 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRPS3 129 " --> pdb=" O ALAS3 126 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYRS3 130 " --> pdb=" O ALAS3 127 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N METS3 137 " --> pdb=" O ILES3 134 " (cutoff:3.500A) Processing helix chain 'S3' and resid 207 through 209 No H-bonds generated for 'chain 'S3' and resid 207 through 209' Processing helix chain 'S7' and resid 25 through 44 removed outlier: 4.092A pdb=" N SERS7 44 " --> pdb=" O ALAS7 40 " (cutoff:3.500A) Processing helix chain 'S7' and resid 55 through 61 Processing helix chain 'S7' and resid 80 through 82 No H-bonds generated for 'chain 'S7' and resid 80 through 82' Processing helix chain 'S7' and resid 94 through 105 Proline residue: S7 98 - end of helix Processing helix chain 'S7' and resid 124 through 126 No H-bonds generated for 'chain 'S7' and resid 124 through 126' Processing helix chain 'S7' and resid 153 through 168 Processing helix chain 'S7' and resid 172 through 178 Processing helix chain 'S8' and resid 14 through 26 Processing helix chain 'S8' and resid 28 through 41 Processing helix chain 'S8' and resid 82 through 86 Processing helix chain 'S8' and resid 121 through 125 Processing helix chain 'S8' and resid 151 through 160 Processing helix chain 'S8' and resid 163 through 171 Processing helix chain 'V3' and resid 48 through 57 removed outlier: 4.596A pdb=" N PHEV3 51 " --> pdb=" O THRV3 48 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEUV3 52 " --> pdb=" O TYRV3 49 " (cutoff:3.500A) Processing helix chain 'S6' and resid 24 through 27 No H-bonds generated for 'chain 'S6' and resid 24 through 27' Processing helix chain 'S4' and resid 19 through 21 No H-bonds generated for 'chain 'S4' and resid 19 through 21' Processing helix chain 'S4' and resid 27 through 31 Processing helix chain 'S4' and resid 49 through 51 No H-bonds generated for 'chain 'S4' and resid 49 through 51' Processing helix chain 'S4' and resid 79 through 81 No H-bonds generated for 'chain 'S4' and resid 79 through 81' Processing helix chain 'S4' and resid 89 through 99 Processing helix chain 'S4' and resid 118 through 121 No H-bonds generated for 'chain 'S4' and resid 118 through 121' Processing helix chain 'A9' and resid 30 through 41 Processing helix chain 'A9' and resid 53 through 58 Processing helix chain 'A9' and resid 60 through 62 No H-bonds generated for 'chain 'A9' and resid 60 through 62' Processing helix chain 'A9' and resid 78 through 84 Processing helix chain 'A9' and resid 109 through 124 Proline residue: A9 114 - end of helix Processing helix chain 'A9' and resid 144 through 158 Processing helix chain 'A9' and resid 178 through 183 Processing helix chain 'A9' and resid 207 through 219 Processing helix chain 'A9' and resid 238 through 249 Processing helix chain 'A9' and resid 281 through 287 Processing helix chain 'A9' and resid 310 through 317 Processing helix chain 'A2' and resid 27 through 38 Processing helix chain 'A2' and resid 41 through 46 Processing helix chain 'A2' and resid 83 through 93 Processing helix chain 'A5' and resid 19 through 35 Processing helix chain 'A5' and resid 42 through 60 removed outlier: 4.507A pdb=" N ALAA5 60 " --> pdb=" O SERA5 56 " (cutoff:3.500A) Processing helix chain 'A5' and resid 65 through 70 Processing helix chain 'A5' and resid 76 through 94 removed outlier: 3.740A pdb=" N ILEA5 80 " --> pdb=" O ILEA5 76 " (cutoff:3.500A) Processing helix chain 'A6' and resid 24 through 39 Processing helix chain 'A6' and resid 42 through 48 Processing helix chain 'A6' and resid 55 through 68 Processing helix chain 'A6' and resid 75 through 93 Processing helix chain 'A6' and resid 99 through 105 Processing helix chain 'A6' and resid 117 through 122 Processing helix chain 'A7' and resid 5 through 14 Processing helix chain 'AL' and resid 9 through 17 Processing helix chain 'AL' and resid 20 through 25 removed outlier: 3.881A pdb=" N LEUAL 24 " --> pdb=" O LEUAL 20 " (cutoff:3.500A) Processing helix chain 'AL' and resid 84 through 90 Processing helix chain 'AA' and resid 8 through 21 Processing helix chain 'AA' and resid 44 through 57 Processing helix chain 'AA' and resid 64 through 68 Processing helix chain 'AA' and resid 73 through 83 Processing sheet with id= A, first strand: chain 'V1' and resid 220 through 224 removed outlier: 6.715A pdb=" N TYRV1 92 " --> pdb=" O THRV1 221 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALAV1 223 " --> pdb=" O TYRV1 92 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VALV1 94 " --> pdb=" O ALAV1 223 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALAV1 133 " --> pdb=" O LEUV1 93 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VALV1 95 " --> pdb=" O ALAV1 133 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYRV1 135 " --> pdb=" O VALV1 95 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALAV1 97 " --> pdb=" O TYRV1 135 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TYRV1 137 " --> pdb=" O ALAV1 97 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASPV1 174 " --> pdb=" O ALAV1 134 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILEV1 136 " --> pdb=" O ASPV1 174 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHEV1 176 " --> pdb=" O ILEV1 136 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILEV1 138 " --> pdb=" O PHEV1 176 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VALV1 178 " --> pdb=" O ILEV1 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'V1' and resid 253 through 258 Processing sheet with id= C, first strand: chain 'V1' and resid 294 through 298 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= D, first strand: chain 'V2' and resid 138 through 142 Processing sheet with id= E, first strand: chain 'S1' and resid 16 through 20 removed outlier: 6.559A pdb=" N TRPS1 77 " --> pdb=" O PHES1 12 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'S1' and resid 56 through 58 Processing sheet with id= G, first strand: chain 'S1' and resid 146 through 148 Processing sheet with id= H, first strand: chain 'S1' and resid 173 through 177 Processing sheet with id= I, first strand: chain 'S1' and resid 223 through 228 Processing sheet with id= J, first strand: chain 'S1' and resid 283 through 285 Processing sheet with id= K, first strand: chain 'S1' and resid 342 through 344 removed outlier: 6.480A pdb=" N METS1 521 " --> pdb=" O ALAS1 316 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILES1 318 " --> pdb=" O METS1 521 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N PHES1 523 " --> pdb=" O ILES1 318 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VALS1 559 " --> pdb=" O TYRS1 545 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLYS1 547 " --> pdb=" O VALS1 559 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEUS1 561 " --> pdb=" O GLYS1 547 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S1' and resid 490 through 493 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) 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: 6.048A pdb=" N LYSS1 405 " --> pdb=" O VALS1 377 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEUS1 379 " --> pdb=" O LYSS1 405 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALAS1 407 " --> pdb=" O LEUS1 379 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASPS1 420 " --> pdb=" O LEUS1 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S2' and resid 47 through 51 Processing sheet with id= N, first strand: chain 'S2' and resid 361 through 369 Processing sheet with id= O, first strand: chain 'S3' and resid 74 through 76 removed outlier: 6.781A pdb=" N LEUS3 48 " --> pdb=" O ARGS3 106 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LYSS3 108 " --> pdb=" O LEUS3 48 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILES3 50 " --> pdb=" O LYSS3 108 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N TYRS3 110 " --> pdb=" O ILES3 50 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILES3 52 " --> pdb=" O TYRS3 110 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'S3' and resid 172 through 177 Processing sheet with id= Q, first strand: chain 'S7' and resid 85 through 89 removed outlier: 6.229A pdb=" N TYRS7 112 " --> pdb=" O METS7 86 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VALS7 88 " --> pdb=" O TYRS7 112 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VALS7 114 " --> pdb=" O VALS7 88 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILES7 144 " --> pdb=" O SERS7 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'S8' and resid 92 through 95 Processing sheet with id= S, first strand: chain 'S6' and resid 50 through 52 Processing sheet with id= T, first strand: chain 'S6' and resid 56 through 59 Processing sheet with id= U, first strand: chain 'S4' and resid 102 through 105 Processing sheet with id= V, first strand: chain 'S4' and resid 64 through 66 Processing sheet with id= W, first strand: chain 'A9' and resid 163 through 168 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) removed outlier: 6.829A pdb=" N SERA9 133 " --> pdb=" O PROA9 168 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VALA9 91 " --> pdb=" O ILEA9 130 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILEA9 132 " --> pdb=" O VALA9 91 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASNA9 93 " --> pdb=" O ILEA9 132 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N HISA9 134 " --> pdb=" O ASNA9 93 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLNA9 44 " --> pdb=" O ALAA9 21 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VALA9 23 " --> pdb=" O GLNA9 44 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILEA9 46 " --> pdb=" O VALA9 23 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILEA9 69 " --> pdb=" O VALA9 47 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYRA9 49 " --> pdb=" O ILEA9 69 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N META9 71 " --> pdb=" O TYRA9 49 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A2' and resid 53 through 56 Processing sheet with id= Y, first strand: chain 'AL' and resid 47 through 50 829 hydrogen bonds defined for protein. 2328 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: 8.53 Time building geometry restraints manager: 10.76 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=" C13 ZMPAA 101 " pdb=" N1 ZMPAA 101 " ideal model delta sigma weight residual 1.487 1.344 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C16 ZMPAA 101 " pdb=" N2 ZMPAA 101 " ideal model delta sigma weight residual 1.474 1.339 0.135 2.00e-02 2.50e+03 4.53e+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=" O7 ZMPAA 101 " pdb=" P1 ZMPAA 101 " ideal model delta sigma weight residual 1.508 1.605 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 28297 not shown) Histogram of bond angle deviations from ideal: 70.10 - 83.68: 72 83.68 - 97.26: 8 97.26 - 110.83: 9457 110.83 - 124.41: 28029 124.41 - 137.99: 790 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 - 20.44: 16525 20.44 - 40.89: 512 40.89 - 61.33: 46 61.33 - 81.78: 15 81.78 - 102.22: 3 Dihedral angle restraints: 17101 sinusoidal: 7102 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 17098 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: 494 2.67 - 3.22: 25208 3.22 - 3.78: 42745 3.78 - 4.34: 56104 4.34 - 4.90: 91146 Nonbonded interactions: 215697 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 2.440 ... (remaining 215692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.920 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: 0.020 Extract box with map and model: 15.230 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 79.410 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.007 0.212 28302 Z= 0.462 Angle : 1.146 22.667 38356 Z= 0.628 Chirality : 1.597 21.133 4177 Planarity : 0.008 0.098 4957 Dihedral : 10.392 102.224 10667 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.054 0.004 TRPV1 413 HIS 0.019 0.002 HISA9 37 PHE 0.033 0.003 PHEV1 81 TYR 0.039 0.003 TYRS7 125 ARG 0.015 0.001 ARGS2 174 *********************** 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 fitting. rotamer outliers: 7 poor density : 1145 time to evaluate : 3.217 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: 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: 0.8238 (t0) REVERT: V1 120 GLU cc_start: 0.7769 (mm-30) cc_final: 0.6957 (mt-10) REVERT: V1 302 SER cc_start: 0.8497 (m) cc_final: 0.7952 (t) REVERT: V1 313 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7614 (tm-30) REVERT: V2 52 ASP cc_start: 0.8828 (t0) cc_final: 0.8616 (t0) REVERT: V2 168 ASP cc_start: 0.8205 (m-30) cc_final: 0.7958 (t0) REVERT: S1 71 MET cc_start: 0.8491 (tpp) cc_final: 0.8274 (tpp) REVERT: S1 187 ILE cc_start: 0.8948 (pt) cc_final: 0.8696 (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: 0.8218 (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: 0.7938 (m-30) REVERT: S2 92 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7901 (mt-10) REVERT: S2 112 MET cc_start: 0.8358 (mmm) cc_final: 0.8142 (mmt) REVERT: S2 149 ASN cc_start: 0.9303 (t0) cc_final: 0.9078 (t0) REVERT: S2 151 ILE cc_start: 0.8663 (tp) cc_final: 0.8367 (tp) REVERT: S2 199 VAL cc_start: 0.8787 (t) cc_final: 0.8546 (t) REVERT: S2 268 ASP cc_start: 0.7285 (t0) cc_final: 0.6962 (t0) REVERT: S2 285 VAL cc_start: 0.9383 (p) cc_final: 0.9073 (m) REVERT: S2 402 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7995 (tm) REVERT: S3 68 SER cc_start: 0.8275 (m) cc_final: 0.7642 (p) REVERT: S3 137 MET cc_start: 0.8667 (mmm) cc_final: 0.8444 (mmm) REVERT: S3 192 GLN cc_start: 0.8030 (tt0) cc_final: 0.7707 (tt0) REVERT: S7 48 MET cc_start: 0.7957 (ptm) cc_final: 0.7744 (ptp) REVERT: S7 71 ARG cc_start: 0.7236 (mtm110) cc_final: 0.5678 (tpm170) REVERT: S7 92 LEU cc_start: 0.9432 (tp) cc_final: 0.9204 (tt) REVERT: S7 105 ASP cc_start: 0.8318 (m-30) cc_final: 0.7893 (m-30) REVERT: S7 112 TYR cc_start: 0.8139 (m-80) cc_final: 0.7598 (m-80) REVERT: S7 125 TYR cc_start: 0.9194 (t80) cc_final: 0.8594 (t80) REVERT: S7 143 ASP cc_start: 0.8360 (m-30) cc_final: 0.7977 (m-30) REVERT: S7 164 GLN cc_start: 0.9079 (mt0) cc_final: 0.8646 (mt0) REVERT: S8 6 ASN cc_start: 0.7184 (m-40) cc_final: 0.6906 (m-40) REVERT: S8 32 ARG cc_start: 0.7692 (ttm170) cc_final: 0.6918 (mmp-170) REVERT: S8 110 ASP cc_start: 0.7615 (m-30) cc_final: 0.6801 (m-30) REVERT: S8 140 SER cc_start: 0.9057 (m) cc_final: 0.8407 (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: 0.8890 (tt) REVERT: S6 17 VAL cc_start: 0.8870 (p) cc_final: 0.8446 (p) REVERT: S4 56 LYS cc_start: 0.8955 (mttt) cc_final: 0.8733 (mttp) REVERT: S4 67 ASN cc_start: 0.8862 (t0) cc_final: 0.8552 (t0) REVERT: S4 70 MET cc_start: 0.7905 (mmm) cc_final: 0.7502 (mmm) REVERT: S4 104 ASP cc_start: 0.8488 (m-30) cc_final: 0.8279 (m-30) REVERT: A9 41 MET cc_start: 0.7800 (ttt) cc_final: 0.7545 (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: 0.8209 (m) REVERT: A9 92 ILE cc_start: 0.8902 (pt) cc_final: 0.8697 (mt) REVERT: A9 123 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6890 (tt0) REVERT: A9 206 TYR cc_start: 0.9070 (t80) cc_final: 0.8699 (t80) REVERT: A9 216 ASN cc_start: 0.9358 (m-40) cc_final: 0.8758 (m110) REVERT: A5 46 TYR cc_start: 0.7856 (m-80) cc_final: 0.7462 (m-80) REVERT: A5 50 ILE cc_start: 0.9262 (tt) cc_final: 0.8794 (tp) REVERT: A5 64 VAL cc_start: 0.8820 (t) cc_final: 0.8467 (p) REVERT: A5 91 ARG cc_start: 0.8038 (mmt90) cc_final: 0.7834 (tpp80) REVERT: A6 73 THR cc_start: 0.8968 (p) cc_final: 0.8680 (t) REVERT: A7 8 GLN cc_start: 0.9017 (tt0) cc_final: 0.8649 (tt0) REVERT: A7 51 ASN cc_start: 0.8239 (p0) cc_final: 0.7718 (p0) REVERT: A7 52 TYR cc_start: 0.8465 (m-10) cc_final: 0.6907 (m-10) REVERT: A7 57 ASP cc_start: 0.8564 (t0) cc_final: 0.7836 (t70) REVERT: A7 100 ILE cc_start: 0.8723 (mm) cc_final: 0.8448 (mm) REVERT: AL 56 PHE cc_start: 0.8542 (t80) cc_final: 0.8317 (t80) REVERT: AL 118 SER cc_start: 0.8779 (t) cc_final: 0.8491 (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: 0.8213 (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: 0.7961 (p0) REVERT: AA 68 GLU cc_start: 0.8632 (tt0) cc_final: 0.8113 (mt-10) REVERT: AM 23 ASN cc_start: 0.8749 (t0) cc_final: 0.8177 (m-40) outliers start: 7 outliers final: 2 residues processed: 1151 average time/residue: 0.4497 time to fit residues: 770.7869 Evaluate side-chains 668 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 665 time to evaluate : 3.251 ------------------------------------------------------------------------------- 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 286 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 265 optimal weight: 0.0170 chunk 102 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 307 optimal weight: 0.0370 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 150 GLN V1 373 ASN V2 37 ASN V2 99 HIS V2 101 GLN ** V2 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 135 GLN S2 157 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 S7 61 HIS ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S8 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A9 288 HIS ** A2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 49 GLN A5 72 GLN A5 82 GLN A6 125 HIS A7 20 GLN AL 72 ASN AA 35 HIS AA 47 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.262 28302 Z= 0.766 Angle : 2.394 50.828 38356 Z= 1.564 Chirality : 0.478 6.446 4177 Planarity : 0.006 0.070 4957 Dihedral : 6.973 85.428 3854 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 3.13 % Allowed : 14.29 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.13), residues: 3417 helix: -0.90 (0.13), residues: 1338 sheet: -1.66 (0.27), residues: 314 loop : -3.10 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPV1 413 HIS 0.012 0.001 HISS1 549 PHE 0.022 0.002 PHEV3 61 TYR 0.029 0.002 TYRAA 17 ARG 0.008 0.001 ARGA6 40 *********************** 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 842 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 749 time to evaluate : 3.455 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: V1 82 MET cc_start: 0.8484 (tpp) cc_final: 0.8082 (tpp) REVERT: V1 120 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7358 (mt-10) REVERT: V1 302 SER cc_start: 0.8699 (m) cc_final: 0.8032 (t) REVERT: V2 168 ASP cc_start: 0.8390 (m-30) cc_final: 0.8095 (t0) REVERT: S1 150 MET cc_start: 0.8753 (mmt) cc_final: 0.8539 (mmt) REVERT: S1 254 MET cc_start: 0.6913 (tmm) cc_final: 0.6610 (tmm) REVERT: S1 328 LEU cc_start: 0.9031 (mt) cc_final: 0.8820 (mt) REVERT: S1 356 THR cc_start: 0.8564 (p) cc_final: 0.8200 (t) REVERT: S2 82 LEU cc_start: 0.8393 (mp) cc_final: 0.8059 (tp) REVERT: S2 127 ASN cc_start: 0.9056 (t0) cc_final: 0.8222 (t0) REVERT: S2 149 ASN cc_start: 0.9283 (t0) cc_final: 0.8979 (t0) REVERT: S2 151 ILE cc_start: 0.8640 (tp) cc_final: 0.8391 (tp) REVERT: S2 227 GLU cc_start: 0.7594 (tp30) cc_final: 0.7393 (tp30) REVERT: S3 47 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7703 (mt-10) REVERT: S3 62 THR cc_start: 0.9342 (m) cc_final: 0.9113 (t) REVERT: S3 105 ILE cc_start: 0.8991 (pt) cc_final: 0.8756 (mt) REVERT: S3 131 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7977 (mt-10) REVERT: S3 133 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8348 (tm-30) REVERT: S3 153 THR cc_start: 0.9067 (p) cc_final: 0.8842 (p) REVERT: S3 192 GLN cc_start: 0.7815 (tt0) cc_final: 0.7543 (tt0) REVERT: S7 58 GLU cc_start: 0.7706 (tp30) cc_final: 0.7112 (tp30) REVERT: S7 62 MET cc_start: 0.7785 (ttp) cc_final: 0.7178 (ttt) REVERT: S7 71 ARG cc_start: 0.7494 (mtm110) cc_final: 0.5344 (mmp-170) REVERT: S7 92 LEU cc_start: 0.9382 (tp) cc_final: 0.8907 (mt) REVERT: S7 105 ASP cc_start: 0.8242 (m-30) cc_final: 0.7854 (m-30) REVERT: S7 112 TYR cc_start: 0.8256 (m-80) cc_final: 0.7690 (m-80) REVERT: S7 125 TYR cc_start: 0.9241 (t80) cc_final: 0.8826 (t80) REVERT: S7 137 ASP cc_start: 0.8157 (t0) cc_final: 0.7954 (t0) REVERT: S7 152 THR cc_start: 0.8266 (m) cc_final: 0.7675 (p) REVERT: S7 164 GLN cc_start: 0.8969 (mt0) cc_final: 0.8489 (mt0) REVERT: S8 32 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7133 (mmp-170) REVERT: S8 110 ASP cc_start: 0.7544 (m-30) cc_final: 0.6717 (m-30) REVERT: S8 143 THR cc_start: 0.8604 (m) cc_final: 0.8320 (p) REVERT: S8 149 TYR cc_start: 0.9104 (m-10) cc_final: 0.8892 (m-80) REVERT: S8 153 LYS cc_start: 0.9013 (tptp) cc_final: 0.8691 (tptt) REVERT: V3 63 MET cc_start: 0.6830 (mmm) cc_final: 0.6549 (mmm) REVERT: S6 32 GLN cc_start: 0.8725 (pp30) cc_final: 0.8288 (pp30) REVERT: S4 56 LYS cc_start: 0.8896 (mttt) cc_final: 0.8666 (mttp) REVERT: S4 67 ASN cc_start: 0.9094 (t0) cc_final: 0.8577 (t0) REVERT: S4 70 MET cc_start: 0.8002 (mmm) cc_final: 0.7232 (mmm) REVERT: A9 52 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: A9 64 ASP cc_start: 0.7528 (t70) cc_final: 0.7049 (t70) REVERT: A9 67 GLN cc_start: 0.8414 (mm110) cc_final: 0.7987 (tp40) REVERT: A9 92 ILE cc_start: 0.8688 (pt) cc_final: 0.8472 (mt) REVERT: A9 244 TYR cc_start: 0.8929 (t80) cc_final: 0.8715 (t80) REVERT: A5 43 TYR cc_start: 0.8549 (t80) cc_final: 0.7957 (t80) REVERT: A5 51 THR cc_start: 0.8795 (m) cc_final: 0.8559 (p) REVERT: A5 65 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8435 (tttp) REVERT: A5 94 ILE cc_start: 0.9155 (tp) cc_final: 0.8660 (mt) REVERT: A6 20 PHE cc_start: 0.8651 (m-10) cc_final: 0.8423 (m-10) REVERT: A6 73 THR cc_start: 0.8895 (p) cc_final: 0.8604 (t) REVERT: A6 113 ARG cc_start: 0.7616 (mtm180) cc_final: 0.7386 (mtp-110) REVERT: A7 51 ASN cc_start: 0.8142 (p0) cc_final: 0.7574 (p0) REVERT: A7 57 ASP cc_start: 0.8580 (t0) cc_final: 0.7685 (t70) REVERT: A7 111 TYR cc_start: 0.7890 (m-80) cc_final: 0.7658 (m-80) REVERT: AL 48 TYR cc_start: 0.8781 (m-80) cc_final: 0.8555 (m-80) REVERT: AL 53 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8453 (mmmt) REVERT: AL 58 ARG cc_start: 0.8326 (mtt180) cc_final: 0.8124 (mtt180) REVERT: AL 88 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7418 (ttm-80) REVERT: AA 12 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8188 (tmtt) REVERT: AA 13 ASP cc_start: 0.8632 (m-30) cc_final: 0.8228 (m-30) REVERT: AA 21 LEU cc_start: 0.9255 (tp) cc_final: 0.9017 (mt) REVERT: AA 52 MET cc_start: 0.8699 (ppp) cc_final: 0.8326 (ppp) REVERT: AA 66 ASP cc_start: 0.8294 (m-30) cc_final: 0.7774 (m-30) REVERT: AA 68 GLU cc_start: 0.8600 (tt0) cc_final: 0.8153 (mt-10) REVERT: AA 83 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6915 (ttpp) REVERT: AM 23 ASN cc_start: 0.8525 (t0) cc_final: 0.8298 (m-40) outliers start: 93 outliers final: 45 residues processed: 808 average time/residue: 0.4021 time to fit residues: 503.7057 Evaluate side-chains 671 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 624 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 220 THR 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 48 LEU 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 236 SER Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S2 residue 284 ASP 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 165 ASP Chi-restraints excluded: chain S3 residue 196 LYS Chi-restraints excluded: chain S7 residue 35 ASP 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 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 105 VAL Chi-restraints excluded: chain A9 residue 52 GLU Chi-restraints excluded: chain A9 residue 115 GLN Chi-restraints excluded: chain A9 residue 176 ASP 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 45 THR 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 AA residue 43 ASP Chi-restraints excluded: chain AA residue 54 MET Chi-restraints excluded: chain AA residue 83 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 171 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 chunk 333 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 247 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 113 HIS ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 179 ASN ** S1 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 421 HIS ** S1 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S1 472 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 46 ASN S2 55 HIS S2 114 ASN S2 135 GLN ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V3 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V3 44 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S4 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A6 25 ASN A7 50 ASN ** AL 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.240 28302 Z= 0.779 Angle : 2.395 50.688 38356 Z= 1.565 Chirality : 0.479 6.368 4177 Planarity : 0.006 0.082 4957 Dihedral : 6.595 87.612 3851 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 4.37 % Allowed : 16.78 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.13), residues: 3417 helix: -0.17 (0.14), residues: 1325 sheet: -1.62 (0.27), residues: 327 loop : -2.86 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPS8 161 HIS 0.010 0.001 HISS1 549 PHE 0.025 0.002 PHEV3 61 TYR 0.029 0.002 TYRS7 28 ARG 0.009 0.001 ARGA9 40 *********************** 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 773 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 643 time to evaluate : 3.561 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: V1 101 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8049 (mm-30) REVERT: V1 120 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7454 (mt-10) REVERT: V1 272 MET cc_start: 0.8426 (tpp) cc_final: 0.7622 (tpp) REVERT: V1 302 SER cc_start: 0.8916 (m) cc_final: 0.8163 (p) REVERT: V1 317 MET cc_start: 0.8202 (mmm) cc_final: 0.7986 (mmm) REVERT: V1 363 THR cc_start: 0.9386 (p) cc_final: 0.9151 (t) REVERT: S1 69 CYS cc_start: 0.8201 (p) cc_final: 0.7992 (p) REVERT: S1 226 GLU cc_start: 0.7790 (tp30) cc_final: 0.7545 (tp30) REVERT: S1 356 THR cc_start: 0.8673 (p) cc_final: 0.8326 (t) REVERT: S1 490 MET cc_start: 0.8653 (tmm) cc_final: 0.8122 (tmm) REVERT: S2 67 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7707 (tm-30) REVERT: S2 149 ASN cc_start: 0.9316 (t0) cc_final: 0.8935 (t0) REVERT: S2 151 ILE cc_start: 0.8791 (tp) cc_final: 0.8473 (tp) REVERT: S3 51 CYS cc_start: 0.8240 (m) cc_final: 0.7780 (m) REVERT: S3 105 ILE cc_start: 0.9083 (pt) cc_final: 0.8803 (mt) REVERT: S3 131 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8178 (mt-10) REVERT: S3 153 THR cc_start: 0.8964 (p) cc_final: 0.8699 (p) REVERT: S3 162 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8726 (m-10) REVERT: S7 58 GLU cc_start: 0.7891 (tp30) cc_final: 0.7271 (tp30) REVERT: S7 62 MET cc_start: 0.7777 (ttp) cc_final: 0.7448 (ttt) REVERT: S7 71 ARG cc_start: 0.7920 (mtm110) cc_final: 0.5483 (mmp-170) REVERT: S7 105 ASP cc_start: 0.8266 (m-30) cc_final: 0.7853 (m-30) REVERT: S7 112 TYR cc_start: 0.8382 (m-80) cc_final: 0.8126 (m-80) REVERT: S7 125 TYR cc_start: 0.9252 (t80) cc_final: 0.8850 (t80) REVERT: S7 130 TYR cc_start: 0.8225 (p90) cc_final: 0.7591 (p90) REVERT: S7 152 THR cc_start: 0.8521 (m) cc_final: 0.7921 (p) REVERT: S7 164 GLN cc_start: 0.9082 (mt0) cc_final: 0.8625 (mt0) REVERT: S8 32 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7176 (mmp-170) REVERT: S8 110 ASP cc_start: 0.7739 (m-30) cc_final: 0.6764 (m-30) REVERT: V3 63 MET cc_start: 0.6958 (mmm) cc_final: 0.6632 (mmm) REVERT: S6 32 GLN cc_start: 0.8851 (pp30) cc_final: 0.8371 (pp30) REVERT: S6 38 ASN cc_start: 0.8346 (t0) cc_final: 0.7935 (t0) REVERT: S4 44 ASN cc_start: 0.8016 (t0) cc_final: 0.7802 (t0) REVERT: S4 56 LYS cc_start: 0.8990 (mttt) cc_final: 0.8723 (mttp) REVERT: S4 67 ASN cc_start: 0.9178 (t0) cc_final: 0.8924 (t0) REVERT: S4 70 MET cc_start: 0.8048 (mmm) cc_final: 0.7545 (mmm) REVERT: A9 52 GLU cc_start: 0.7872 (tp30) cc_final: 0.7612 (tp30) REVERT: A9 64 ASP cc_start: 0.7695 (t70) cc_final: 0.6754 (m-30) REVERT: A9 92 ILE cc_start: 0.8813 (pt) cc_final: 0.8594 (mt) REVERT: A9 177 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7879 (tpp80) REVERT: A5 34 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A5 40 ASN cc_start: 0.8897 (p0) cc_final: 0.8467 (t0) REVERT: A5 94 ILE cc_start: 0.9108 (tp) cc_final: 0.8610 (mt) REVERT: A5 104 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7432 (mt-10) REVERT: A6 39 TYR cc_start: 0.8944 (t80) cc_final: 0.8415 (t80) REVERT: A6 41 GLU cc_start: 0.8894 (tp30) cc_final: 0.8573 (tp30) REVERT: A6 73 THR cc_start: 0.8935 (p) cc_final: 0.8663 (t) REVERT: A7 51 ASN cc_start: 0.8125 (p0) cc_final: 0.7710 (p0) REVERT: AL 34 ARG cc_start: 0.7413 (mtm110) cc_final: 0.6722 (ttp-110) REVERT: AL 61 TRP cc_start: 0.8816 (p90) cc_final: 0.8517 (p90) REVERT: AL 134 ILE cc_start: 0.8974 (pt) cc_final: 0.8709 (mp) REVERT: AL 135 GLN cc_start: 0.8660 (tp40) cc_final: 0.8008 (tm-30) REVERT: AA 9 GLU cc_start: 0.8742 (mp0) cc_final: 0.8351 (mp0) REVERT: AA 12 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8000 (tmtt) REVERT: AA 13 ASP cc_start: 0.8639 (m-30) cc_final: 0.8172 (m-30) REVERT: AA 21 LEU cc_start: 0.9221 (tp) cc_final: 0.8977 (mt) REVERT: AA 49 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7374 (pt0) REVERT: AA 52 MET cc_start: 0.8724 (ppp) cc_final: 0.8140 (ppp) REVERT: AA 66 ASP cc_start: 0.8151 (m-30) cc_final: 0.7703 (m-30) REVERT: AA 68 GLU cc_start: 0.8618 (tt0) cc_final: 0.8248 (mt-10) outliers start: 130 outliers final: 97 residues processed: 726 average time/residue: 0.3903 time to fit residues: 444.9305 Evaluate side-chains 679 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 580 time to evaluate : 3.079 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain V1 residue 266 CYS 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 8 VAL Chi-restraints excluded: chain V2 residue 48 LEU Chi-restraints excluded: chain V2 residue 113 SER Chi-restraints excluded: chain S1 residue 30 CYS Chi-restraints excluded: chain S1 residue 33 VAL Chi-restraints excluded: chain S1 residue 51 ASN Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 107 ILE Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 180 ASP 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 295 THR Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 378 LEU Chi-restraints excluded: chain S1 residue 414 ASP Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S2 residue 73 VAL Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 199 VAL Chi-restraints excluded: chain S2 residue 284 ASP Chi-restraints excluded: chain S2 residue 323 ILE Chi-restraints excluded: chain S2 residue 354 GLU Chi-restraints excluded: chain S2 residue 403 ASP 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 79 THR Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 109 THR Chi-restraints excluded: chain S3 residue 162 PHE Chi-restraints excluded: chain S3 residue 165 ASP Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 87 ILE 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 S8 residue 40 TYR Chi-restraints excluded: chain S8 residue 47 THR 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 159 ASP Chi-restraints excluded: chain S8 residue 162 GLU Chi-restraints excluded: chain V3 residue 44 HIS 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 44 ILE Chi-restraints excluded: chain S6 residue 78 GLU 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 77 ASP Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 111 VAL Chi-restraints excluded: chain A9 residue 126 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 53 LEU 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 34 LEU Chi-restraints excluded: chain A5 residue 58 VAL Chi-restraints excluded: chain A5 residue 64 VAL Chi-restraints excluded: chain A5 residue 112 LYS Chi-restraints excluded: chain A6 residue 45 THR Chi-restraints excluded: chain A6 residue 47 HIS 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 A6 residue 119 SER Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 40 LEU Chi-restraints excluded: chain AL residue 24 LEU 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 AA residue 32 VAL Chi-restraints excluded: chain AA residue 43 ASP Chi-restraints excluded: chain AA residue 77 VAL 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 304 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 309 optimal weight: 6.9990 chunk 327 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 293 optimal weight: 0.7980 chunk 88 optimal weight: 0.0870 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 37 ASN ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 159 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** ** 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 46 GLN S4 50 ASN ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 24 GLN A5 82 GLN A6 25 ASN AL 116 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 28302 Z= 0.754 Angle : 2.377 50.594 38356 Z= 1.556 Chirality : 0.479 6.332 4177 Planarity : 0.005 0.067 4957 Dihedral : 6.230 88.750 3851 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 3.80 % Allowed : 19.07 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.14), residues: 3417 helix: 0.26 (0.14), residues: 1320 sheet: -1.42 (0.27), residues: 327 loop : -2.75 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPS8 161 HIS 0.015 0.001 HISV3 44 PHE 0.022 0.001 PHEV3 61 TYR 0.028 0.002 TYRAA 17 ARG 0.006 0.000 ARGS8 32 *********************** 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 741 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 628 time to evaluate : 3.421 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: V1 120 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7504 (mt-10) REVERT: V1 213 VAL cc_start: 0.9497 (t) cc_final: 0.9160 (m) REVERT: V1 272 MET cc_start: 0.8318 (tpp) cc_final: 0.7592 (tpp) REVERT: V1 363 THR cc_start: 0.9319 (p) cc_final: 0.9114 (t) REVERT: V2 104 THR cc_start: 0.6623 (OUTLIER) cc_final: 0.3778 (m) REVERT: V2 163 ASP cc_start: 0.7675 (m-30) cc_final: 0.7424 (m-30) REVERT: S1 69 CYS cc_start: 0.8081 (p) cc_final: 0.7836 (p) REVERT: S1 490 MET cc_start: 0.8616 (tmm) cc_final: 0.8059 (tmm) REVERT: S2 82 LEU cc_start: 0.8463 (mp) cc_final: 0.8138 (tp) REVERT: S2 109 VAL cc_start: 0.9337 (t) cc_final: 0.9135 (m) REVERT: S2 149 ASN cc_start: 0.9350 (t0) cc_final: 0.8930 (t0) REVERT: S2 151 ILE cc_start: 0.8712 (tp) cc_final: 0.8480 (tp) REVERT: S2 342 MET cc_start: 0.8946 (tpp) cc_final: 0.8600 (tpp) REVERT: S3 51 CYS cc_start: 0.8418 (m) cc_final: 0.7924 (m) REVERT: S3 105 ILE cc_start: 0.9010 (pt) cc_final: 0.8787 (mt) REVERT: S3 131 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8313 (mt-10) REVERT: S3 147 ASP cc_start: 0.7761 (m-30) cc_final: 0.7556 (m-30) REVERT: S3 153 THR cc_start: 0.8916 (p) cc_final: 0.8701 (p) REVERT: S3 200 ASN cc_start: 0.8352 (p0) cc_final: 0.8146 (p0) REVERT: S7 62 MET cc_start: 0.7898 (ttp) cc_final: 0.7449 (ttt) REVERT: S7 71 ARG cc_start: 0.7888 (mtm110) cc_final: 0.5383 (mmp-170) REVERT: S7 92 LEU cc_start: 0.9320 (tp) cc_final: 0.9056 (mt) REVERT: S7 105 ASP cc_start: 0.8250 (m-30) cc_final: 0.7825 (m-30) REVERT: S7 112 TYR cc_start: 0.8304 (m-80) cc_final: 0.7936 (m-80) REVERT: S7 125 TYR cc_start: 0.9126 (t80) cc_final: 0.8739 (t80) REVERT: S7 130 TYR cc_start: 0.8055 (p90) cc_final: 0.7601 (p90) REVERT: S7 152 THR cc_start: 0.8534 (m) cc_final: 0.7975 (p) REVERT: S7 156 LEU cc_start: 0.8825 (tp) cc_final: 0.8508 (tp) REVERT: S8 110 ASP cc_start: 0.7839 (m-30) cc_final: 0.7257 (m-30) REVERT: V3 55 ASN cc_start: 0.9283 (t0) cc_final: 0.9041 (t0) REVERT: V3 56 LEU cc_start: 0.9070 (tp) cc_final: 0.8828 (tp) REVERT: S6 32 GLN cc_start: 0.8894 (pp30) cc_final: 0.8346 (pp30) REVERT: S6 38 ASN cc_start: 0.8213 (t0) cc_final: 0.7945 (t0) REVERT: S4 44 ASN cc_start: 0.7830 (t0) cc_final: 0.7565 (t0) REVERT: S4 56 LYS cc_start: 0.8927 (mttt) cc_final: 0.8665 (mttp) REVERT: S4 67 ASN cc_start: 0.9230 (t0) cc_final: 0.9010 (t0) REVERT: S4 70 MET cc_start: 0.7953 (mmm) cc_final: 0.6911 (mmt) REVERT: A9 57 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8753 (ttm) REVERT: A9 64 ASP cc_start: 0.7518 (t70) cc_final: 0.6826 (m-30) REVERT: A5 40 ASN cc_start: 0.8889 (p0) cc_final: 0.8471 (t0) REVERT: A5 51 THR cc_start: 0.9012 (m) cc_final: 0.8798 (p) REVERT: A5 94 ILE cc_start: 0.9121 (tp) cc_final: 0.8594 (mt) REVERT: A5 104 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6957 (mt-10) REVERT: A6 39 TYR cc_start: 0.8857 (t80) cc_final: 0.8345 (t80) REVERT: A6 41 GLU cc_start: 0.8847 (tp30) cc_final: 0.8458 (tp30) REVERT: A6 73 THR cc_start: 0.8917 (p) cc_final: 0.8609 (t) REVERT: A7 51 ASN cc_start: 0.8111 (p0) cc_final: 0.7681 (p0) REVERT: A7 57 ASP cc_start: 0.8361 (t0) cc_final: 0.7527 (t70) REVERT: AL 134 ILE cc_start: 0.8938 (pt) cc_final: 0.8712 (mp) REVERT: AL 135 GLN cc_start: 0.8650 (tp40) cc_final: 0.8001 (tm-30) REVERT: AA 9 GLU cc_start: 0.8906 (mp0) cc_final: 0.8701 (mp0) REVERT: AA 12 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8041 (tmtt) REVERT: AA 13 ASP cc_start: 0.8644 (m-30) cc_final: 0.8207 (m-30) REVERT: AA 21 LEU cc_start: 0.9236 (tp) cc_final: 0.8994 (mt) REVERT: AA 47 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8387 (tp40) REVERT: AA 52 MET cc_start: 0.8765 (ppp) cc_final: 0.8117 (ppp) REVERT: AA 66 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: AA 79 TYR cc_start: 0.8544 (t80) cc_final: 0.8332 (t80) outliers start: 113 outliers final: 84 residues processed: 699 average time/residue: 0.3943 time to fit residues: 433.2224 Evaluate side-chains 680 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 592 time to evaluate : 3.206 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain V1 residue 266 CYS 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 389 ILE Chi-restraints excluded: chain V2 residue 48 LEU Chi-restraints excluded: chain V2 residue 104 THR 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 191 PHE Chi-restraints excluded: chain S1 residue 30 CYS Chi-restraints excluded: chain S1 residue 33 VAL Chi-restraints excluded: chain S1 residue 51 ASN Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 113 GLU Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 180 ASP Chi-restraints excluded: chain S1 residue 187 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 378 LEU Chi-restraints excluded: chain S1 residue 414 ASP 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 284 ASP Chi-restraints excluded: chain S2 residue 403 ASP 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 79 THR Chi-restraints excluded: chain S3 residue 99 LEU Chi-restraints excluded: chain S3 residue 109 THR Chi-restraints excluded: chain S7 residue 35 ASP 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 S8 residue 18 THR 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 S8 residue 162 GLU Chi-restraints excluded: chain V3 residue 36 THR Chi-restraints excluded: chain V3 residue 44 HIS Chi-restraints excluded: chain V3 residue 54 LEU 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 78 GLU 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 57 MET Chi-restraints excluded: chain A9 residue 77 ASP Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 111 VAL Chi-restraints excluded: chain A9 residue 176 ASP 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 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 A5 residue 112 LYS 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 101 LYS Chi-restraints excluded: chain AL residue 24 LEU 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 AL residue 111 THR Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 43 ASP Chi-restraints excluded: chain AA residue 47 GLN Chi-restraints excluded: chain AA residue 66 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 272 optimal weight: 0.1980 chunk 186 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 243 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V1 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 155 GLN ** 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 472 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 116 GLN S2 190 HIS ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 61 HIS ** S7 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V3 44 HIS ** 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 82 GLN AL 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.239 28302 Z= 0.795 Angle : 2.399 50.780 38356 Z= 1.566 Chirality : 0.479 6.343 4177 Planarity : 0.005 0.077 4957 Dihedral : 6.303 88.909 3851 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 4.88 % Allowed : 19.47 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3417 helix: 0.38 (0.14), residues: 1321 sheet: -1.56 (0.27), residues: 346 loop : -2.75 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPV1 31 HIS 0.007 0.001 HISS1 549 PHE 0.026 0.002 PHES4 122 TYR 0.036 0.002 TYRAL 48 ARG 0.009 0.001 ARGA2 67 *********************** 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 734 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 589 time to evaluate : 3.125 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: symmetry clash REVERT: V1 82 MET cc_start: 0.8867 (mmm) cc_final: 0.8664 (tmm) REVERT: V1 213 VAL cc_start: 0.9564 (t) cc_final: 0.9264 (m) REVERT: V1 302 SER cc_start: 0.8920 (m) cc_final: 0.8124 (p) REVERT: V2 10 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7300 (mtm-85) REVERT: S1 490 MET cc_start: 0.8597 (tmm) cc_final: 0.8062 (tmm) REVERT: S1 627 SER cc_start: 0.8974 (t) cc_final: 0.8765 (m) REVERT: S2 82 LEU cc_start: 0.8453 (mp) cc_final: 0.8101 (tp) REVERT: S2 103 PHE cc_start: 0.8652 (m-80) cc_final: 0.8107 (m-10) REVERT: S2 149 ASN cc_start: 0.9402 (t0) cc_final: 0.9077 (t0) REVERT: S3 105 ILE cc_start: 0.9164 (pt) cc_final: 0.8830 (mt) REVERT: S3 131 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8226 (mt-10) REVERT: S3 153 THR cc_start: 0.8961 (p) cc_final: 0.8711 (p) REVERT: S3 200 ASN cc_start: 0.8279 (p0) cc_final: 0.8074 (p0) REVERT: S7 62 MET cc_start: 0.7815 (ttp) cc_final: 0.7529 (ttt) REVERT: S7 92 LEU cc_start: 0.9334 (tp) cc_final: 0.8982 (mt) REVERT: S7 105 ASP cc_start: 0.8331 (m-30) cc_final: 0.7952 (m-30) REVERT: S7 112 TYR cc_start: 0.8462 (m-80) cc_final: 0.8065 (m-80) REVERT: S7 125 TYR cc_start: 0.9219 (t80) cc_final: 0.8902 (t80) REVERT: S7 130 TYR cc_start: 0.8311 (p90) cc_final: 0.7899 (p90) REVERT: S7 152 THR cc_start: 0.8647 (m) cc_final: 0.8394 (p) REVERT: S8 110 ASP cc_start: 0.7920 (m-30) cc_final: 0.7317 (m-30) REVERT: S8 161 TRP cc_start: 0.9119 (OUTLIER) cc_final: 0.8612 (p90) REVERT: V3 55 ASN cc_start: 0.9270 (t0) cc_final: 0.9037 (t0) REVERT: V3 63 MET cc_start: 0.7407 (mmm) cc_final: 0.7064 (mmm) REVERT: S6 32 GLN cc_start: 0.8893 (pp30) cc_final: 0.8495 (pp30) REVERT: S6 38 ASN cc_start: 0.8355 (t0) cc_final: 0.7996 (t0) REVERT: S4 44 ASN cc_start: 0.7954 (t0) cc_final: 0.7752 (t0) REVERT: S4 56 LYS cc_start: 0.8994 (mttt) cc_final: 0.8727 (mttp) REVERT: S4 70 MET cc_start: 0.8131 (mmm) cc_final: 0.7017 (mmt) REVERT: A9 29 PHE cc_start: 0.8777 (t80) cc_final: 0.8522 (t80) REVERT: A9 57 MET cc_start: 0.8935 (ttm) cc_final: 0.8732 (ttm) REVERT: A9 64 ASP cc_start: 0.7667 (t70) cc_final: 0.6721 (m-30) REVERT: A5 40 ASN cc_start: 0.8914 (p0) cc_final: 0.8404 (t0) REVERT: A5 65 LYS cc_start: 0.8808 (ttmm) cc_final: 0.8440 (tttp) REVERT: A5 104 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7157 (mt-10) REVERT: A6 39 TYR cc_start: 0.8964 (t80) cc_final: 0.8073 (t80) REVERT: A6 41 GLU cc_start: 0.8931 (tp30) cc_final: 0.8427 (tp30) REVERT: A6 73 THR cc_start: 0.8957 (p) cc_final: 0.8670 (t) REVERT: A7 51 ASN cc_start: 0.8239 (p0) cc_final: 0.7856 (p0) REVERT: AL 27 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8196 (tt) REVERT: AL 61 TRP cc_start: 0.8930 (p90) cc_final: 0.8585 (p90) REVERT: AL 134 ILE cc_start: 0.8915 (pt) cc_final: 0.8633 (mp) REVERT: AL 135 GLN cc_start: 0.8655 (tp40) cc_final: 0.8235 (tm-30) REVERT: AA 12 LYS cc_start: 0.8346 (ttpt) cc_final: 0.8009 (tmtt) REVERT: AA 13 ASP cc_start: 0.8614 (m-30) cc_final: 0.8166 (m-30) REVERT: AA 21 LEU cc_start: 0.9256 (tp) cc_final: 0.9000 (mt) REVERT: AA 52 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.7661 (ppp) outliers start: 145 outliers final: 107 residues processed: 683 average time/residue: 0.3955 time to fit residues: 427.8512 Evaluate side-chains 656 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 545 time to evaluate : 3.401 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain V1 residue 266 CYS Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 298 ILE 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 10 ARG Chi-restraints excluded: chain V2 residue 48 LEU Chi-restraints excluded: chain V2 residue 132 THR Chi-restraints excluded: chain S1 residue 30 CYS Chi-restraints excluded: chain S1 residue 33 VAL Chi-restraints excluded: chain S1 residue 51 ASN 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 180 ASP 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 253 ARG Chi-restraints excluded: chain S1 residue 295 THR Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 378 LEU Chi-restraints excluded: chain S1 residue 414 ASP Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 536 ASP Chi-restraints excluded: chain S1 residue 661 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 284 ASP Chi-restraints excluded: chain S2 residue 403 ASP 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 79 THR Chi-restraints excluded: chain S3 residue 102 ASN Chi-restraints excluded: chain S3 residue 109 THR Chi-restraints excluded: chain S3 residue 117 VAL 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 85 VAL Chi-restraints excluded: chain S7 residue 87 ILE Chi-restraints excluded: chain S7 residue 93 THR 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 S8 residue 18 THR 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 131 ILE Chi-restraints excluded: chain S8 residue 161 TRP Chi-restraints excluded: chain S8 residue 162 GLU Chi-restraints excluded: chain V3 residue 36 THR Chi-restraints excluded: chain V3 residue 44 HIS 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 44 ILE 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 68 ILE Chi-restraints excluded: chain A9 residue 77 ASP Chi-restraints excluded: chain A9 residue 88 SER 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 180 ASN Chi-restraints excluded: chain A9 residue 279 THR Chi-restraints excluded: chain A2 residue 15 LEU Chi-restraints excluded: chain A2 residue 17 GLU 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 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 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 119 SER 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 65 THR Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AL residue 92 CYS 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 43 ASP Chi-restraints excluded: chain AA residue 52 MET Chi-restraints excluded: chain AA residue 77 VAL Chi-restraints excluded: chain AM residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 110 optimal weight: 0.6980 chunk 295 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 192 optimal weight: 0.1980 chunk 80 optimal weight: 0.1980 chunk 327 optimal weight: 0.9990 chunk 272 optimal weight: 0.0770 chunk 151 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 172 optimal weight: 0.9980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V1 361 GLN ** V2 101 GLN ** 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 444 GLN S1 491 ASN ** S1 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 149 ASN ** 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 ** S7 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 127 HIS V3 42 GLN ** V3 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S6 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 47 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 28302 Z= 0.754 Angle : 2.373 50.603 38356 Z= 1.554 Chirality : 0.478 6.327 4177 Planarity : 0.005 0.071 4957 Dihedral : 5.985 86.384 3851 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.60 % Allowed : 21.79 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3417 helix: 0.60 (0.14), residues: 1329 sheet: -1.34 (0.28), residues: 341 loop : -2.63 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPS8 161 HIS 0.024 0.001 HISS7 61 PHE 0.022 0.001 PHEV3 61 TYR 0.029 0.002 TYRS7 28 ARG 0.007 0.000 ARGAL 131 *********************** 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 705 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 598 time to evaluate : 3.460 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: V1 185 ILE cc_start: 0.8959 (pt) cc_final: 0.8542 (tp) REVERT: V1 213 VAL cc_start: 0.9462 (t) cc_final: 0.9164 (m) REVERT: V1 302 SER cc_start: 0.8579 (m) cc_final: 0.8019 (t) REVERT: V1 317 MET cc_start: 0.8260 (tpt) cc_final: 0.8032 (tpp) REVERT: V1 363 THR cc_start: 0.9291 (p) cc_final: 0.9073 (t) REVERT: V2 104 THR cc_start: 0.7038 (OUTLIER) cc_final: 0.5253 (m) REVERT: S1 357 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7678 (p0) REVERT: S1 378 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8718 (pp) REVERT: S1 490 MET cc_start: 0.8516 (tmm) cc_final: 0.7987 (tmm) REVERT: S2 149 ASN cc_start: 0.9378 (t0) cc_final: 0.8999 (t0) REVERT: S2 371 LYS cc_start: 0.9101 (mmtp) cc_final: 0.8389 (mmtm) REVERT: S2 422 ASP cc_start: 0.7974 (p0) cc_final: 0.6770 (p0) REVERT: S3 95 ASN cc_start: 0.8689 (m-40) cc_final: 0.8273 (m-40) REVERT: S3 131 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8205 (mt-10) REVERT: S7 62 MET cc_start: 0.7740 (ttp) cc_final: 0.7497 (ttt) REVERT: S7 69 MET cc_start: 0.8383 (mmm) cc_final: 0.7780 (mmm) REVERT: S7 71 ARG cc_start: 0.8011 (mtm110) cc_final: 0.5335 (mmp-170) REVERT: S7 92 LEU cc_start: 0.9249 (tp) cc_final: 0.8865 (mt) REVERT: S7 105 ASP cc_start: 0.8291 (m-30) cc_final: 0.7884 (m-30) REVERT: S7 112 TYR cc_start: 0.8164 (m-80) cc_final: 0.7736 (m-80) REVERT: S7 125 TYR cc_start: 0.9003 (t80) cc_final: 0.8665 (t80) REVERT: S7 130 TYR cc_start: 0.8088 (p90) cc_final: 0.7659 (p90) REVERT: S7 152 THR cc_start: 0.8591 (m) cc_final: 0.8333 (p) REVERT: S8 110 ASP cc_start: 0.7852 (m-30) cc_final: 0.7215 (m-30) REVERT: S8 173 TYR cc_start: 0.9103 (p90) cc_final: 0.8711 (p90) REVERT: V3 55 ASN cc_start: 0.9199 (t0) cc_final: 0.8951 (t0) REVERT: V3 63 MET cc_start: 0.7451 (mmm) cc_final: 0.7041 (mmm) REVERT: S6 32 GLN cc_start: 0.8882 (pp30) cc_final: 0.8542 (pp30) REVERT: S6 38 ASN cc_start: 0.8311 (t0) cc_final: 0.7977 (t0) REVERT: S4 44 ASN cc_start: 0.7854 (t0) cc_final: 0.7507 (t0) REVERT: S4 56 LYS cc_start: 0.8966 (mttt) cc_final: 0.8714 (mttp) REVERT: S4 70 MET cc_start: 0.8035 (mmm) cc_final: 0.6938 (mmt) REVERT: S4 106 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A9 64 ASP cc_start: 0.7374 (t70) cc_final: 0.6753 (m-30) REVERT: A9 177 ARG cc_start: 0.8246 (tpp80) cc_final: 0.7761 (tpp80) REVERT: A5 40 ASN cc_start: 0.8909 (p0) cc_final: 0.8346 (t0) REVERT: A5 65 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8367 (tttp) REVERT: A5 104 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6835 (mt-10) REVERT: A6 39 TYR cc_start: 0.8824 (t80) cc_final: 0.7954 (t80) REVERT: A6 41 GLU cc_start: 0.8898 (tp30) cc_final: 0.8295 (tp30) REVERT: A6 73 THR cc_start: 0.8878 (p) cc_final: 0.8577 (t) REVERT: A7 51 ASN cc_start: 0.8132 (p0) cc_final: 0.7726 (p0) REVERT: A7 57 ASP cc_start: 0.8305 (t0) cc_final: 0.7489 (t70) REVERT: AL 27 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8151 (tt) REVERT: AL 56 PHE cc_start: 0.8509 (t80) cc_final: 0.8159 (t80) REVERT: AL 61 TRP cc_start: 0.8825 (p90) cc_final: 0.7982 (p90) REVERT: AL 81 MET cc_start: 0.7855 (mtt) cc_final: 0.7638 (mtt) REVERT: AL 134 ILE cc_start: 0.8847 (pt) cc_final: 0.8601 (mp) REVERT: AL 135 GLN cc_start: 0.8590 (tp40) cc_final: 0.8227 (tm-30) REVERT: AA 12 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7967 (tmtt) REVERT: AA 21 LEU cc_start: 0.9210 (tp) cc_final: 0.8981 (mt) REVERT: AA 49 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7548 (pt0) REVERT: AA 52 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.7601 (ppp) outliers start: 107 outliers final: 76 residues processed: 668 average time/residue: 0.3954 time to fit residues: 417.8576 Evaluate side-chains 651 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 570 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 107 ASP 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 362 CYS Chi-restraints excluded: chain V1 residue 389 ILE Chi-restraints excluded: chain V2 residue 10 ARG Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 110 LEU Chi-restraints excluded: chain S1 residue 33 VAL Chi-restraints excluded: chain S1 residue 52 CYS Chi-restraints excluded: chain S1 residue 77 TRP Chi-restraints excluded: chain S1 residue 113 GLU Chi-restraints excluded: chain S1 residue 159 CYS Chi-restraints excluded: chain S1 residue 187 ILE Chi-restraints excluded: chain S1 residue 216 THR 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 S1 residue 357 ASP Chi-restraints excluded: chain S1 residue 378 LEU Chi-restraints excluded: chain S1 residue 414 ASP Chi-restraints excluded: chain S1 residue 444 GLN Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 536 ASP 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 284 ASP Chi-restraints excluded: chain S2 residue 340 THR Chi-restraints excluded: chain S2 residue 354 GLU Chi-restraints excluded: chain S2 residue 403 ASP 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 109 THR Chi-restraints excluded: chain S3 residue 117 VAL Chi-restraints excluded: chain S3 residue 188 VAL 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 S8 residue 18 THR 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 36 THR Chi-restraints excluded: chain V3 residue 42 GLN 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 79 LEU Chi-restraints excluded: chain S4 residue 97 GLU Chi-restraints excluded: chain S4 residue 105 VAL Chi-restraints excluded: chain A9 residue 77 ASP Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP 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 A5 residue 64 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 27 LEU Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AL residue 120 THR Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 43 ASP Chi-restraints excluded: chain AA residue 52 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 316 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 276 optimal weight: 10.0000 chunk 183 optimal weight: 0.0670 chunk 326 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 101 GLN ** 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** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 149 ASN ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 61 HIS V3 44 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A9 3 HIS ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A5 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.238 28302 Z= 0.761 Angle : 2.379 50.661 38356 Z= 1.557 Chirality : 0.478 6.327 4177 Planarity : 0.005 0.071 4957 Dihedral : 5.904 83.116 3851 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.17 % Allowed : 21.59 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3417 helix: 0.70 (0.15), residues: 1335 sheet: -1.28 (0.27), residues: 354 loop : -2.63 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPS8 161 HIS 0.007 0.001 HISS1 549 PHE 0.023 0.001 PHEV3 61 TYR 0.028 0.002 TYRS7 28 ARG 0.007 0.000 ARGAL 131 *********************** 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 700 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 576 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V1 185 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8579 (tp) REVERT: V1 213 VAL cc_start: 0.9514 (t) cc_final: 0.9266 (m) REVERT: V1 302 SER cc_start: 0.8617 (m) cc_final: 0.8092 (t) REVERT: V1 335 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8389 (pt) REVERT: V2 28 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: V2 104 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.5016 (m) REVERT: S1 52 CYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8835 (p) REVERT: S1 357 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7678 (p0) REVERT: S1 364 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8099 (tt) REVERT: S1 378 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8742 (pp) REVERT: S1 490 MET cc_start: 0.8584 (tmm) cc_final: 0.7993 (tmm) REVERT: S1 693 GLU cc_start: 0.7593 (tp30) cc_final: 0.7367 (tp30) REVERT: S2 82 LEU cc_start: 0.8345 (mp) cc_final: 0.7860 (tp) REVERT: S2 149 ASN cc_start: 0.9321 (t160) cc_final: 0.9006 (t0) REVERT: S2 261 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.6560 (mpt-90) REVERT: S2 371 LYS cc_start: 0.9182 (mmtp) cc_final: 0.8341 (mmtm) REVERT: S2 422 ASP cc_start: 0.7964 (p0) cc_final: 0.6673 (p0) REVERT: S3 95 ASN cc_start: 0.8704 (m-40) cc_final: 0.8257 (m-40) REVERT: S3 131 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8198 (mt-10) REVERT: S7 105 ASP cc_start: 0.8308 (m-30) cc_final: 0.7917 (m-30) REVERT: S7 112 TYR cc_start: 0.8098 (m-80) cc_final: 0.7678 (m-80) REVERT: S7 125 TYR cc_start: 0.9098 (t80) cc_final: 0.8823 (t80) REVERT: S7 130 TYR cc_start: 0.8194 (p90) cc_final: 0.7883 (p90) REVERT: S7 152 THR cc_start: 0.8642 (m) cc_final: 0.8368 (p) REVERT: S8 110 ASP cc_start: 0.7903 (m-30) cc_final: 0.6801 (m-30) REVERT: S8 161 TRP cc_start: 0.9113 (OUTLIER) cc_final: 0.8420 (p90) REVERT: S8 162 GLU cc_start: 0.7950 (tp30) cc_final: 0.7676 (tp30) REVERT: S8 173 TYR cc_start: 0.9105 (p90) cc_final: 0.8665 (p90) REVERT: V3 55 ASN cc_start: 0.9212 (t0) cc_final: 0.8908 (t0) REVERT: V3 63 MET cc_start: 0.7520 (mmm) cc_final: 0.7061 (mmm) REVERT: S6 32 GLN cc_start: 0.8894 (pp30) cc_final: 0.8574 (pp30) REVERT: S6 38 ASN cc_start: 0.8184 (t0) cc_final: 0.7842 (t0) REVERT: S6 89 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8919 (pp) REVERT: S4 44 ASN cc_start: 0.7870 (t0) cc_final: 0.7548 (t0) REVERT: S4 56 LYS cc_start: 0.8982 (mttt) cc_final: 0.8734 (mttp) REVERT: S4 63 GLU cc_start: 0.8566 (pm20) cc_final: 0.8245 (tt0) REVERT: S4 70 MET cc_start: 0.8111 (mmm) cc_final: 0.7567 (mmm) REVERT: A9 64 ASP cc_start: 0.7494 (t70) cc_final: 0.6709 (m-30) REVERT: A9 177 ARG cc_start: 0.8209 (tpp80) cc_final: 0.7728 (tpp80) REVERT: A9 206 TYR cc_start: 0.8198 (t80) cc_final: 0.7832 (t80) REVERT: A5 40 ASN cc_start: 0.8880 (p0) cc_final: 0.8443 (t0) REVERT: A5 104 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6944 (mt-10) REVERT: A6 39 TYR cc_start: 0.8866 (t80) cc_final: 0.8233 (t80) REVERT: A6 41 GLU cc_start: 0.8898 (tp30) cc_final: 0.8336 (tp30) REVERT: A6 73 THR cc_start: 0.8911 (p) cc_final: 0.8617 (t) REVERT: A7 51 ASN cc_start: 0.8137 (p0) cc_final: 0.7794 (p0) REVERT: AL 27 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8177 (tt) REVERT: AL 43 LYS cc_start: 0.8066 (tmmt) cc_final: 0.7818 (pptt) REVERT: AL 61 TRP cc_start: 0.8895 (p90) cc_final: 0.7903 (p90) REVERT: AL 81 MET cc_start: 0.7945 (mtt) cc_final: 0.7727 (mtt) REVERT: AL 134 ILE cc_start: 0.8865 (pt) cc_final: 0.8620 (mp) REVERT: AL 135 GLN cc_start: 0.8640 (tp40) cc_final: 0.8325 (tm-30) REVERT: AA 12 LYS cc_start: 0.8414 (ttpt) cc_final: 0.8064 (tmtt) REVERT: AA 13 ASP cc_start: 0.8436 (m-30) cc_final: 0.7990 (m-30) REVERT: AA 21 LEU cc_start: 0.9253 (tp) cc_final: 0.9010 (mt) REVERT: AA 49 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7529 (pt0) REVERT: AA 52 MET cc_start: 0.8688 (ppp) cc_final: 0.7608 (ppp) outliers start: 124 outliers final: 89 residues processed: 653 average time/residue: 0.3889 time to fit residues: 401.9868 Evaluate side-chains 654 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 553 time to evaluate : 3.410 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain V1 residue 266 CYS Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 298 ILE Chi-restraints excluded: chain V1 residue 306 LEU Chi-restraints excluded: chain V1 residue 335 ILE 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 28 TYR Chi-restraints excluded: chain V2 residue 48 LEU Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 110 LEU Chi-restraints excluded: chain S1 residue 33 VAL 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 236 SER Chi-restraints excluded: chain S1 residue 253 ARG Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 324 ASP Chi-restraints excluded: chain S1 residue 357 ASP Chi-restraints excluded: chain S1 residue 364 LEU Chi-restraints excluded: chain S1 residue 378 LEU Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 536 ASP Chi-restraints excluded: chain S1 residue 661 LEU Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 144 ILE 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 284 ASP Chi-restraints excluded: chain S2 residue 403 ASP 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 79 THR Chi-restraints excluded: chain S3 residue 109 THR Chi-restraints excluded: chain S3 residue 117 VAL Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S3 residue 188 VAL Chi-restraints excluded: chain S7 residue 35 ASP Chi-restraints excluded: chain S7 residue 48 MET Chi-restraints excluded: chain S7 residue 67 TYR 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 S8 residue 18 THR 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 131 ILE Chi-restraints excluded: chain S8 residue 161 TRP Chi-restraints excluded: chain V3 residue 36 THR Chi-restraints excluded: chain V3 residue 42 GLN Chi-restraints excluded: chain S6 residue 7 THR 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 23 THR Chi-restraints excluded: chain S4 residue 25 VAL Chi-restraints excluded: chain S4 residue 130 VAL Chi-restraints excluded: chain A9 residue 57 MET Chi-restraints excluded: chain A9 residue 77 ASP Chi-restraints excluded: chain A9 residue 88 SER Chi-restraints excluded: chain A9 residue 91 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 180 ASN 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 A5 residue 64 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 A7 residue 10 LEU 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 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AL residue 120 THR Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 43 ASP Chi-restraints excluded: chain AA residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 202 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 0.0020 chunk 207 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V1 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 101 GLN ** 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** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN S7 61 HIS V3 42 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 82 GLN AL 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.240 28302 Z= 0.756 Angle : 2.380 50.616 38356 Z= 1.556 Chirality : 0.478 6.333 4177 Planarity : 0.005 0.070 4957 Dihedral : 5.823 79.652 3851 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.17 % Allowed : 22.06 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3417 helix: 0.82 (0.15), residues: 1321 sheet: -1.23 (0.27), residues: 366 loop : -2.59 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPS8 161 HIS 0.007 0.001 HISS1 549 PHE 0.023 0.001 PHEV3 61 TYR 0.028 0.002 TYRS7 28 ARG 0.006 0.000 ARGAL 131 *********************** 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 688 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 564 time to evaluate : 3.272 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 185 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8646 (tp) REVERT: V1 213 VAL cc_start: 0.9493 (t) cc_final: 0.9239 (m) REVERT: V1 335 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8414 (pt) REVERT: V2 28 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8160 (m-10) REVERT: V2 104 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.4992 (m) REVERT: S1 357 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7589 (p0) REVERT: S1 364 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8106 (tt) REVERT: S1 490 MET cc_start: 0.8557 (tmm) cc_final: 0.8026 (tmm) REVERT: S1 693 GLU cc_start: 0.7664 (tp30) cc_final: 0.7452 (tp30) REVERT: S2 149 ASN cc_start: 0.9260 (t160) cc_final: 0.8959 (t0) REVERT: S2 261 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6507 (mpt-90) REVERT: S3 95 ASN cc_start: 0.8619 (m-40) cc_final: 0.8276 (m-40) REVERT: S3 131 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8212 (mt-10) REVERT: S7 105 ASP cc_start: 0.8326 (m-30) cc_final: 0.7914 (m-30) REVERT: S7 112 TYR cc_start: 0.8054 (m-80) cc_final: 0.7685 (m-80) REVERT: S7 125 TYR cc_start: 0.9049 (t80) cc_final: 0.8847 (t80) REVERT: S7 130 TYR cc_start: 0.8243 (p90) cc_final: 0.7860 (p90) REVERT: S7 152 THR cc_start: 0.8665 (m) cc_final: 0.8459 (p) REVERT: S7 165 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8219 (mtpt) REVERT: S8 110 ASP cc_start: 0.7935 (m-30) cc_final: 0.7047 (m-30) REVERT: S8 161 TRP cc_start: 0.9116 (OUTLIER) cc_final: 0.8394 (p90) REVERT: S8 173 TYR cc_start: 0.9062 (p90) cc_final: 0.8576 (p90) REVERT: V3 55 ASN cc_start: 0.9202 (t0) cc_final: 0.8891 (t0) REVERT: V3 63 MET cc_start: 0.7541 (mmm) cc_final: 0.7062 (mmp) REVERT: S6 32 GLN cc_start: 0.8871 (pp30) cc_final: 0.8612 (pp30) REVERT: S6 38 ASN cc_start: 0.8191 (t0) cc_final: 0.7844 (t0) REVERT: S6 83 THR cc_start: 0.9620 (m) cc_final: 0.9218 (p) REVERT: S6 89 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8877 (pp) REVERT: S4 44 ASN cc_start: 0.7898 (t0) cc_final: 0.7549 (t0) REVERT: S4 56 LYS cc_start: 0.8950 (mttt) cc_final: 0.8731 (mttp) REVERT: S4 63 GLU cc_start: 0.8592 (pm20) cc_final: 0.8272 (tt0) REVERT: S4 70 MET cc_start: 0.8129 (mmm) cc_final: 0.7554 (mmm) REVERT: S4 106 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A9 64 ASP cc_start: 0.7465 (t70) cc_final: 0.6686 (m-30) REVERT: A9 89 ASN cc_start: 0.8823 (t0) cc_final: 0.8475 (t0) REVERT: A9 177 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7748 (tpp80) REVERT: A5 40 ASN cc_start: 0.8872 (p0) cc_final: 0.8491 (t0) REVERT: A5 104 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6898 (mt-10) REVERT: A6 39 TYR cc_start: 0.8843 (t80) cc_final: 0.8567 (t80) REVERT: A6 41 GLU cc_start: 0.8892 (tp30) cc_final: 0.8344 (tp30) REVERT: A6 73 THR cc_start: 0.8916 (p) cc_final: 0.8618 (t) REVERT: A7 51 ASN cc_start: 0.8093 (p0) cc_final: 0.7790 (p0) REVERT: A7 57 ASP cc_start: 0.8187 (t70) cc_final: 0.7406 (t70) REVERT: A7 108 ASP cc_start: 0.7032 (t0) cc_final: 0.6500 (t0) REVERT: AL 27 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8137 (tt) REVERT: AL 43 LYS cc_start: 0.8067 (tmmt) cc_final: 0.7262 (tppt) REVERT: AL 61 TRP cc_start: 0.8896 (p90) cc_final: 0.7882 (p90) REVERT: AL 81 MET cc_start: 0.7909 (mtt) cc_final: 0.7677 (mtt) REVERT: AL 134 ILE cc_start: 0.8862 (pt) cc_final: 0.8630 (mp) REVERT: AL 135 GLN cc_start: 0.8659 (tp40) cc_final: 0.8296 (tm-30) REVERT: AA 12 LYS cc_start: 0.8332 (ttpt) cc_final: 0.8001 (tmtt) REVERT: AA 13 ASP cc_start: 0.8438 (m-30) cc_final: 0.7988 (m-30) REVERT: AA 21 LEU cc_start: 0.9250 (tp) cc_final: 0.9014 (mt) REVERT: AA 24 LYS cc_start: 0.7606 (tttm) cc_final: 0.7401 (tttm) REVERT: AA 52 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8063 (ppp) outliers start: 124 outliers final: 93 residues processed: 642 average time/residue: 0.3894 time to fit residues: 395.8237 Evaluate side-chains 646 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 542 time to evaluate : 3.379 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain V1 residue 297 VAL Chi-restraints excluded: chain V1 residue 306 LEU Chi-restraints excluded: chain V1 residue 335 ILE 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 28 TYR Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 110 LEU Chi-restraints excluded: chain S1 residue 33 VAL Chi-restraints excluded: chain S1 residue 77 TRP Chi-restraints excluded: chain S1 residue 113 GLU 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 236 SER Chi-restraints excluded: chain S1 residue 253 ARG Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 324 ASP Chi-restraints excluded: chain S1 residue 357 ASP Chi-restraints excluded: chain S1 residue 364 LEU Chi-restraints excluded: chain S1 residue 378 LEU Chi-restraints excluded: chain S1 residue 414 ASP Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 536 ASP Chi-restraints excluded: chain S1 residue 661 LEU Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 144 ILE Chi-restraints excluded: chain S2 residue 199 VAL Chi-restraints excluded: chain S2 residue 203 LEU Chi-restraints excluded: chain S2 residue 209 ASP Chi-restraints excluded: chain S2 residue 229 LEU Chi-restraints excluded: chain S2 residue 261 ARG Chi-restraints excluded: chain S2 residue 284 ASP Chi-restraints excluded: chain S2 residue 403 ASP 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 109 THR Chi-restraints excluded: chain S3 residue 117 VAL Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S3 residue 188 VAL 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 61 HIS Chi-restraints excluded: chain S7 residue 67 TYR Chi-restraints excluded: chain S7 residue 93 THR 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 S8 residue 18 THR 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 131 ILE Chi-restraints excluded: chain S8 residue 161 TRP Chi-restraints excluded: chain V3 residue 36 THR Chi-restraints excluded: chain V3 residue 75 HIS Chi-restraints excluded: chain S6 residue 7 THR Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 44 ILE Chi-restraints excluded: chain S6 residue 78 GLU Chi-restraints excluded: chain S6 residue 89 LEU Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 23 THR Chi-restraints excluded: chain S4 residue 25 VAL Chi-restraints excluded: chain S4 residue 79 LEU Chi-restraints excluded: chain S4 residue 97 GLU Chi-restraints excluded: chain A9 residue 57 MET Chi-restraints excluded: chain A9 residue 77 ASP Chi-restraints excluded: chain A9 residue 91 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP 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 A5 residue 64 VAL Chi-restraints excluded: chain A5 residue 112 LYS Chi-restraints excluded: chain A6 residue 47 HIS 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 A7 residue 101 LYS Chi-restraints excluded: chain AL residue 27 LEU 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 AA residue 32 VAL Chi-restraints excluded: chain AA residue 51 ILE Chi-restraints excluded: chain AA residue 52 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 297 optimal weight: 0.0070 chunk 313 optimal weight: 0.6980 chunk 285 optimal weight: 4.9990 chunk 304 optimal weight: 0.0980 chunk 312 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 275 optimal weight: 0.6980 chunk 287 optimal weight: 2.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V1 29 HIS ** V2 101 GLN ** 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 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 82 GLN ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A5 82 GLN A5 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 28302 Z= 0.755 Angle : 2.378 50.579 38356 Z= 1.555 Chirality : 0.478 6.328 4177 Planarity : 0.005 0.074 4957 Dihedral : 5.686 77.005 3851 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.26 % Allowed : 23.10 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 3417 helix: 0.84 (0.15), residues: 1320 sheet: -1.08 (0.28), residues: 354 loop : -2.51 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPS8 161 HIS 0.021 0.001 HISS7 61 PHE 0.021 0.001 PHEV3 61 TYR 0.028 0.002 TYRS7 28 ARG 0.010 0.000 ARGS2 105 *********************** 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 685 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 588 time to evaluate : 3.419 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: V1 185 ILE cc_start: 0.9016 (pt) cc_final: 0.8745 (tp) REVERT: V1 213 VAL cc_start: 0.9439 (t) cc_final: 0.9227 (m) REVERT: V2 28 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8015 (m-10) REVERT: V2 82 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6755 (mt-10) REVERT: S1 357 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7565 (p0) REVERT: S1 490 MET cc_start: 0.8559 (tmm) cc_final: 0.8013 (tmm) REVERT: S1 684 MET cc_start: 0.8379 (mmp) cc_final: 0.8139 (mmt) REVERT: S2 71 GLU cc_start: 0.7988 (tp30) cc_final: 0.7779 (tp30) REVERT: S2 149 ASN cc_start: 0.9215 (t160) cc_final: 0.8932 (t0) REVERT: S2 371 LYS cc_start: 0.9301 (mmtm) cc_final: 0.8683 (mmtm) REVERT: S2 391 ILE cc_start: 0.9269 (mp) cc_final: 0.9067 (mm) REVERT: S2 422 ASP cc_start: 0.7593 (p0) cc_final: 0.6730 (p0) REVERT: S3 21 GLN cc_start: 0.8293 (mt0) cc_final: 0.8070 (mt0) REVERT: S3 95 ASN cc_start: 0.8590 (m-40) cc_final: 0.8301 (m-40) REVERT: S3 131 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8170 (mt-10) REVERT: S3 192 GLN cc_start: 0.8793 (tp40) cc_final: 0.8063 (tt0) REVERT: S7 105 ASP cc_start: 0.8313 (m-30) cc_final: 0.8001 (m-30) REVERT: S7 112 TYR cc_start: 0.8104 (m-80) cc_final: 0.7504 (m-80) REVERT: S7 125 TYR cc_start: 0.8957 (t80) cc_final: 0.8750 (t80) REVERT: S7 130 TYR cc_start: 0.8244 (p90) cc_final: 0.7797 (p90) REVERT: S7 152 THR cc_start: 0.8623 (m) cc_final: 0.8394 (p) REVERT: S7 165 LYS cc_start: 0.8414 (mtmm) cc_final: 0.8138 (mtpt) REVERT: S8 110 ASP cc_start: 0.7930 (m-30) cc_final: 0.6998 (m-30) REVERT: S8 161 TRP cc_start: 0.9079 (OUTLIER) cc_final: 0.8285 (p90) REVERT: S8 162 GLU cc_start: 0.7918 (tp30) cc_final: 0.7680 (tp30) REVERT: S8 173 TYR cc_start: 0.8999 (p90) cc_final: 0.8475 (p90) REVERT: V3 55 ASN cc_start: 0.9178 (t0) cc_final: 0.8861 (t0) REVERT: V3 63 MET cc_start: 0.7581 (mmm) cc_final: 0.7097 (mmp) REVERT: S6 32 GLN cc_start: 0.8916 (pp30) cc_final: 0.8678 (pp30) REVERT: S6 38 ASN cc_start: 0.8134 (t0) cc_final: 0.7805 (t0) REVERT: S6 54 SER cc_start: 0.8064 (t) cc_final: 0.7809 (m) REVERT: S6 83 THR cc_start: 0.9626 (m) cc_final: 0.9252 (p) REVERT: S6 89 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8854 (pp) REVERT: S4 44 ASN cc_start: 0.7781 (t0) cc_final: 0.7438 (t0) REVERT: S4 63 GLU cc_start: 0.8580 (pm20) cc_final: 0.8255 (tt0) REVERT: S4 70 MET cc_start: 0.8170 (mmm) cc_final: 0.7512 (mmm) REVERT: S4 106 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7383 (mt-10) REVERT: A9 64 ASP cc_start: 0.7336 (t70) cc_final: 0.6669 (m-30) REVERT: A9 89 ASN cc_start: 0.8839 (t0) cc_final: 0.8484 (t0) REVERT: A9 177 ARG cc_start: 0.8309 (tpp80) cc_final: 0.7914 (tpp80) REVERT: A9 206 TYR cc_start: 0.8157 (t80) cc_final: 0.7789 (t80) REVERT: A5 40 ASN cc_start: 0.8880 (p0) cc_final: 0.8582 (t0) REVERT: A5 104 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6680 (mt-10) REVERT: A6 39 TYR cc_start: 0.8818 (t80) cc_final: 0.8504 (t80) REVERT: A6 41 GLU cc_start: 0.8842 (tp30) cc_final: 0.8266 (tp30) REVERT: A6 73 THR cc_start: 0.8889 (p) cc_final: 0.8586 (t) REVERT: A7 40 LEU cc_start: 0.9006 (mp) cc_final: 0.8784 (mt) REVERT: A7 51 ASN cc_start: 0.8065 (p0) cc_final: 0.7760 (p0) REVERT: AL 27 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8142 (tt) REVERT: AL 43 LYS cc_start: 0.8130 (tmmt) cc_final: 0.7169 (tppt) REVERT: AL 61 TRP cc_start: 0.8904 (p90) cc_final: 0.7924 (p90) REVERT: AL 81 MET cc_start: 0.7874 (mtt) cc_final: 0.7646 (mtt) REVERT: AL 135 GLN cc_start: 0.8624 (tp40) cc_final: 0.8309 (tm-30) REVERT: AA 12 LYS cc_start: 0.8399 (ttpt) cc_final: 0.8051 (tmtt) REVERT: AA 13 ASP cc_start: 0.8433 (m-30) cc_final: 0.7977 (m-30) REVERT: AA 21 LEU cc_start: 0.9250 (tp) cc_final: 0.9023 (mt) REVERT: AA 52 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8079 (ppp) REVERT: AA 83 LYS cc_start: 0.7074 (ttpp) cc_final: 0.6827 (ttpp) outliers start: 97 outliers final: 79 residues processed: 655 average time/residue: 0.3804 time to fit residues: 393.9349 Evaluate side-chains 642 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 557 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 107 ASP Chi-restraints excluded: chain V1 residue 222 VAL 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 28 TYR Chi-restraints excluded: chain V2 residue 48 LEU Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 110 LEU Chi-restraints excluded: chain S1 residue 33 VAL Chi-restraints excluded: chain S1 residue 77 TRP Chi-restraints excluded: chain S1 residue 113 GLU 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 216 THR 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 S1 residue 324 ASP Chi-restraints excluded: chain S1 residue 357 ASP Chi-restraints excluded: chain S1 residue 378 LEU Chi-restraints excluded: chain S1 residue 414 ASP Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 536 ASP Chi-restraints excluded: chain S1 residue 661 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 209 ASP Chi-restraints excluded: chain S2 residue 229 LEU Chi-restraints excluded: chain S2 residue 284 ASP Chi-restraints excluded: chain S2 residue 403 ASP 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 109 THR Chi-restraints excluded: chain S3 residue 117 VAL Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S3 residue 188 VAL Chi-restraints excluded: chain S7 residue 48 MET Chi-restraints excluded: chain S7 residue 67 TYR 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 S8 residue 18 THR 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 36 THR Chi-restraints excluded: chain S6 residue 7 THR Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 78 GLU Chi-restraints excluded: chain S6 residue 89 LEU Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 23 THR Chi-restraints excluded: chain S4 residue 25 VAL Chi-restraints excluded: chain S4 residue 79 LEU Chi-restraints excluded: chain A9 residue 77 ASP Chi-restraints excluded: chain A9 residue 91 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP 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 A5 residue 112 LYS Chi-restraints excluded: chain A6 residue 47 HIS Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 101 LYS Chi-restraints excluded: chain AL residue 27 LEU Chi-restraints excluded: chain AL residue 65 THR Chi-restraints excluded: chain AL residue 77 VAL Chi-restraints excluded: chain AL residue 78 ASP Chi-restraints excluded: chain AL residue 120 THR Chi-restraints excluded: chain AA residue 32 VAL Chi-restraints excluded: chain AA residue 51 ILE Chi-restraints excluded: chain AA residue 52 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 1.9990 chunk 199 optimal weight: 0.9980 chunk 321 optimal weight: 0.4980 chunk 196 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 223 optimal weight: 4.9990 chunk 337 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 268 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V2 101 GLN ** 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** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S3 200 ASN S7 61 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 61 GLN A5 82 GLN A7 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.239 28302 Z= 0.759 Angle : 2.385 50.609 38356 Z= 1.558 Chirality : 0.478 6.330 4177 Planarity : 0.005 0.069 4957 Dihedral : 5.690 74.558 3851 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 3.36 % Allowed : 23.27 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 3417 helix: 0.79 (0.15), residues: 1332 sheet: -1.04 (0.28), residues: 363 loop : -2.53 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPS8 161 HIS 0.007 0.001 HISS1 549 PHE 0.022 0.001 PHEV3 61 TYR 0.024 0.002 TYRS7 28 ARG 0.008 0.000 ARGAL 131 ********************** 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 665 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 565 time to evaluate : 3.235 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 185 ILE cc_start: 0.9013 (pt) cc_final: 0.8740 (tp) REVERT: V1 213 VAL cc_start: 0.9457 (t) cc_final: 0.9256 (m) REVERT: V2 28 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8143 (m-10) REVERT: V2 82 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6708 (mt-10) REVERT: V2 104 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.4732 (m) REVERT: V2 162 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7059 (mt-10) REVERT: S1 357 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7395 (p0) REVERT: S1 490 MET cc_start: 0.8580 (tmm) cc_final: 0.8014 (tmm) REVERT: S2 149 ASN cc_start: 0.9256 (t160) cc_final: 0.8906 (t0) REVERT: S2 193 TYR cc_start: 0.8843 (t80) cc_final: 0.8633 (t80) REVERT: S2 201 GLN cc_start: 0.8171 (tt0) cc_final: 0.7830 (tm-30) REVERT: S2 261 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.6362 (mpt-90) REVERT: S2 371 LYS cc_start: 0.9315 (mmtm) cc_final: 0.8736 (mmtm) REVERT: S2 391 ILE cc_start: 0.9263 (mp) cc_final: 0.9052 (mm) REVERT: S2 422 ASP cc_start: 0.7678 (p0) cc_final: 0.6877 (p0) REVERT: S3 21 GLN cc_start: 0.8334 (mt0) cc_final: 0.8101 (mt0) REVERT: S3 95 ASN cc_start: 0.8617 (m-40) cc_final: 0.8286 (m-40) REVERT: S3 131 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8180 (mt-10) REVERT: S3 192 GLN cc_start: 0.8833 (tp40) cc_final: 0.8085 (tt0) REVERT: S7 62 MET cc_start: 0.7380 (ttt) cc_final: 0.6706 (ttt) REVERT: S7 69 MET cc_start: 0.7816 (mmm) cc_final: 0.7096 (mmt) REVERT: S7 105 ASP cc_start: 0.8341 (m-30) cc_final: 0.7913 (m-30) REVERT: S7 112 TYR cc_start: 0.8125 (m-80) cc_final: 0.7550 (m-80) REVERT: S7 130 TYR cc_start: 0.8267 (p90) cc_final: 0.7882 (p90) REVERT: S7 152 THR cc_start: 0.8674 (m) cc_final: 0.8444 (p) REVERT: S8 110 ASP cc_start: 0.7943 (m-30) cc_final: 0.7064 (m-30) REVERT: S8 161 TRP cc_start: 0.9121 (OUTLIER) cc_final: 0.8327 (p90) REVERT: V3 55 ASN cc_start: 0.9196 (t0) cc_final: 0.8884 (t0) REVERT: V3 63 MET cc_start: 0.7604 (mmm) cc_final: 0.7118 (mmp) REVERT: S6 32 GLN cc_start: 0.8913 (pp30) cc_final: 0.8664 (pp30) REVERT: S6 38 ASN cc_start: 0.8219 (t0) cc_final: 0.7896 (t0) REVERT: S6 83 THR cc_start: 0.9631 (m) cc_final: 0.9262 (p) REVERT: S6 89 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8886 (pp) REVERT: S4 44 ASN cc_start: 0.7863 (t0) cc_final: 0.7495 (t0) REVERT: S4 63 GLU cc_start: 0.8564 (pm20) cc_final: 0.8302 (tt0) REVERT: S4 70 MET cc_start: 0.8193 (mmm) cc_final: 0.7609 (mmm) REVERT: S4 106 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A9 64 ASP cc_start: 0.7424 (t70) cc_final: 0.6665 (m-30) REVERT: A9 177 ARG cc_start: 0.8269 (tpp80) cc_final: 0.7893 (tpp80) REVERT: A9 206 TYR cc_start: 0.8302 (t80) cc_final: 0.7797 (t80) REVERT: A5 40 ASN cc_start: 0.8871 (p0) cc_final: 0.8572 (t0) REVERT: A5 104 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6722 (mt-10) REVERT: A6 39 TYR cc_start: 0.8829 (t80) cc_final: 0.8259 (t80) REVERT: A6 41 GLU cc_start: 0.8919 (tp30) cc_final: 0.8344 (tp30) REVERT: A6 73 THR cc_start: 0.8903 (p) cc_final: 0.8627 (t) REVERT: A7 39 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8396 (mtmt) REVERT: A7 51 ASN cc_start: 0.8111 (p0) cc_final: 0.7819 (p0) REVERT: A7 57 ASP cc_start: 0.7733 (t70) cc_final: 0.7427 (t70) REVERT: AL 27 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8160 (tt) REVERT: AL 43 LYS cc_start: 0.8308 (tmmt) cc_final: 0.7349 (tppt) REVERT: AL 61 TRP cc_start: 0.8912 (p90) cc_final: 0.7895 (p90) REVERT: AL 81 MET cc_start: 0.7903 (mtt) cc_final: 0.7655 (mtm) REVERT: AA 12 LYS cc_start: 0.8346 (ttpt) cc_final: 0.8018 (tmtt) REVERT: AA 13 ASP cc_start: 0.8437 (m-30) cc_final: 0.8096 (m-30) REVERT: AA 21 LEU cc_start: 0.9265 (tp) cc_final: 0.9020 (mt) REVERT: AA 52 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7688 (ppp) REVERT: AA 83 LYS cc_start: 0.7107 (ttpp) cc_final: 0.6779 (ttpp) outliers start: 100 outliers final: 84 residues processed: 636 average time/residue: 0.3929 time to fit residues: 394.9519 Evaluate side-chains 643 residues out of total 2983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 551 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V1 residue 107 ASP Chi-restraints excluded: chain V1 residue 222 VAL 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 28 TYR Chi-restraints excluded: chain V2 residue 48 LEU Chi-restraints excluded: chain V2 residue 104 THR Chi-restraints excluded: chain V2 residue 110 LEU Chi-restraints excluded: chain S1 residue 27 LEU Chi-restraints excluded: chain S1 residue 33 VAL Chi-restraints excluded: chain S1 residue 77 TRP Chi-restraints excluded: chain S1 residue 113 GLU 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 236 SER Chi-restraints excluded: chain S1 residue 322 LEU Chi-restraints excluded: chain S1 residue 324 ASP Chi-restraints excluded: chain S1 residue 357 ASP Chi-restraints excluded: chain S1 residue 378 LEU Chi-restraints excluded: chain S1 residue 414 ASP Chi-restraints excluded: chain S1 residue 453 LEU Chi-restraints excluded: chain S1 residue 536 ASP Chi-restraints excluded: chain S1 residue 541 CYS Chi-restraints excluded: chain S1 residue 636 VAL Chi-restraints excluded: chain S1 residue 661 LEU Chi-restraints excluded: chain S2 residue 114 ASN Chi-restraints excluded: chain S2 residue 139 VAL Chi-restraints excluded: chain S2 residue 171 PHE 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 284 ASP Chi-restraints excluded: chain S2 residue 354 GLU Chi-restraints excluded: chain S2 residue 403 ASP 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 109 THR Chi-restraints excluded: chain S3 residue 117 VAL Chi-restraints excluded: chain S3 residue 136 ASP Chi-restraints excluded: chain S3 residue 188 VAL 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 67 TYR 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 S8 residue 18 THR 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 36 THR Chi-restraints excluded: chain S6 residue 7 THR Chi-restraints excluded: chain S6 residue 17 VAL Chi-restraints excluded: chain S6 residue 89 LEU Chi-restraints excluded: chain S4 residue 12 THR Chi-restraints excluded: chain S4 residue 23 THR Chi-restraints excluded: chain S4 residue 25 VAL Chi-restraints excluded: chain S4 residue 79 LEU Chi-restraints excluded: chain A9 residue 77 ASP Chi-restraints excluded: chain A9 residue 91 VAL Chi-restraints excluded: chain A9 residue 126 VAL Chi-restraints excluded: chain A9 residue 176 ASP Chi-restraints excluded: chain A9 residue 287 ILE 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 A5 residue 112 LYS Chi-restraints excluded: chain A6 residue 47 HIS Chi-restraints excluded: chain A6 residue 95 VAL Chi-restraints excluded: chain A7 residue 10 LEU Chi-restraints excluded: chain A7 residue 25 LEU Chi-restraints excluded: chain A7 residue 101 LYS Chi-restraints excluded: chain AL residue 27 LEU Chi-restraints excluded: chain AL residue 65 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 52 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 164 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 286 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 247 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 269 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 276 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V2 101 GLN ** 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** ** S1 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 61 HIS ** S6 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A9 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 61 GLN A5 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.100870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.086406 restraints weight = 61223.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088842 restraints weight = 35810.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.090532 restraints weight = 23697.180| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.239 28302 Z= 0.761 Angle : 2.390 50.621 38356 Z= 1.560 Chirality : 0.478 6.332 4177 Planarity : 0.005 0.069 4957 Dihedral : 5.697 72.606 3851 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 3.56 % Allowed : 23.30 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 3417 helix: 0.79 (0.15), residues: 1332 sheet: -1.03 (0.28), residues: 363 loop : -2.52 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPS8 161 HIS 0.007 0.001 HISS1 549 PHE 0.024 0.001 PHEV2 211 TYR 0.034 0.002 TYRAL 124 ARG 0.008 0.000 ARGAL 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7639.50 seconds wall clock time: 138 minutes 36.44 seconds (8316.44 seconds total)