Starting phenix.real_space_refine on Sat Sep 28 01:24:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/09_2024/8csq_26967_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/09_2024/8csq_26967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/09_2024/8csq_26967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/09_2024/8csq_26967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/09_2024/8csq_26967_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csq_26967/09_2024/8csq_26967_neut.cif" } resolution = 2.54 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= 0.039 sd= 1.386 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: 9 Type Number sf(0) Gaussians K 4 8.98 5 Fe 8 7.16 5 Zn 1 6.06 5 P 807 5.49 5 Mg 27 5.21 5 S 252 5.16 5 C 39883 2.51 5 N 12116 2.21 5 O 14608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 67706 Number of models: 1 Model: "" Number of chains: 40 Chain: "0" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1754 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "1" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2098 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain breaks: 1 Chain: "3" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 395 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "4" Number of atoms: 4585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4585 Classifications: {'peptide': 566} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 539} Chain breaks: 3 Chain: "5" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2568 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 23, 'TRANS': 295} Chain: "7" Number of atoms: 3145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3145 Classifications: {'peptide': 398} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 366} Chain breaks: 1 Chain: "8" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2543 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 18, 'TRANS': 307} Chain: "A" Number of atoms: 17027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 17027 Classifications: {'RNA': 802} Modifications used: {'rna2p_pur': 71, 'rna2p_pyr': 57, 'rna3p_pur': 346, 'rna3p_pyr': 328} Link IDs: {'rna2p': 127, 'rna3p': 674} Chain breaks: 9 Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1789 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 10, 'TRANS': 209} Chain: "C" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1042 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1838 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 839 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1724 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 13, 'TRANS': 194} Chain: "G" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2384 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 10, 'TRANS': 280} Chain breaks: 1 Chain: "H" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1064 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 8, 'TRANS': 121} Chain breaks: 1 Chain: "J" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 839 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 97} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 296 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain breaks: 1 Chain: "L" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1363 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "M" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 913 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1570 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 21, 'TRANS': 168} Chain: "P" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "R" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2382 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain: "S" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1100 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "T" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1344 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain: "U" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1468 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 5, 'TRANS': 168} Chain: "V" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2946 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 9, 'TRANS': 349} Chain breaks: 1 Chain: "W" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "X" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2849 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 332} Chain: "Y" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1043 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "Z" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain breaks: 1 Chain: "a" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1785 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "7" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Unusual residues: {' K': 4, ' MG': 25} Classifications: {'undetermined': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14253 SG CYS 7 404 101.559 108.438 153.209 1.00 19.70 S ATOM 13774 SG CYS 7 347 105.684 103.947 150.425 1.00 30.57 S ATOM 13669 SG CYS 7 333 99.613 105.869 148.111 1.00 19.24 S ATOM 13716 SG CYS 7 339 104.969 109.317 147.912 1.00 17.52 S ATOM 49472 SG CYS O 94 114.523 152.095 98.509 1.00 27.72 S ATOM 49558 SG CYS O 105 117.210 152.626 95.968 1.00 25.97 S ATOM 49579 SG CYS O 108 116.130 155.574 98.003 1.00 27.87 S ATOM 49867 SG CYS O 143 113.672 154.153 95.450 1.00 24.24 S ATOM 51063 SG CYS P 100 125.456 65.540 48.961 1.00 47.11 S ATOM 39614 SG CYS E 105 125.303 68.448 44.204 1.00 59.43 S ATOM 50812 SG CYS P 68 125.981 64.703 42.685 1.00 47.55 S ATOM 47417 SG CYS M 26 93.225 164.015 76.755 1.00 28.06 S ATOM 56115 SG CYS T 149 97.383 163.552 76.775 1.00 31.23 S ATOM 56043 SG CYS T 139 95.301 164.940 71.131 1.00 27.78 S ATOM 56057 SG CYS T 141 97.880 164.964 73.768 1.00 26.91 S Time building chain proxies: 28.03, per 1000 atoms: 0.41 Number of scatterers: 67706 At special positions: 0 Unit cell: (226.206, 234.702, 220.896, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 Fe 8 26.01 K 4 19.00 S 252 16.00 P 807 15.00 Mg 27 11.99 O 14608 8.00 N 12116 7.00 C 39883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.01 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 201 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 100 " pdb="FE2 FES P 201 " - pdb=" SG CYS E 105 " pdb="FE2 FES P 201 " - pdb=" SG CYS P 68 " pdb="FE1 FES P 201 " - pdb=" SG CYS P 65 " pdb=" FES T 201 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 141 " pdb="FE2 FES T 201 " - pdb=" SG CYS T 139 " pdb="FE1 FES T 201 " - pdb=" SG CYS T 149 " pdb="FE1 FES T 201 " - pdb=" SG CYS M 26 " pdb=" SF4 7 501 " pdb="FE3 SF4 7 501 " - pdb=" SG CYS 7 333 " pdb="FE1 SF4 7 501 " - pdb=" SG CYS 7 404 " pdb="FE4 SF4 7 501 " - pdb=" SG CYS 7 339 " pdb="FE2 SF4 7 501 " - pdb=" SG CYS 7 347 " Number of angles added : 24 Zn2+ tetrahedral coordination pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 105 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 108 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 143 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 94 " Number of angles added : 6 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11894 Finding SS restraints... Secondary structure from input PDB file: 281 helices and 43 sheets defined 53.3% alpha, 12.3% beta 229 base pairs and 396 stacking pairs defined. Time for finding SS restraints: 21.91 Creating SS restraints... Processing helix chain '0' and resid 9 through 26 removed outlier: 3.961A pdb=" N GLU 0 13 " --> pdb=" O ARG 0 9 " (cutoff:3.500A) Processing helix chain '0' and resid 29 through 34 Processing helix chain '0' and resid 51 through 53 No H-bonds generated for 'chain '0' and resid 51 through 53' Processing helix chain '0' and resid 54 through 61 Processing helix chain '0' and resid 63 through 69 Processing helix chain '0' and resid 70 through 76 removed outlier: 7.804A pdb=" N LEU 0 73 " --> pdb=" O ARG 0 70 " (cutoff:3.500A) Processing helix chain '0' and resid 83 through 89 Processing helix chain '0' and resid 143 through 145 No H-bonds generated for 'chain '0' and resid 143 through 145' Processing helix chain '0' and resid 146 through 152 Processing helix chain '0' and resid 167 through 181 Processing helix chain '1' and resid 55 through 60 Processing helix chain '1' and resid 65 through 69 Processing helix chain '1' and resid 102 through 107 removed outlier: 3.537A pdb=" N LEU 1 106 " --> pdb=" O ASN 1 102 " (cutoff:3.500A) Processing helix chain '1' and resid 115 through 126 Processing helix chain '1' and resid 127 through 130 Processing helix chain '1' and resid 139 through 147 removed outlier: 3.671A pdb=" N LYS 1 145 " --> pdb=" O GLU 1 141 " (cutoff:3.500A) Processing helix chain '1' and resid 165 through 169 removed outlier: 3.908A pdb=" N ARG 1 169 " --> pdb=" O PRO 1 166 " (cutoff:3.500A) Processing helix chain '1' and resid 178 through 180 No H-bonds generated for 'chain '1' and resid 178 through 180' Processing helix chain '1' and resid 183 through 195 Processing helix chain '1' and resid 214 through 234 removed outlier: 3.741A pdb=" N ASN 1 218 " --> pdb=" O LEU 1 214 " (cutoff:3.500A) Processing helix chain '1' and resid 237 through 242 Processing helix chain '1' and resid 256 through 273 Processing helix chain '1' and resid 287 through 302 Processing helix chain '1' and resid 305 through 321 Processing helix chain '3' and resid 154 through 181 Processing helix chain '4' and resid 68 through 78 removed outlier: 3.808A pdb=" N VAL 4 78 " --> pdb=" O LEU 4 74 " (cutoff:3.500A) Processing helix chain '4' and resid 99 through 124 Processing helix chain '4' and resid 125 through 128 Processing helix chain '4' and resid 137 through 141 Processing helix chain '4' and resid 153 through 163 removed outlier: 3.537A pdb=" N LEU 4 157 " --> pdb=" O SER 4 153 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 180 Processing helix chain '4' and resid 184 through 199 Processing helix chain '4' and resid 242 through 251 Processing helix chain '4' and resid 255 through 269 Processing helix chain '4' and resid 271 through 285 Processing helix chain '4' and resid 290 through 304 Processing helix chain '4' and resid 308 through 326 Processing helix chain '4' and resid 331 through 343 removed outlier: 3.727A pdb=" N PHE 4 335 " --> pdb=" O ASN 4 331 " (cutoff:3.500A) Processing helix chain '4' and resid 344 through 348 removed outlier: 7.203A pdb=" N VAL 4 347 " --> pdb=" O ARG 4 344 " (cutoff:3.500A) Processing helix chain '4' and resid 349 through 363 Processing helix chain '4' and resid 368 through 380 removed outlier: 3.642A pdb=" N TYR 4 372 " --> pdb=" O SER 4 368 " (cutoff:3.500A) Processing helix chain '4' and resid 391 through 401 removed outlier: 3.951A pdb=" N ASP 4 395 " --> pdb=" O PHE 4 391 " (cutoff:3.500A) Processing helix chain '4' and resid 409 through 413 removed outlier: 4.165A pdb=" N ASP 4 413 " --> pdb=" O PRO 4 410 " (cutoff:3.500A) Processing helix chain '4' and resid 414 through 427 Processing helix chain '4' and resid 428 through 441 removed outlier: 3.592A pdb=" N ALA 4 432 " --> pdb=" O ASP 4 428 " (cutoff:3.500A) Processing helix chain '4' and resid 443 through 449 removed outlier: 4.194A pdb=" N GLY 4 449 " --> pdb=" O LYS 4 446 " (cutoff:3.500A) Processing helix chain '4' and resid 450 through 469 Processing helix chain '4' and resid 470 through 482 Processing helix chain '4' and resid 489 through 504 Processing helix chain '4' and resid 505 through 507 No H-bonds generated for 'chain '4' and resid 505 through 507' Processing helix chain '4' and resid 508 through 519 Processing helix chain '4' and resid 524 through 537 Processing helix chain '4' and resid 541 through 561 Processing helix chain '4' and resid 572 through 586 Processing helix chain '4' and resid 588 through 602 removed outlier: 3.600A pdb=" N ALA 4 592 " --> pdb=" O ARG 4 588 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY 4 597 " --> pdb=" O TRP 4 593 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 4 598 " --> pdb=" O LYS 4 594 " (cutoff:3.500A) Processing helix chain '4' and resid 607 through 622 Processing helix chain '4' and resid 623 through 637 removed outlier: 3.567A pdb=" N PHE 4 637 " --> pdb=" O LEU 4 633 " (cutoff:3.500A) Processing helix chain '4' and resid 641 through 653 Processing helix chain '4' and resid 656 through 667 Processing helix chain '5' and resid 17 through 25 Processing helix chain '5' and resid 40 through 51 Processing helix chain '5' and resid 67 through 76 Processing helix chain '5' and resid 87 through 89 No H-bonds generated for 'chain '5' and resid 87 through 89' Processing helix chain '5' and resid 90 through 101 Processing helix chain '5' and resid 116 through 120 removed outlier: 4.027A pdb=" N LYS 5 119 " --> pdb=" O LYS 5 116 " (cutoff:3.500A) Processing helix chain '5' and resid 143 through 161 removed outlier: 4.170A pdb=" N THR 5 148 " --> pdb=" O PHE 5 144 " (cutoff:3.500A) Proline residue: 5 149 - end of helix Processing helix chain '5' and resid 162 through 167 removed outlier: 3.840A pdb=" N TYR 5 167 " --> pdb=" O PRO 5 164 " (cutoff:3.500A) Processing helix chain '5' and resid 178 through 185 Processing helix chain '5' and resid 194 through 202 Processing helix chain '5' and resid 213 through 217 Processing helix chain '5' and resid 241 through 254 Processing helix chain '5' and resid 259 through 265 removed outlier: 3.931A pdb=" N GLY 5 263 " --> pdb=" O TYR 5 259 " (cutoff:3.500A) Processing helix chain '5' and resid 266 through 268 No H-bonds generated for 'chain '5' and resid 266 through 268' Processing helix chain '5' and resid 272 through 285 Processing helix chain '5' and resid 291 through 295 Processing helix chain '5' and resid 296 through 313 Processing helix chain '5' and resid 321 through 328 removed outlier: 3.563A pdb=" N ARG 5 328 " --> pdb=" O GLU 5 324 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 47 Processing helix chain '7' and resid 64 through 75 Processing helix chain '7' and resid 80 through 96 Processing helix chain '7' and resid 102 through 116 Processing helix chain '7' and resid 134 through 140 Processing helix chain '7' and resid 151 through 181 removed outlier: 6.191A pdb=" N ASP 7 164 " --> pdb=" O ALA 7 160 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLY 7 165 " --> pdb=" O ALA 7 161 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE 7 177 " --> pdb=" O ALA 7 173 " (cutoff:3.500A) Processing helix chain '7' and resid 197 through 208 Processing helix chain '7' and resid 220 through 232 Processing helix chain '7' and resid 267 through 271 Processing helix chain '7' and resid 273 through 287 Processing helix chain '7' and resid 299 through 315 Processing helix chain '7' and resid 416 through 421 Processing helix chain '7' and resid 421 through 431 Processing helix chain '8' and resid 86 through 99 removed outlier: 3.847A pdb=" N LEU 8 90 " --> pdb=" O ARG 8 86 " (cutoff:3.500A) Processing helix chain '8' and resid 101 through 108 removed outlier: 3.637A pdb=" N LEU 8 105 " --> pdb=" O ASP 8 101 " (cutoff:3.500A) Processing helix chain '8' and resid 111 through 116 removed outlier: 3.609A pdb=" N ARG 8 116 " --> pdb=" O GLU 8 112 " (cutoff:3.500A) Processing helix chain '8' and resid 116 through 139 removed outlier: 3.787A pdb=" N GLN 8 121 " --> pdb=" O THR 8 117 " (cutoff:3.500A) Proline residue: 8 122 - end of helix Processing helix chain '8' and resid 139 through 145 removed outlier: 3.723A pdb=" N ILE 8 143 " --> pdb=" O GLN 8 139 " (cutoff:3.500A) Processing helix chain '8' and resid 154 through 163 removed outlier: 3.541A pdb=" N ALA 8 158 " --> pdb=" O VAL 8 154 " (cutoff:3.500A) Processing helix chain '8' and resid 167 through 189 removed outlier: 3.744A pdb=" N VAL 8 189 " --> pdb=" O ALA 8 185 " (cutoff:3.500A) Processing helix chain '8' and resid 203 through 219 removed outlier: 3.531A pdb=" N CYS 8 215 " --> pdb=" O ALA 8 211 " (cutoff:3.500A) Processing helix chain '8' and resid 241 through 251 Processing helix chain '8' and resid 251 through 256 Processing helix chain '8' and resid 271 through 276 Proline residue: 8 276 - end of helix Processing helix chain '8' and resid 277 through 288 removed outlier: 3.547A pdb=" N LEU 8 281 " --> pdb=" O ALA 8 277 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA 8 287 " --> pdb=" O GLN 8 283 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL 8 288 " --> pdb=" O ALA 8 284 " (cutoff:3.500A) Processing helix chain '8' and resid 308 through 319 removed outlier: 3.934A pdb=" N ILE 8 312 " --> pdb=" O HIS 8 308 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N HIS 8 313 " --> pdb=" O PRO 8 309 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS 8 314 " --> pdb=" O GLY 8 310 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA 8 317 " --> pdb=" O HIS 8 313 " (cutoff:3.500A) Processing helix chain '8' and resid 320 through 322 No H-bonds generated for 'chain '8' and resid 320 through 322' Processing helix chain '8' and resid 326 through 335 Processing helix chain '8' and resid 352 through 362 Processing helix chain '8' and resid 362 through 367 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.518A pdb=" N HIS B 69 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.905A pdb=" N PHE B 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 87 Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 99 through 104 Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 117 through 138 removed outlier: 3.554A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 206 through 215 removed outlier: 4.245A pdb=" N ARG B 210 " --> pdb=" O HIS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 274 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 81 through 100 Processing helix chain 'C' and resid 128 through 148 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.548A pdb=" N ASP D 287 " --> pdb=" O ARG D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 341 through 355 Processing helix chain 'D' and resid 358 through 367 Processing helix chain 'D' and resid 374 through 378 Processing helix chain 'D' and resid 407 through 415 Processing helix chain 'E' and resid 14 through 32 Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.969A pdb=" N SER E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 70 removed outlier: 3.663A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 103 through 128 Processing helix chain 'F' and resid 130 through 137 removed outlier: 4.118A pdb=" N ALA F 135 " --> pdb=" O GLU F 132 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE F 137 " --> pdb=" O GLN F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 153 Processing helix chain 'F' and resid 175 through 192 Processing helix chain 'F' and resid 200 through 214 removed outlier: 3.600A pdb=" N HIS F 214 " --> pdb=" O LEU F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 232 removed outlier: 3.636A pdb=" N MET F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 93 Processing helix chain 'G' and resid 100 through 112 Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 150 through 154 Processing helix chain 'G' and resid 155 through 175 Processing helix chain 'G' and resid 201 through 210 Processing helix chain 'G' and resid 214 through 231 Processing helix chain 'G' and resid 234 through 243 Processing helix chain 'G' and resid 300 through 304 Processing helix chain 'G' and resid 306 through 320 removed outlier: 3.562A pdb=" N ARG G 310 " --> pdb=" O ILE G 306 " (cutoff:3.500A) Proline residue: G 316 - end of helix removed outlier: 3.635A pdb=" N VAL G 320 " --> pdb=" O PRO G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 353 Processing helix chain 'G' and resid 354 through 356 No H-bonds generated for 'chain 'G' and resid 354 through 356' Processing helix chain 'G' and resid 357 through 367 Processing helix chain 'H' and resid 84 through 102 Processing helix chain 'H' and resid 150 through 163 Processing helix chain 'H' and resid 181 through 185 removed outlier: 3.599A pdb=" N LYS H 185 " --> pdb=" O GLU H 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 40 Processing helix chain 'K' and resid 49 through 58 Processing helix chain 'K' and resid 107 through 117 Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.862A pdb=" N GLN L 77 " --> pdb=" O LYS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.993A pdb=" N VAL L 85 " --> pdb=" O ILE L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 93 Processing helix chain 'L' and resid 94 through 98 Processing helix chain 'L' and resid 99 through 116 removed outlier: 3.925A pdb=" N MET L 103 " --> pdb=" O ASN L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 146 removed outlier: 3.948A pdb=" N LYS L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 174 Processing helix chain 'L' and resid 174 through 185 Processing helix chain 'L' and resid 200 through 225 Processing helix chain 'M' and resid 69 through 79 Processing helix chain 'M' and resid 84 through 94 Processing helix chain 'M' and resid 100 through 124 removed outlier: 3.516A pdb=" N ILE M 104 " --> pdb=" O HIS M 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 112 Processing helix chain 'O' and resid 55 through 60 removed outlier: 4.128A pdb=" N LEU O 59 " --> pdb=" O PRO O 55 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU O 60 " --> pdb=" O TRP O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 60' Processing helix chain 'O' and resid 61 through 69 Processing helix chain 'O' and resid 119 through 125 removed outlier: 3.690A pdb=" N GLN O 125 " --> pdb=" O LYS O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 141 removed outlier: 3.937A pdb=" N THR O 140 " --> pdb=" O TYR O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 160 Processing helix chain 'O' and resid 190 through 196 Processing helix chain 'O' and resid 200 through 204 Processing helix chain 'O' and resid 209 through 220 Processing helix chain 'P' and resid 76 through 81 Processing helix chain 'P' and resid 82 through 84 No H-bonds generated for 'chain 'P' and resid 82 through 84' Processing helix chain 'P' and resid 93 through 98 Processing helix chain 'P' and resid 100 through 117 Processing helix chain 'P' and resid 126 through 130 Processing helix chain 'R' and resid 72 through 84 Processing helix chain 'R' and resid 86 through 91 Processing helix chain 'R' and resid 107 through 126 Processing helix chain 'R' and resid 146 through 149 Processing helix chain 'R' and resid 166 through 170 removed outlier: 3.589A pdb=" N ARG R 170 " --> pdb=" O HIS R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 197 Processing helix chain 'R' and resid 207 through 210 removed outlier: 3.603A pdb=" N PHE R 210 " --> pdb=" O PRO R 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 207 through 210' Processing helix chain 'R' and resid 211 through 221 Processing helix chain 'R' and resid 223 through 235 Processing helix chain 'R' and resid 239 through 257 Processing helix chain 'R' and resid 258 through 262 Processing helix chain 'R' and resid 267 through 278 Processing helix chain 'R' and resid 281 through 291 Processing helix chain 'R' and resid 293 through 308 Processing helix chain 'R' and resid 311 through 321 Processing helix chain 'R' and resid 324 through 335 removed outlier: 3.819A pdb=" N ILE R 328 " --> pdb=" O GLY R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 356 Processing helix chain 'S' and resid 11 through 22 Processing helix chain 'S' and resid 31 through 38 Processing helix chain 'S' and resid 65 through 78 removed outlier: 4.204A pdb=" N ARG S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE S 70 " --> pdb=" O HIS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 94 through 109 Processing helix chain 'S' and resid 113 through 129 Processing helix chain 'T' and resid 7 through 11 Processing helix chain 'T' and resid 12 through 18 Processing helix chain 'T' and resid 38 through 40 No H-bonds generated for 'chain 'T' and resid 38 through 40' Processing helix chain 'T' and resid 41 through 51 Processing helix chain 'T' and resid 51 through 59 Processing helix chain 'T' and resid 94 through 107 Processing helix chain 'T' and resid 109 through 124 removed outlier: 3.842A pdb=" N LEU T 123 " --> pdb=" O GLU T 119 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER T 124 " --> pdb=" O LYS T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 143 Processing helix chain 'T' and resid 156 through 159 Processing helix chain 'T' and resid 160 through 165 Processing helix chain 'U' and resid 35 through 39 removed outlier: 3.562A pdb=" N ILE U 39 " --> pdb=" O LYS U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 88 Processing helix chain 'U' and resid 88 through 165 removed outlier: 4.018A pdb=" N LYS U 165 " --> pdb=" O GLN U 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 182 Processing helix chain 'V' and resid 31 through 36 Processing helix chain 'V' and resid 37 through 42 Processing helix chain 'V' and resid 49 through 63 Processing helix chain 'V' and resid 68 through 78 removed outlier: 3.502A pdb=" N ILE V 72 " --> pdb=" O SER V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 97 removed outlier: 3.551A pdb=" N ASP V 86 " --> pdb=" O ARG V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 104 Processing helix chain 'V' and resid 105 through 119 Processing helix chain 'V' and resid 121 through 131 Processing helix chain 'V' and resid 131 through 136 Processing helix chain 'V' and resid 140 through 154 Processing helix chain 'V' and resid 156 through 171 Processing helix chain 'V' and resid 175 through 191 Processing helix chain 'V' and resid 197 through 215 Proline residue: V 211 - end of helix removed outlier: 3.912A pdb=" N LYS V 214 " --> pdb=" O LEU V 210 " (cutoff:3.500A) Processing helix chain 'V' and resid 217 through 239 Processing helix chain 'V' and resid 239 through 245 removed outlier: 3.662A pdb=" N VAL V 243 " --> pdb=" O GLY V 239 " (cutoff:3.500A) Processing helix chain 'V' and resid 254 through 268 Processing helix chain 'V' and resid 277 through 291 Processing helix chain 'V' and resid 322 through 345 Proline residue: V 328 - end of helix Processing helix chain 'V' and resid 351 through 405 removed outlier: 5.263A pdb=" N SER V 365 " --> pdb=" O LYS V 361 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR V 366 " --> pdb=" O GLU V 362 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 86 Processing helix chain 'W' and resid 87 through 93 removed outlier: 4.008A pdb=" N GLY W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 134 removed outlier: 3.660A pdb=" N LYS W 133 " --> pdb=" O ASP W 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 55 through 59 removed outlier: 3.617A pdb=" N HIS X 59 " --> pdb=" O PRO X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 64 Processing helix chain 'X' and resid 71 through 79 Processing helix chain 'X' and resid 84 through 95 Processing helix chain 'X' and resid 102 through 114 Processing helix chain 'X' and resid 133 through 148 removed outlier: 3.619A pdb=" N GLN X 148 " --> pdb=" O PHE X 144 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 163 removed outlier: 3.541A pdb=" N TRP X 161 " --> pdb=" O ALA X 158 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS X 163 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 180 through 195 removed outlier: 3.506A pdb=" N TRP X 187 " --> pdb=" O GLU X 183 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN X 190 " --> pdb=" O THR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 202 removed outlier: 4.358A pdb=" N GLN X 201 " --> pdb=" O ARG X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 232 removed outlier: 3.973A pdb=" N VAL X 225 " --> pdb=" O PRO X 221 " (cutoff:3.500A) Processing helix chain 'X' and resid 235 through 254 Processing helix chain 'X' and resid 265 through 268 Processing helix chain 'X' and resid 283 through 286 Processing helix chain 'X' and resid 287 through 295 removed outlier: 3.921A pdb=" N LYS X 295 " --> pdb=" O HIS X 291 " (cutoff:3.500A) Processing helix chain 'X' and resid 324 through 338 removed outlier: 6.869A pdb=" N LYS X 331 " --> pdb=" O GLU X 327 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N GLU X 332 " --> pdb=" O LEU X 328 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY X 333 " --> pdb=" O LEU X 329 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 363 Processing helix chain 'X' and resid 373 through 385 Processing helix chain 'X' and resid 387 through 397 removed outlier: 3.920A pdb=" N TYR X 397 " --> pdb=" O ARG X 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 277 through 289 removed outlier: 3.809A pdb=" N VAL Y 289 " --> pdb=" O GLN Y 285 " (cutoff:3.500A) Processing helix chain 'Y' and resid 296 through 307 Processing helix chain 'Y' and resid 327 through 333 removed outlier: 3.610A pdb=" N HIS Y 331 " --> pdb=" O GLU Y 327 " (cutoff:3.500A) Processing helix chain 'Y' and resid 334 through 339 removed outlier: 3.520A pdb=" N LEU Y 338 " --> pdb=" O GLU Y 335 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU Y 339 " --> pdb=" O LYS Y 336 " (cutoff:3.500A) Processing helix chain 'Y' and resid 345 through 359 Processing helix chain 'Y' and resid 365 through 383 Processing helix chain 'Z' and resid 5 through 20 Processing helix chain 'Z' and resid 31 through 39 removed outlier: 3.533A pdb=" N LYS Z 35 " --> pdb=" O MET Z 31 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 68 Processing helix chain 'a' and resid 125 through 135 Processing helix chain 'a' and resid 189 through 196 removed outlier: 4.002A pdb=" N SER a 196 " --> pdb=" O LYS a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 226 Processing helix chain 'a' and resid 237 through 241 Processing helix chain 'a' and resid 244 through 255 removed outlier: 4.255A pdb=" N LEU a 248 " --> pdb=" O LYS a 244 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU a 249 " --> pdb=" O SER a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 315 through 326 Processing helix chain 'a' and resid 344 through 360 Processing helix chain 'a' and resid 363 through 368 removed outlier: 3.765A pdb=" N VAL a 368 " --> pdb=" O PRO a 365 " (cutoff:3.500A) Processing helix chain 'a' and resid 393 through 402 Processing helix chain 'a' and resid 405 through 424 Processing sheet with id=AA1, first strand: chain '0' and resid 123 through 124 Processing sheet with id=AA2, first strand: chain '0' and resid 123 through 124 removed outlier: 6.013A pdb=" N ILE 0 117 " --> pdb=" O LEU 0 97 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU 0 97 " --> pdb=" O ILE 0 117 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR 0 119 " --> pdb=" O TRP 0 95 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N TRP 0 95 " --> pdb=" O THR 0 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain '1' and resid 198 through 199 removed outlier: 3.633A pdb=" N VAL 1 204 " --> pdb=" O CYS 1 199 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG H 75 " --> pdb=" O THR H 175 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU H 177 " --> pdb=" O TYR H 73 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N TYR H 73 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU H 72 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR H 149 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS H 74 " --> pdb=" O HIS H 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 105 through 109 removed outlier: 4.182A pdb=" N SER H 105 " --> pdb=" O GLU H 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '4' and resid 64 through 65 Processing sheet with id=AA7, first strand: chain '5' and resid 106 through 109 removed outlier: 3.780A pdb=" N GLN 5 171 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE 5 210 " --> pdb=" O VAL 5 227 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N HIS 5 229 " --> pdb=" O HIS 5 208 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS 5 208 " --> pdb=" O HIS 5 229 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR 5 231 " --> pdb=" O VAL 5 206 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL 5 206 " --> pdb=" O THR 5 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '7' and resid 36 through 37 Processing sheet with id=AA9, first strand: chain '7' and resid 61 through 62 removed outlier: 6.596A pdb=" N VAL 7 61 " --> pdb=" O HIS 7 354 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N HIS 7 290 " --> pdb=" O ARG 7 376 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE 7 259 " --> pdb=" O GLY 7 289 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N PHE 7 291 " --> pdb=" O PHE 7 259 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL 7 261 " --> pdb=" O PHE 7 291 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL 7 293 " --> pdb=" O VAL 7 261 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL 7 263 " --> pdb=" O VAL 7 293 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL 7 295 " --> pdb=" O VAL 7 263 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA 7 265 " --> pdb=" O VAL 7 295 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASN 7 297 " --> pdb=" O ALA 7 265 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA 7 265 " --> pdb=" O PHE 7 192 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 7 189 " --> pdb=" O MET 7 215 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL 7 217 " --> pdb=" O LEU 7 189 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP 7 191 " --> pdb=" O VAL 7 217 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR 7 214 " --> pdb=" O PHE 7 246 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG 7 248 " --> pdb=" O TYR 7 214 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS 7 216 " --> pdb=" O ARG 7 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '7' and resid 61 through 62 removed outlier: 6.596A pdb=" N VAL 7 61 " --> pdb=" O HIS 7 354 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA 7 375 " --> pdb=" O VAL 7 329 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL 7 329 " --> pdb=" O ALA 7 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '7' and resid 387 through 388 Processing sheet with id=AB3, first strand: chain '7' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain '8' and resid 296 through 298 removed outlier: 7.032A pdb=" N VAL 8 147 " --> pdb=" O SER 8 296 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N TYR 8 298 " --> pdb=" O VAL 8 147 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ALA 8 149 " --> pdb=" O TYR 8 298 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER 8 63 " --> pdb=" O CYS 8 146 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA 8 148 " --> pdb=" O SER 8 63 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL 8 64 " --> pdb=" O PHE 8 346 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR 8 345 " --> pdb=" O SER 8 370 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '8' and resid 257 through 262 removed outlier: 8.286A pdb=" N CYS 8 235 " --> pdb=" O TYR 8 230 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR 8 230 " --> pdb=" O CYS 8 235 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL 8 237 " --> pdb=" O SER 8 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 94 removed outlier: 5.828A pdb=" N LEU B 91 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE B 116 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS B 93 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 108 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 165 through 167 removed outlier: 6.331A pdb=" N ILE B 142 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N HIS B 167 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE B 144 " --> pdb=" O HIS B 167 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU B 143 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR B 219 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL B 236 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY B 221 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AB9, first strand: chain 'C' and resid 70 through 71 removed outlier: 3.537A pdb=" N ARG C 113 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.538A pdb=" N VAL C 123 " --> pdb=" O VAL C 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 219 through 228 removed outlier: 6.410A pdb=" N LEU D 244 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL D 225 " --> pdb=" O ARG D 242 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG D 242 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN D 227 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER D 240 " --> pdb=" O ASN D 227 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 294 through 298 removed outlier: 6.729A pdb=" N ARG D 315 " --> pdb=" O ALA D 334 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL D 336 " --> pdb=" O ARG D 315 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 382 through 385 removed outlier: 6.848A pdb=" N VAL D 370 " --> pdb=" O VAL D 384 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 35 through 53 removed outlier: 7.138A pdb=" N ARG E 37 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N TYR E 69 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU E 39 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP E 67 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASN E 41 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU E 65 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY E 43 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN E 59 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 11.394A pdb=" N TYR E 49 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N GLN E 57 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS E 11 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL E 88 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 156 through 163 removed outlier: 3.515A pdb=" N LYS F 163 " --> pdb=" O ARG F 166 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 198 through 199 Processing sheet with id=AC8, first strand: chain 'G' and resid 261 through 262 removed outlier: 6.336A pdb=" N LYS G 294 " --> pdb=" O CYS G 330 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL G 332 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 57 through 68 removed outlier: 6.839A pdb=" N ARG J 82 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR J 65 " --> pdb=" O CYS J 80 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N CYS J 80 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR J 67 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ARG J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU J 123 " --> pdb=" O VAL J 92 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 82 through 83 removed outlier: 6.814A pdb=" N TYR M 32 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER M 53 " --> pdb=" O TYR M 32 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE M 34 " --> pdb=" O LEU M 51 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU R 181 " --> pdb=" O LEU R 142 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 12 through 22 removed outlier: 15.660A pdb=" N TRP N 12 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 11.963A pdb=" N LEU N 33 " --> pdb=" O TRP N 12 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL N 14 " --> pdb=" O THR N 31 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR N 31 " --> pdb=" O VAL N 14 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS N 27 " --> pdb=" O ILE N 18 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR N 20 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR N 25 " --> pdb=" O THR N 20 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N VAL N 77 " --> pdb=" O THR N 48 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE N 50 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS N 79 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU N 65 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE N 84 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE N 63 " --> pdb=" O ILE N 84 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 100 through 101 removed outlier: 3.570A pdb=" N THR N 104 " --> pdb=" O ALA N 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 63 through 68 removed outlier: 6.696A pdb=" N TYR T 79 " --> pdb=" O LYS T 28 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET T 30 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG T 77 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL T 32 " --> pdb=" O PHE T 75 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE T 75 " --> pdb=" O VAL T 32 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 190 through 191 Processing sheet with id=AD6, first strand: chain 'V' and resid 275 through 276 removed outlier: 6.264A pdb=" N LEU V 275 " --> pdb=" O GLU V 348 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'W' and resid 122 through 125 removed outlier: 3.634A pdb=" N HIS W 106 " --> pdb=" O TYR W 113 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP W 115 " --> pdb=" O ILE W 104 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ILE W 104 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS W 98 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL W 140 " --> pdb=" O ILE W 172 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE W 172 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU W 142 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU W 170 " --> pdb=" O LEU W 142 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU W 144 " --> pdb=" O VAL W 168 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL W 168 " --> pdb=" O LEU W 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 150 through 151 Processing sheet with id=AD9, first strand: chain 'X' and resid 67 through 70 removed outlier: 4.370A pdb=" N ALA X 97 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 151 through 155 removed outlier: 6.458A pdb=" N LEU X 258 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL X 307 " --> pdb=" O LEU X 258 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL X 260 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA X 309 " --> pdb=" O VAL X 260 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL X 262 " --> pdb=" O ALA X 309 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG X 123 " --> pdb=" O ILE X 341 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE X 343 " --> pdb=" O ARG X 123 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU X 125 " --> pdb=" O ILE X 343 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL X 345 " --> pdb=" O LEU X 125 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR X 127 " --> pdb=" O VAL X 345 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 169 through 170 Processing sheet with id=AE3, first strand: chain 'X' and resid 208 through 209 Processing sheet with id=AE4, first strand: chain 'a' and resid 154 through 158 removed outlier: 6.510A pdb=" N ARG a 112 " --> pdb=" O GLN a 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE a 164 " --> pdb=" O ARG a 112 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU a 114 " --> pdb=" O ILE a 164 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU a 166 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL a 116 " --> pdb=" O LEU a 166 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU a 199 " --> pdb=" O VAL a 113 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG a 115 " --> pdb=" O LEU a 199 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL a 201 " --> pdb=" O ARG a 115 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL a 117 " --> pdb=" O VAL a 201 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU a 203 " --> pdb=" O VAL a 117 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU a 119 " --> pdb=" O LEU a 203 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP a 205 " --> pdb=" O LEU a 119 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER a 231 " --> pdb=" O LYS a 303 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE a 305 " --> pdb=" O SER a 231 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU a 233 " --> pdb=" O ILE a 305 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N MET a 307 " --> pdb=" O LEU a 233 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET a 235 " --> pdb=" O MET a 307 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 154 through 158 removed outlier: 6.510A pdb=" N ARG a 112 " --> pdb=" O GLN a 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE a 164 " --> pdb=" O ARG a 112 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU a 114 " --> pdb=" O ILE a 164 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU a 166 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL a 116 " --> pdb=" O LEU a 166 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 258 through 259 Processing sheet with id=AE7, first strand: chain 'a' and resid 369 through 377 removed outlier: 6.234A pdb=" N GLN a 386 " --> pdb=" O ALA a 373 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP a 375 " --> pdb=" O VAL a 384 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL a 384 " --> pdb=" O TRP a 375 " (cutoff:3.500A) 2551 hydrogen bonds defined for protein. 7242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 559 hydrogen bonds 1010 hydrogen bond angles 0 basepair planarities 229 basepair parallelities 396 stacking parallelities Total time for adding SS restraints: 37.48 Time building geometry restraints manager: 15.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 32666 1.43 - 1.65: 37748 1.65 - 1.87: 388 1.87 - 2.09: 0 2.09 - 2.31: 20 Bond restraints: 70822 Sorted by residual: bond pdb=" N1 GDP X 503 " pdb=" C2 GDP X 503 " ideal model delta sigma weight residual 1.337 1.558 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C6 GDP X 503 " pdb=" O6 GDP X 503 " ideal model delta sigma weight residual 1.250 1.416 -0.166 2.00e-02 2.50e+03 6.91e+01 bond pdb=" C5 GDP X 503 " pdb=" C4 GDP X 503 " ideal model delta sigma weight residual 1.490 1.351 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C2 GDP X 503 " pdb=" N2 GDP X 503 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C2 GDP X 503 " pdb=" N3 GDP X 503 " ideal model delta sigma weight residual 1.350 1.453 -0.103 2.00e-02 2.50e+03 2.68e+01 ... (remaining 70817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 98319 2.27 - 4.55: 1138 4.55 - 6.82: 96 6.82 - 9.09: 12 9.09 - 11.37: 2 Bond angle restraints: 99567 Sorted by residual: angle pdb=" CA PRO 8 59 " pdb=" N PRO 8 59 " pdb=" CD PRO 8 59 " ideal model delta sigma weight residual 112.00 103.30 8.70 1.40e+00 5.10e-01 3.87e+01 angle pdb=" CA PRO 7 103 " pdb=" N PRO 7 103 " pdb=" CD PRO 7 103 " ideal model delta sigma weight residual 112.00 104.39 7.61 1.40e+00 5.10e-01 2.96e+01 angle pdb=" C VAL 4 508 " pdb=" N ILE 4 509 " pdb=" CA ILE 4 509 " ideal model delta sigma weight residual 120.24 123.22 -2.98 6.30e-01 2.52e+00 2.24e+01 angle pdb=" C PHE 5 90 " pdb=" N ILE 5 91 " pdb=" CA ILE 5 91 " ideal model delta sigma weight residual 120.24 122.90 -2.66 6.30e-01 2.52e+00 1.78e+01 angle pdb=" C3' C A1330 " pdb=" O3' C A1330 " pdb=" P A A1331 " ideal model delta sigma weight residual 120.20 125.59 -5.39 1.50e+00 4.44e-01 1.29e+01 ... (remaining 99562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 41263 35.01 - 70.02: 2118 70.02 - 105.03: 330 105.03 - 140.03: 14 140.03 - 175.04: 7 Dihedral angle restraints: 43732 sinusoidal: 25408 harmonic: 18324 Sorted by residual: dihedral pdb=" CA LYS J 72 " pdb=" C LYS J 72 " pdb=" N PRO J 73 " pdb=" CA PRO J 73 " ideal model delta harmonic sigma weight residual 180.00 123.29 56.71 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" O4' C A 870 " pdb=" C1' C A 870 " pdb=" N1 C A 870 " pdb=" C2 C A 870 " ideal model delta sinusoidal sigma weight residual 200.00 33.50 166.50 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' C A1233 " pdb=" C1' C A1233 " pdb=" N1 C A1233 " pdb=" C2 C A1233 " ideal model delta sinusoidal sigma weight residual 200.00 44.18 155.82 1 1.50e+01 4.44e-03 8.16e+01 ... (remaining 43729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.210: 11634 4.210 - 8.419: 0 8.419 - 12.629: 0 12.629 - 16.838: 0 16.838 - 21.048: 4 Chirality restraints: 11638 Sorted by residual: chirality pdb="FE2 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S3 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.49 21.05 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S3 SF4 7 501 " both_signs ideal model delta sigma weight residual False 10.55 -10.47 21.03 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4 7 501 " pdb=" S1 SF4 7 501 " pdb=" S2 SF4 7 501 " pdb=" S4 SF4 7 501 " both_signs ideal model delta sigma weight residual False -10.55 10.43 -20.98 2.00e-01 2.50e+01 1.10e+04 ... (remaining 11635 not shown) Planarity restraints: 9784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU 7 102 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO 7 103 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO 7 103 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO 7 103 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG T 160 " 0.402 9.50e-02 1.11e+02 1.80e-01 2.03e+01 pdb=" NE ARG T 160 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG T 160 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG T 160 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG T 160 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET 8 58 " -0.073 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO 8 59 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO 8 59 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO 8 59 " -0.057 5.00e-02 4.00e+02 ... (remaining 9781 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.59: 538 2.59 - 3.23: 62307 3.23 - 3.87: 142620 3.87 - 4.50: 195466 4.50 - 5.14: 285532 Nonbonded interactions: 686463 Sorted by model distance: nonbonded pdb=" OP1 C A 806 " pdb="MG MG A1709 " model vdw 1.958 2.170 nonbonded pdb=" OP1 A A 801 " pdb="MG MG A1709 " model vdw 1.961 2.170 nonbonded pdb=" OP2 A A 731 " pdb="MG MG A1714 " model vdw 1.963 2.170 nonbonded pdb=" O2' A A 738 " pdb=" O2 C A 739 " model vdw 1.965 3.040 nonbonded pdb=" OG1 THR X 135 " pdb="MG MG X 502 " model vdw 1.973 2.170 ... (remaining 686458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 2.300 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 165.580 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.221 70822 Z= 0.262 Angle : 0.642 11.368 99567 Z= 0.344 Chirality : 0.391 21.048 11638 Planarity : 0.006 0.180 9784 Dihedral : 18.545 175.042 31838 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.11), residues: 6167 helix: 1.46 (0.10), residues: 2949 sheet: 0.03 (0.19), residues: 667 loop : 0.25 (0.13), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP 1 239 HIS 0.013 0.001 HIS R 247 PHE 0.028 0.002 PHE 4 335 TYR 0.037 0.002 TYR 4 486 ARG 0.011 0.001 ARG T 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 988 time to evaluate : 5.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 318 ARG cc_start: 0.6996 (mmp80) cc_final: 0.6547 (mmm160) REVERT: 4 260 CYS cc_start: 0.6487 (p) cc_final: 0.6229 (p) REVERT: C 19 ARG cc_start: 0.5146 (mmt-90) cc_final: 0.4234 (tpt-90) REVERT: G 138 ILE cc_start: 0.8033 (tp) cc_final: 0.7645 (pt) REVERT: G 314 MET cc_start: 0.8609 (ttp) cc_final: 0.8237 (ttp) REVERT: G 321 ASP cc_start: 0.7277 (m-30) cc_final: 0.6749 (m-30) REVERT: J 36 MET cc_start: 0.9218 (mtp) cc_final: 0.8868 (mtp) REVERT: N 59 THR cc_start: 0.8430 (m) cc_final: 0.8195 (m) REVERT: N 105 TYR cc_start: 0.8860 (m-80) cc_final: 0.8545 (m-80) REVERT: O 62 GLU cc_start: 0.6883 (tp30) cc_final: 0.6510 (tp30) REVERT: O 164 ILE cc_start: 0.9049 (mt) cc_final: 0.8794 (mp) REVERT: O 177 PHE cc_start: 0.8856 (m-80) cc_final: 0.8640 (m-80) REVERT: O 235 MET cc_start: 0.8750 (tpp) cc_final: 0.8383 (tpt) REVERT: P 87 PHE cc_start: 0.7143 (m-80) cc_final: 0.6886 (m-80) REVERT: P 120 MET cc_start: 0.8311 (ttt) cc_final: 0.8039 (ttt) REVERT: R 116 ARG cc_start: 0.8241 (ttp80) cc_final: 0.7054 (ttp-110) REVERT: R 277 ASN cc_start: 0.8439 (m-40) cc_final: 0.8190 (m110) REVERT: U 44 MET cc_start: 0.7605 (mmm) cc_final: 0.7373 (mmm) REVERT: V 276 CYS cc_start: 0.7484 (m) cc_final: 0.7082 (m) REVERT: W 83 MET cc_start: 0.8776 (mtt) cc_final: 0.8506 (mtt) REVERT: W 110 ASN cc_start: 0.7376 (m-40) cc_final: 0.7148 (m110) REVERT: Y 351 MET cc_start: 0.6999 (mmm) cc_final: 0.6538 (mmm) outliers start: 0 outliers final: 3 residues processed: 988 average time/residue: 1.7498 time to fit residues: 2187.7774 Evaluate side-chains 704 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 701 time to evaluate : 5.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain Z residue 63 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 584 optimal weight: 6.9990 chunk 524 optimal weight: 4.9990 chunk 291 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 353 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 542 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 329 optimal weight: 0.9980 chunk 403 optimal weight: 5.9990 chunk 628 optimal weight: 0.6980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 3 158 GLN 4 175 GLN 4 189 ASN 4 326 GLN 4 417 GLN 4 545 GLN 4 602 HIS 5 208 HIS 5 229 HIS 5 251 ASN 5 294 GLN 7 60 HIS 7 98 HIS 7 290 HIS 7 383 HIS 7 400 HIS 8 83 ASN B 74 ASN B 266 GLN C 57 HIS C 130 HIS C 156 GLN G 255 GLN K 113 HIS K 119 GLN O 207 GLN R 221 GLN R 247 HIS R 299 ASN R 308 HIS R 315 GLN S 47 GLN S 91 ASN S 107 GLN T 37 HIS T 85 GLN U 79 GLN U 110 GLN U 186 ASN X 81 HIS X 110 HIS ** X 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 159 HIS a 260 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.300 70822 Z= 0.342 Angle : 0.828 50.566 99567 Z= 0.490 Chirality : 0.123 6.386 11638 Planarity : 0.005 0.077 9784 Dihedral : 19.649 168.834 19029 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.26 % Allowed : 8.72 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.11), residues: 6167 helix: 1.72 (0.09), residues: 2955 sheet: 0.27 (0.19), residues: 656 loop : 0.29 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 1 239 HIS 0.012 0.001 HIS R 247 PHE 0.025 0.002 PHE 4 345 TYR 0.021 0.002 TYR V 91 ARG 0.009 0.001 ARG U 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 727 time to evaluate : 5.182 Fit side-chains REVERT: 0 192 ASN cc_start: 0.8864 (t0) cc_final: 0.8567 (t0) REVERT: 1 268 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7760 (mt0) REVERT: 1 288 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6675 (mt-10) REVERT: 1 318 ARG cc_start: 0.6934 (mmp80) cc_final: 0.6677 (mmm160) REVERT: 3 163 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7291 (mtm-85) REVERT: 4 200 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.5855 (t0) REVERT: 4 328 VAL cc_start: 0.7335 (m) cc_final: 0.7052 (t) REVERT: 4 506 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6876 (mm) REVERT: 4 507 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: 4 533 MET cc_start: 0.6285 (mtm) cc_final: 0.6083 (mtt) REVERT: 5 96 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5908 (mtp) REVERT: B 181 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8384 (tp) REVERT: C 19 ARG cc_start: 0.5129 (mmt-90) cc_final: 0.4228 (tpt-90) REVERT: C 94 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7210 (mptt) REVERT: D 330 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8411 (mmtp) REVERT: G 138 ILE cc_start: 0.8079 (tp) cc_final: 0.7687 (pt) REVERT: G 314 MET cc_start: 0.8551 (ttp) cc_final: 0.8122 (ttp) REVERT: G 321 ASP cc_start: 0.7245 (m-30) cc_final: 0.6912 (m-30) REVERT: J 36 MET cc_start: 0.9211 (mtp) cc_final: 0.8776 (mtp) REVERT: K 51 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5697 (mmm160) REVERT: O 62 GLU cc_start: 0.6784 (tp30) cc_final: 0.6395 (tp30) REVERT: O 63 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: O 145 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8416 (ttpt) REVERT: O 164 ILE cc_start: 0.9052 (mt) cc_final: 0.8781 (mp) REVERT: O 177 PHE cc_start: 0.8879 (m-80) cc_final: 0.8668 (m-80) REVERT: O 235 MET cc_start: 0.8718 (tpp) cc_final: 0.8428 (tpt) REVERT: P 87 PHE cc_start: 0.7172 (m-80) cc_final: 0.6897 (m-80) REVERT: P 120 MET cc_start: 0.8362 (ttt) cc_final: 0.8094 (ttt) REVERT: P 131 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6427 (pptt) REVERT: R 72 ASP cc_start: 0.7034 (t70) cc_final: 0.6791 (t0) REVERT: R 116 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7308 (ttp-110) REVERT: R 127 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8085 (tttt) REVERT: R 133 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7339 (mm-30) REVERT: R 331 PHE cc_start: 0.7728 (t80) cc_final: 0.7486 (t80) REVERT: R 344 LEU cc_start: 0.7737 (tt) cc_final: 0.7441 (tp) REVERT: V 77 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7680 (t0) REVERT: V 396 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: V 398 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5848 (mt-10) REVERT: W 109 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: W 110 ASN cc_start: 0.7450 (m-40) cc_final: 0.7249 (m110) REVERT: X 227 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6474 (tp30) REVERT: Y 351 MET cc_start: 0.7028 (mmm) cc_final: 0.6624 (mmm) REVERT: Z 21 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6435 (mm-30) outliers start: 123 outliers final: 50 residues processed: 783 average time/residue: 1.6503 time to fit residues: 1649.5325 Evaluate side-chains 739 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 669 time to evaluate : 5.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 37 ASP Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 183 VAL Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 262 MET Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 8 residue 117 THR Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 51 ARG Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain O residue 145 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 131 LYS Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 196 LEU Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 227 GLU Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain a residue 156 ILE Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 211 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 349 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 523 optimal weight: 4.9990 chunk 427 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 629 optimal weight: 0.6980 chunk 680 optimal weight: 9.9990 chunk 560 optimal weight: 5.9990 chunk 624 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 505 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 0 107 GLN 0 181 ASN 4 189 ASN 4 562 GLN 5 171 GLN 5 208 HIS 7 69 ASN 7 144 HIS ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 313 HIS B 124 HIS B 266 GLN C 130 HIS H 51 HIS K 117 HIS ** O 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 246 HIS R 315 GLN S 47 GLN S 91 ASN S 107 GLN T 18 GLN Y 296 ASN a 123 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.247 70822 Z= 0.446 Angle : 0.880 50.489 99567 Z= 0.513 Chirality : 0.126 6.475 11638 Planarity : 0.006 0.066 9784 Dihedral : 19.674 165.320 19022 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.31 % Allowed : 9.88 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.02 % 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: 1.07 (0.11), residues: 6167 helix: 1.41 (0.09), residues: 2953 sheet: 0.29 (0.20), residues: 652 loop : 0.12 (0.12), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 1 66 HIS 0.012 0.002 HIS R 247 PHE 0.026 0.002 PHE 5 230 TYR 0.024 0.002 TYR V 91 ARG 0.022 0.001 ARG 4 585 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 701 time to evaluate : 5.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 26 ASN cc_start: 0.8042 (m-40) cc_final: 0.7826 (m110) REVERT: 0 195 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6818 (ptm160) REVERT: 1 268 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: 1 288 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6678 (mt-10) REVERT: 1 318 ARG cc_start: 0.6978 (mmp80) cc_final: 0.6627 (mmm160) REVERT: 3 163 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7667 (mtp85) REVERT: 4 67 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8017 (mtmm) REVERT: 4 200 ASP cc_start: 0.6397 (OUTLIER) cc_final: 0.6120 (t0) REVERT: 4 430 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: 4 507 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: 4 650 MET cc_start: 0.3620 (OUTLIER) cc_final: 0.3080 (mpp) REVERT: 5 96 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.6072 (mtm) REVERT: 8 83 ASN cc_start: 0.7242 (m-40) cc_final: 0.7019 (m110) REVERT: B 181 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8440 (tp) REVERT: C 19 ARG cc_start: 0.4976 (mmt-90) cc_final: 0.4217 (tpt-90) REVERT: D 330 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8407 (mmtp) REVERT: G 245 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7066 (tpt90) REVERT: G 267 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6574 (mtp) REVERT: J 36 MET cc_start: 0.9213 (mtp) cc_final: 0.8783 (mtp) REVERT: K 51 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.5728 (mmm160) REVERT: O 62 GLU cc_start: 0.6859 (tp30) cc_final: 0.6507 (tp30) REVERT: O 235 MET cc_start: 0.8845 (tpp) cc_final: 0.8464 (tpt) REVERT: P 87 PHE cc_start: 0.7234 (m-80) cc_final: 0.6971 (m-80) REVERT: R 72 ASP cc_start: 0.7157 (t70) cc_final: 0.6837 (t0) REVERT: R 112 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: R 116 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7334 (ttp-110) REVERT: R 127 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8131 (tttt) REVERT: R 133 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7474 (mm-30) REVERT: R 331 PHE cc_start: 0.7836 (t80) cc_final: 0.7431 (t80) REVERT: T 9 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8610 (tp) REVERT: T 120 LYS cc_start: 0.7629 (mtpp) cc_final: 0.7378 (tttp) REVERT: U 80 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7711 (ttp-110) REVERT: V 77 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7756 (t0) REVERT: V 396 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7086 (mm-40) REVERT: V 398 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5841 (mt-10) REVERT: W 109 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: W 110 ASN cc_start: 0.7535 (m-40) cc_final: 0.7327 (m110) REVERT: Y 351 MET cc_start: 0.7076 (mmm) cc_final: 0.6604 (mmm) REVERT: Z 13 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6387 (ttm170) REVERT: Z 21 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6388 (mm-30) outliers start: 180 outliers final: 76 residues processed: 799 average time/residue: 1.6639 time to fit residues: 1697.0459 Evaluate side-chains 760 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 661 time to evaluate : 5.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 151 THR Chi-restraints excluded: chain 0 residue 180 LYS Chi-restraints excluded: chain 0 residue 195 ARG Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 183 VAL Chi-restraints excluded: chain 4 residue 187 THR Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 262 MET Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 430 GLU Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 576 LEU Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 117 THR Chi-restraints excluded: chain 8 residue 180 GLU Chi-restraints excluded: chain 8 residue 206 PHE Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain 8 residue 377 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 51 ARG Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 334 THR Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 196 LEU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 354 VAL Chi-restraints excluded: chain Z residue 13 ARG Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain a residue 211 THR Chi-restraints excluded: chain a residue 259 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 621 optimal weight: 0.6980 chunk 473 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 422 optimal weight: 7.9990 chunk 631 optimal weight: 0.5980 chunk 668 optimal weight: 0.0970 chunk 330 optimal weight: 2.9990 chunk 598 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 179 GLN 0 181 ASN 4 189 ASN 4 417 GLN 4 562 GLN 5 208 HIS ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 266 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS F 146 HIS G 318 HIS H 51 HIS O 65 GLN O 204 ASN R 315 GLN S 47 GLN S 91 ASN S 107 GLN W 173 GLN X 81 HIS ** Y 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 70822 Z= 0.269 Angle : 0.790 50.526 99567 Z= 0.474 Chirality : 0.123 6.367 11638 Planarity : 0.004 0.080 9784 Dihedral : 19.549 167.847 19022 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.59 % Allowed : 11.92 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.11), residues: 6167 helix: 1.77 (0.10), residues: 2945 sheet: 0.51 (0.20), residues: 642 loop : 0.22 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 3 177 HIS 0.007 0.001 HIS 7 52 PHE 0.021 0.001 PHE Y 259 TYR 0.017 0.001 TYR V 91 ARG 0.007 0.000 ARG X 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 706 time to evaluate : 5.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 26 ASN cc_start: 0.8054 (m-40) cc_final: 0.7818 (m110) REVERT: 0 65 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8755 (mt) REVERT: 0 192 ASN cc_start: 0.8847 (t0) cc_final: 0.8505 (t0) REVERT: 1 268 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: 1 288 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6431 (mt-10) REVERT: 4 67 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7883 (mtmm) REVERT: 4 200 ASP cc_start: 0.6485 (OUTLIER) cc_final: 0.6211 (t0) REVERT: 4 507 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: 4 650 MET cc_start: 0.3760 (OUTLIER) cc_final: 0.3367 (mpm) REVERT: 8 83 ASN cc_start: 0.7147 (m-40) cc_final: 0.6933 (m110) REVERT: B 268 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7168 (tt0) REVERT: C 19 ARG cc_start: 0.5019 (mmt-90) cc_final: 0.4208 (tpt-90) REVERT: D 330 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8372 (mmtp) REVERT: G 245 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6899 (tpt90) REVERT: J 36 MET cc_start: 0.9215 (mtp) cc_final: 0.8782 (mtp) REVERT: K 51 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5848 (mmm160) REVERT: O 63 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6751 (tt0) REVERT: O 92 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8508 (mttm) REVERT: O 235 MET cc_start: 0.8863 (tpp) cc_final: 0.8446 (tpt) REVERT: P 87 PHE cc_start: 0.7257 (m-80) cc_final: 0.7011 (m-80) REVERT: R 72 ASP cc_start: 0.7082 (t70) cc_final: 0.6802 (t0) REVERT: R 112 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: R 127 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8068 (tttt) REVERT: R 133 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7452 (mm-30) REVERT: R 344 LEU cc_start: 0.7730 (tt) cc_final: 0.7510 (tt) REVERT: T 9 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8575 (tp) REVERT: T 120 LYS cc_start: 0.7650 (mtpp) cc_final: 0.7400 (tttp) REVERT: U 80 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7657 (ttp-110) REVERT: V 77 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7757 (t0) REVERT: V 358 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6547 (mm-40) REVERT: V 396 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: W 109 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: Y 351 MET cc_start: 0.7115 (mmm) cc_final: 0.6764 (mmm) REVERT: Z 13 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6319 (ttm170) outliers start: 141 outliers final: 57 residues processed: 789 average time/residue: 1.6513 time to fit residues: 1671.8581 Evaluate side-chains 749 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 671 time to evaluate : 5.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 37 ASP Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 239 TRP Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 200 ASP Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 5 residue 326 LEU Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 423 ASP Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 180 GLU Chi-restraints excluded: chain 8 residue 206 PHE Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 51 ARG Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 61 GLN Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Z residue 13 ARG Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 211 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 557 optimal weight: 3.9990 chunk 379 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 498 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 570 optimal weight: 4.9990 chunk 462 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 341 optimal weight: 9.9990 chunk 600 optimal weight: 8.9990 chunk 168 optimal weight: 0.0470 overall best weight: 3.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 179 GLN 0 181 ASN 4 189 ASN 4 417 GLN 4 562 GLN 5 208 HIS ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 319 GLN B 126 GLN B 266 GLN G 318 HIS ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 GLN O 204 ASN R 277 ASN S 47 GLN S 91 ASN S 107 GLN T 14 GLN T 18 GLN ** Y 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 70822 Z= 0.387 Angle : 0.841 50.490 99567 Z= 0.496 Chirality : 0.125 6.435 11638 Planarity : 0.005 0.071 9784 Dihedral : 19.523 166.661 19022 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.25 % Allowed : 12.32 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.11), residues: 6167 helix: 1.57 (0.09), residues: 2954 sheet: 0.46 (0.20), residues: 637 loop : 0.13 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP a 299 HIS 0.008 0.001 HIS 7 52 PHE 0.023 0.002 PHE 5 165 TYR 0.022 0.002 TYR a 322 ARG 0.008 0.001 ARG 7 429 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 689 time to evaluate : 5.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 26 ASN cc_start: 0.8105 (m-40) cc_final: 0.7876 (m110) REVERT: 0 65 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8811 (mt) REVERT: 1 268 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7687 (mt0) REVERT: 1 288 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6471 (mt-10) REVERT: 4 67 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8016 (mtmm) REVERT: 4 262 MET cc_start: 0.5718 (tpt) cc_final: 0.5516 (tpt) REVERT: 4 507 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: 4 650 MET cc_start: 0.3765 (OUTLIER) cc_final: 0.3340 (mpp) REVERT: 5 96 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5932 (mtm) REVERT: 8 83 ASN cc_start: 0.7241 (m-40) cc_final: 0.7032 (m110) REVERT: 8 100 TYR cc_start: 0.7418 (p90) cc_final: 0.7076 (p90) REVERT: 8 319 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7718 (tm130) REVERT: B 204 GLU cc_start: 0.7731 (mp0) cc_final: 0.7516 (mm-30) REVERT: B 268 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: C 19 ARG cc_start: 0.5016 (mmt-90) cc_final: 0.4238 (tpt-90) REVERT: D 330 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8421 (mmtp) REVERT: G 243 ARG cc_start: 0.7429 (mtp180) cc_final: 0.7124 (ttp80) REVERT: G 245 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6907 (tpt90) REVERT: J 36 MET cc_start: 0.9219 (mtp) cc_final: 0.8871 (mtp) REVERT: K 51 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5783 (mmm160) REVERT: O 63 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6775 (tt0) REVERT: O 235 MET cc_start: 0.8854 (tpp) cc_final: 0.8487 (tpt) REVERT: P 87 PHE cc_start: 0.7302 (m-80) cc_final: 0.7026 (m-80) REVERT: R 72 ASP cc_start: 0.7137 (t70) cc_final: 0.6826 (t0) REVERT: R 112 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: R 127 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8115 (tttt) REVERT: T 9 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8642 (tp) REVERT: T 66 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8122 (mpp) REVERT: T 120 LYS cc_start: 0.7579 (mtpp) cc_final: 0.7336 (tttp) REVERT: U 80 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7653 (ttp-110) REVERT: V 77 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7713 (t0) REVERT: V 358 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6506 (mm-40) REVERT: V 396 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7124 (mm-40) REVERT: V 398 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5935 (mt-10) REVERT: W 109 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: Y 351 MET cc_start: 0.7178 (mmm) cc_final: 0.6762 (mmm) REVERT: Z 13 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6314 (ttm170) REVERT: Z 21 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6333 (mm-30) REVERT: a 266 MET cc_start: 0.3413 (mmm) cc_final: 0.3129 (mmm) outliers start: 177 outliers final: 93 residues processed: 795 average time/residue: 1.6248 time to fit residues: 1658.9039 Evaluate side-chains 779 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 662 time to evaluate : 5.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 151 THR Chi-restraints excluded: chain 0 residue 154 THR Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 196 ILE Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 138 ASP Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 506 LEU Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 534 LEU Chi-restraints excluded: chain 4 residue 576 LEU Chi-restraints excluded: chain 4 residue 595 MET Chi-restraints excluded: chain 4 residue 598 LEU Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 170 THR Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 5 residue 228 VAL Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 423 ASP Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 180 GLU Chi-restraints excluded: chain 8 residue 195 SER Chi-restraints excluded: chain 8 residue 206 PHE Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 231 LEU Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain 8 residue 319 GLN Chi-restraints excluded: chain 8 residue 377 THR Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 330 LYS Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 122 LYS Chi-restraints excluded: chain K residue 51 ARG Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 282 ASP Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 65 MET Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 168 ILE Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 13 ARG Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain a residue 128 THR Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 211 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 225 optimal weight: 7.9990 chunk 602 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 392 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 669 optimal weight: 0.0770 chunk 555 optimal weight: 2.9990 chunk 309 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 221 optimal weight: 8.9990 chunk 351 optimal weight: 2.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 179 GLN 0 181 ASN 4 189 ASN 4 417 GLN 4 562 GLN 5 208 HIS 8 199 GLN ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 319 GLN B 64 ASN B 265 GLN B 266 GLN G 318 HIS K 113 HIS O 65 GLN O 204 ASN R 277 ASN R 299 ASN R 315 GLN S 47 GLN S 91 ASN S 107 GLN X 81 HIS ** Y 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 70822 Z= 0.265 Angle : 0.785 50.544 99567 Z= 0.471 Chirality : 0.123 6.365 11638 Planarity : 0.004 0.069 9784 Dihedral : 19.458 169.124 19022 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.83 % Favored : 98.15 % Rotamer: Outliers : 2.50 % Allowed : 13.48 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.11), residues: 6167 helix: 1.81 (0.10), residues: 2958 sheet: 0.51 (0.20), residues: 640 loop : 0.24 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP a 299 HIS 0.008 0.001 HIS 7 52 PHE 0.026 0.001 PHE a 302 TYR 0.023 0.001 TYR a 322 ARG 0.005 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 690 time to evaluate : 5.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8753 (mt) REVERT: 0 192 ASN cc_start: 0.8875 (t0) cc_final: 0.8533 (t0) REVERT: 1 268 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: 1 288 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6452 (mt-10) REVERT: 4 67 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7883 (mtmm) REVERT: 4 262 MET cc_start: 0.5727 (tpt) cc_final: 0.5515 (tpt) REVERT: 4 507 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: 4 650 MET cc_start: 0.3737 (OUTLIER) cc_final: 0.3435 (mpm) REVERT: 5 96 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5882 (mtm) REVERT: 7 241 TYR cc_start: 0.7168 (t80) cc_final: 0.6896 (t80) REVERT: 8 100 TYR cc_start: 0.7323 (p90) cc_final: 0.6977 (p90) REVERT: 8 319 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7775 (tm130) REVERT: B 112 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: B 181 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8409 (tp) REVERT: B 268 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: C 19 ARG cc_start: 0.4988 (mmt-90) cc_final: 0.4223 (tpt-90) REVERT: G 243 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7084 (ttp80) REVERT: J 36 MET cc_start: 0.9210 (mtp) cc_final: 0.8866 (mtp) REVERT: K 51 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5839 (mmm160) REVERT: M 13 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7454 (ttt-90) REVERT: O 63 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: O 99 LYS cc_start: 0.7958 (mttm) cc_final: 0.7744 (mttp) REVERT: O 235 MET cc_start: 0.8854 (tpp) cc_final: 0.8469 (tpt) REVERT: P 87 PHE cc_start: 0.7298 (m-80) cc_final: 0.7037 (m-80) REVERT: R 72 ASP cc_start: 0.7068 (t70) cc_final: 0.6778 (t0) REVERT: R 112 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: R 127 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8091 (tttt) REVERT: R 315 GLN cc_start: 0.5927 (mm-40) cc_final: 0.5713 (mm110) REVERT: R 344 LEU cc_start: 0.7745 (tt) cc_final: 0.7489 (tt) REVERT: T 9 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8661 (tp) REVERT: U 80 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7658 (ttp-110) REVERT: V 77 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7740 (t0) REVERT: V 358 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6471 (mm-40) REVERT: V 396 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6454 (tm-30) REVERT: W 83 MET cc_start: 0.8811 (mtt) cc_final: 0.8514 (mtt) REVERT: W 109 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: Y 351 MET cc_start: 0.7178 (mmm) cc_final: 0.6849 (mmm) REVERT: a 266 MET cc_start: 0.3334 (mmm) cc_final: 0.3039 (mmm) outliers start: 136 outliers final: 60 residues processed: 769 average time/residue: 1.6089 time to fit residues: 1593.1344 Evaluate side-chains 741 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 660 time to evaluate : 5.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 194 GLN Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 239 TRP Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 650 MET Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 5 residue 326 LEU Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 206 PHE Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain 8 residue 319 GLN Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 51 ARG Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 211 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 645 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 381 optimal weight: 0.9990 chunk 488 optimal weight: 6.9990 chunk 378 optimal weight: 2.9990 chunk 563 optimal weight: 6.9990 chunk 373 optimal weight: 1.9990 chunk 666 optimal weight: 20.0000 chunk 417 optimal weight: 6.9990 chunk 406 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 0 32 GLN 0 179 GLN 0 181 ASN 4 189 ASN 4 417 GLN 4 562 GLN 5 208 HIS 8 83 ASN ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 266 GLN K 113 HIS O 65 GLN O 204 ASN R 277 ASN S 47 GLN S 91 ASN S 107 GLN U 117 HIS X 81 HIS ** Y 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 70822 Z= 0.277 Angle : 0.786 50.494 99567 Z= 0.472 Chirality : 0.123 6.368 11638 Planarity : 0.004 0.092 9784 Dihedral : 19.391 171.008 19022 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.99 % Favored : 97.99 % Rotamer: Outliers : 2.48 % Allowed : 13.83 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.11), residues: 6167 helix: 1.86 (0.10), residues: 2956 sheet: 0.55 (0.20), residues: 642 loop : 0.26 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP a 299 HIS 0.008 0.001 HIS 7 52 PHE 0.022 0.001 PHE 7 43 TYR 0.017 0.001 TYR a 322 ARG 0.006 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 680 time to evaluate : 5.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8749 (mt) REVERT: 0 192 ASN cc_start: 0.8821 (t0) cc_final: 0.8485 (t0) REVERT: 1 268 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: 4 67 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7900 (mtmm) REVERT: 4 262 MET cc_start: 0.5693 (tpt) cc_final: 0.5466 (tpt) REVERT: 4 507 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6460 (mp0) REVERT: 4 562 GLN cc_start: 0.5005 (OUTLIER) cc_final: 0.4552 (mm110) REVERT: 4 650 MET cc_start: 0.3738 (ptm) cc_final: 0.3537 (mpp) REVERT: 5 96 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.5876 (mtm) REVERT: 7 241 TYR cc_start: 0.7175 (t80) cc_final: 0.6898 (t80) REVERT: 8 100 TYR cc_start: 0.7257 (p90) cc_final: 0.6940 (p90) REVERT: B 112 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: B 181 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8416 (tp) REVERT: C 19 ARG cc_start: 0.5025 (mmt-90) cc_final: 0.4243 (tpt-90) REVERT: E 100 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: F 47 ASP cc_start: 0.6967 (t0) cc_final: 0.6597 (t70) REVERT: J 36 MET cc_start: 0.9213 (mtp) cc_final: 0.8773 (mtp) REVERT: K 51 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5742 (mmm160) REVERT: M 13 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7435 (ttt-90) REVERT: O 235 MET cc_start: 0.8853 (tpp) cc_final: 0.8480 (tpt) REVERT: P 87 PHE cc_start: 0.7306 (m-80) cc_final: 0.7043 (m-80) REVERT: R 72 ASP cc_start: 0.7074 (t70) cc_final: 0.6792 (t0) REVERT: R 112 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: R 127 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8062 (tttt) REVERT: T 9 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8664 (tp) REVERT: T 66 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8085 (mpp) REVERT: U 80 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7720 (ttp-110) REVERT: V 77 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7720 (t0) REVERT: V 358 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6429 (mm-40) REVERT: V 396 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6454 (tm-30) REVERT: V 398 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5876 (mt-10) REVERT: W 83 MET cc_start: 0.8809 (mtt) cc_final: 0.8514 (mtt) REVERT: W 109 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: Y 351 MET cc_start: 0.7154 (mmm) cc_final: 0.6841 (mmm) REVERT: Z 21 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6295 (mm-30) REVERT: a 266 MET cc_start: 0.3550 (mmm) cc_final: 0.3205 (mmm) outliers start: 135 outliers final: 77 residues processed: 755 average time/residue: 1.6105 time to fit residues: 1569.2541 Evaluate side-chains 756 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 658 time to evaluate : 5.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 194 GLN Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 72 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 161 ILE Chi-restraints excluded: chain 4 residue 183 VAL Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 452 GLN Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 562 GLN Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 5 residue 326 LEU Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 423 ASP Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 206 PHE Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 51 ARG Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain S residue 93 LYS Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 92 LYS Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 211 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 412 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 chunk 398 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 131 optimal weight: 0.0370 chunk 129 optimal weight: 0.9990 chunk 424 optimal weight: 8.9990 chunk 454 optimal weight: 0.8980 chunk 329 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 524 optimal weight: 2.9990 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 0 32 GLN 0 179 GLN 0 181 ASN 4 189 ASN ** 4 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 208 HIS 8 83 ASN ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 266 GLN E 59 ASN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN S 47 GLN S 91 ASN S 107 GLN T 14 GLN ** Y 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 70822 Z= 0.300 Angle : 0.799 50.513 99567 Z= 0.477 Chirality : 0.124 6.376 11638 Planarity : 0.004 0.075 9784 Dihedral : 19.356 171.469 19022 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.08 % Favored : 97.91 % Rotamer: Outliers : 2.59 % Allowed : 14.09 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.11), residues: 6167 helix: 1.82 (0.10), residues: 2954 sheet: 0.55 (0.20), residues: 645 loop : 0.25 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP a 299 HIS 0.008 0.001 HIS 7 52 PHE 0.025 0.001 PHE 7 43 TYR 0.027 0.002 TYR a 322 ARG 0.007 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 677 time to evaluate : 5.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8771 (mt) REVERT: 0 192 ASN cc_start: 0.8881 (t0) cc_final: 0.8559 (t0) REVERT: 1 268 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7626 (mt0) REVERT: 1 288 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6451 (mt-10) REVERT: 4 67 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7920 (mtmm) REVERT: 4 507 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: 4 599 PHE cc_start: 0.5190 (OUTLIER) cc_final: 0.4758 (m-80) REVERT: 4 650 MET cc_start: 0.3768 (ptm) cc_final: 0.3544 (mpp) REVERT: 5 96 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5887 (mtm) REVERT: 7 241 TYR cc_start: 0.7143 (t80) cc_final: 0.6866 (t80) REVERT: 8 100 TYR cc_start: 0.7264 (p90) cc_final: 0.6931 (p90) REVERT: B 181 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8423 (tp) REVERT: C 19 ARG cc_start: 0.5027 (mmt-90) cc_final: 0.4189 (tpp-160) REVERT: E 100 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6848 (mp10) REVERT: F 47 ASP cc_start: 0.6987 (t0) cc_final: 0.6628 (t70) REVERT: G 243 ARG cc_start: 0.7309 (mtp180) cc_final: 0.7055 (ttp80) REVERT: G 256 LEU cc_start: 0.7235 (pp) cc_final: 0.6870 (pt) REVERT: J 36 MET cc_start: 0.9213 (mtp) cc_final: 0.8864 (mtp) REVERT: K 51 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.5777 (mmm160) REVERT: M 13 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7438 (ttt-90) REVERT: O 235 MET cc_start: 0.8851 (tpp) cc_final: 0.8491 (tpt) REVERT: P 87 PHE cc_start: 0.7321 (m-80) cc_final: 0.7045 (m-80) REVERT: R 72 ASP cc_start: 0.7089 (t70) cc_final: 0.6802 (t0) REVERT: R 112 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: R 127 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8086 (tttt) REVERT: R 344 LEU cc_start: 0.7754 (tt) cc_final: 0.7483 (tt) REVERT: T 9 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8674 (tp) REVERT: T 66 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8075 (mpp) REVERT: T 132 ARG cc_start: 0.7797 (mmt-90) cc_final: 0.7579 (tpp-160) REVERT: U 80 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7719 (ttp-110) REVERT: V 77 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7727 (t0) REVERT: V 358 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6476 (mm-40) REVERT: V 396 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6501 (tm-30) REVERT: V 398 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5872 (mt-10) REVERT: W 83 MET cc_start: 0.8819 (mtt) cc_final: 0.8532 (mtt) REVERT: W 109 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: Y 351 MET cc_start: 0.7164 (mmm) cc_final: 0.6778 (mmm) REVERT: Z 21 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6285 (mm-30) REVERT: Z 32 LYS cc_start: 0.7234 (mmmm) cc_final: 0.6777 (tptm) REVERT: Z 65 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6731 (mp) REVERT: a 266 MET cc_start: 0.3553 (mmm) cc_final: 0.3138 (mmm) REVERT: a 301 HIS cc_start: 0.5957 (OUTLIER) cc_final: 0.5697 (m-70) outliers start: 141 outliers final: 82 residues processed: 754 average time/residue: 1.6439 time to fit residues: 1597.8789 Evaluate side-chains 778 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 673 time to evaluate : 5.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 72 VAL Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 183 VAL Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 237 THR Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 452 GLN Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 508 VAL Chi-restraints excluded: chain 4 residue 599 PHE Chi-restraints excluded: chain 4 residue 632 GLU Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 5 residue 326 LEU Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 206 PHE Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 51 ARG Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 92 LYS Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 22 VAL Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 211 THR Chi-restraints excluded: chain a residue 301 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 606 optimal weight: 0.0770 chunk 638 optimal weight: 4.9990 chunk 582 optimal weight: 2.9990 chunk 621 optimal weight: 1.9990 chunk 374 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 488 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 561 optimal weight: 4.9990 chunk 587 optimal weight: 0.7980 chunk 619 optimal weight: 3.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 0 32 GLN 0 111 HIS 0 179 GLN 0 181 ASN ** 4 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 GLN 5 208 HIS 8 83 ASN ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 266 GLN ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 65 GLN R 277 ASN R 315 GLN S 47 GLN S 91 ASN S 107 GLN T 14 GLN T 20 ASN ** Y 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 70822 Z= 0.298 Angle : 0.799 50.493 99567 Z= 0.476 Chirality : 0.123 6.372 11638 Planarity : 0.004 0.077 9784 Dihedral : 19.327 172.020 19022 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.03 % Favored : 97.96 % Rotamer: Outliers : 2.35 % Allowed : 14.31 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.11), residues: 6167 helix: 1.83 (0.10), residues: 2951 sheet: 0.56 (0.20), residues: 645 loop : 0.24 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP a 299 HIS 0.008 0.001 HIS 7 52 PHE 0.026 0.001 PHE 7 43 TYR 0.017 0.001 TYR 5 202 ARG 0.007 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 681 time to evaluate : 5.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8772 (mt) REVERT: 0 192 ASN cc_start: 0.8890 (t0) cc_final: 0.8570 (t0) REVERT: 1 268 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: 1 288 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6445 (mt-10) REVERT: 4 67 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7899 (mtmm) REVERT: 4 507 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: 4 599 PHE cc_start: 0.5218 (OUTLIER) cc_final: 0.4682 (m-80) REVERT: 4 650 MET cc_start: 0.3722 (ptm) cc_final: 0.3493 (mpp) REVERT: 5 96 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5876 (mtm) REVERT: 7 241 TYR cc_start: 0.7128 (t80) cc_final: 0.6857 (t80) REVERT: 8 100 TYR cc_start: 0.7316 (p90) cc_final: 0.6988 (p90) REVERT: B 181 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8425 (tp) REVERT: C 19 ARG cc_start: 0.4990 (mmt-90) cc_final: 0.4199 (tpp-160) REVERT: E 100 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6878 (mp10) REVERT: G 243 ARG cc_start: 0.7315 (mtp180) cc_final: 0.7071 (ttp80) REVERT: G 256 LEU cc_start: 0.7328 (pp) cc_final: 0.6953 (pt) REVERT: J 36 MET cc_start: 0.9211 (mtp) cc_final: 0.8860 (mtp) REVERT: K 51 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5747 (mmm160) REVERT: M 13 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7449 (ttt-90) REVERT: O 63 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6481 (tt0) REVERT: O 235 MET cc_start: 0.8847 (tpp) cc_final: 0.8495 (tpt) REVERT: P 87 PHE cc_start: 0.7327 (m-80) cc_final: 0.7040 (m-80) REVERT: R 72 ASP cc_start: 0.7123 (t70) cc_final: 0.6846 (t0) REVERT: R 112 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: R 127 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8077 (tttt) REVERT: R 315 GLN cc_start: 0.5966 (mm-40) cc_final: 0.5745 (mm110) REVERT: T 9 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8664 (tp) REVERT: T 66 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8012 (mpp) REVERT: T 132 ARG cc_start: 0.7790 (mmt-90) cc_final: 0.7579 (tpp-160) REVERT: U 80 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7720 (ttp-110) REVERT: V 77 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7704 (t0) REVERT: V 358 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6535 (mm-40) REVERT: V 396 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: V 398 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5862 (mt-10) REVERT: W 83 MET cc_start: 0.8823 (mtt) cc_final: 0.8537 (mtt) REVERT: W 109 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: Y 351 MET cc_start: 0.7160 (mmm) cc_final: 0.6774 (mmm) REVERT: Z 21 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6259 (mm-30) REVERT: Z 32 LYS cc_start: 0.7248 (mmmm) cc_final: 0.6900 (tppt) REVERT: Z 65 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6679 (mp) REVERT: a 226 TYR cc_start: 0.4428 (m-10) cc_final: 0.3249 (m-10) REVERT: a 266 MET cc_start: 0.3458 (mmm) cc_final: 0.3036 (mmm) REVERT: a 267 ARG cc_start: 0.4901 (OUTLIER) cc_final: 0.4038 (ppt170) outliers start: 128 outliers final: 80 residues processed: 753 average time/residue: 1.6970 time to fit residues: 1643.5103 Evaluate side-chains 766 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 662 time to evaluate : 5.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 72 VAL Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 183 VAL Chi-restraints excluded: chain 4 residue 192 LEU Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 599 PHE Chi-restraints excluded: chain 4 residue 632 GLU Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 5 residue 326 LEU Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 51 ARG Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 168 ILE Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 92 LYS Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 211 THR Chi-restraints excluded: chain a residue 267 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 408 optimal weight: 0.9980 chunk 657 optimal weight: 9.9990 chunk 401 optimal weight: 0.9980 chunk 311 optimal weight: 8.9990 chunk 456 optimal weight: 2.9990 chunk 689 optimal weight: 5.9990 chunk 634 optimal weight: 1.9990 chunk 548 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 424 optimal weight: 8.9990 chunk 336 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 0 32 GLN 0 179 GLN 1 321 ASN ** 4 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 562 GLN 5 208 HIS 8 83 ASN ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 265 GLN B 266 GLN K 113 HIS R 277 ASN S 47 GLN S 91 ASN S 107 GLN T 14 GLN T 20 ASN ** Y 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 301 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 70822 Z= 0.277 Angle : 0.791 50.513 99567 Z= 0.473 Chirality : 0.123 6.366 11638 Planarity : 0.004 0.078 9784 Dihedral : 19.292 173.364 19022 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.04 % Favored : 97.94 % Rotamer: Outliers : 2.13 % Allowed : 14.69 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.11), residues: 6167 helix: 1.90 (0.10), residues: 2947 sheet: 0.58 (0.20), residues: 645 loop : 0.29 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP a 299 HIS 0.009 0.001 HIS 7 52 PHE 0.028 0.001 PHE 7 43 TYR 0.017 0.001 TYR 5 202 ARG 0.008 0.000 ARG H 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12334 Ramachandran restraints generated. 6167 Oldfield, 0 Emsley, 6167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 670 time to evaluate : 5.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 65 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8746 (mt) REVERT: 0 192 ASN cc_start: 0.8845 (t0) cc_final: 0.8522 (t0) REVERT: 1 268 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: 1 288 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6433 (mt-10) REVERT: 4 67 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7870 (mtmm) REVERT: 4 507 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: 4 562 GLN cc_start: 0.5096 (OUTLIER) cc_final: 0.3860 (pp30) REVERT: 4 599 PHE cc_start: 0.5104 (OUTLIER) cc_final: 0.4531 (m-80) REVERT: 4 650 MET cc_start: 0.3678 (ptm) cc_final: 0.3452 (mpp) REVERT: 5 96 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5948 (mtm) REVERT: 7 241 TYR cc_start: 0.7086 (t80) cc_final: 0.6791 (t80) REVERT: 8 100 TYR cc_start: 0.7338 (p90) cc_final: 0.7028 (p90) REVERT: B 181 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8424 (tp) REVERT: C 19 ARG cc_start: 0.5026 (mmt-90) cc_final: 0.4187 (tpp-160) REVERT: E 100 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6902 (mp10) REVERT: G 243 ARG cc_start: 0.7298 (mtp180) cc_final: 0.7051 (ttp80) REVERT: G 256 LEU cc_start: 0.7317 (pp) cc_final: 0.6939 (pt) REVERT: J 36 MET cc_start: 0.9211 (mtp) cc_final: 0.8861 (mtp) REVERT: K 51 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5721 (mmm160) REVERT: M 13 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7441 (ttt-90) REVERT: O 63 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6279 (tm-30) REVERT: O 235 MET cc_start: 0.8845 (tpp) cc_final: 0.8500 (tpt) REVERT: P 87 PHE cc_start: 0.7329 (m-80) cc_final: 0.7067 (m-80) REVERT: R 72 ASP cc_start: 0.7138 (t70) cc_final: 0.6883 (t0) REVERT: R 112 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: R 127 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8061 (tttt) REVERT: T 9 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8656 (tp) REVERT: T 66 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8018 (mpp) REVERT: T 132 ARG cc_start: 0.7786 (mmt-90) cc_final: 0.7576 (tpp-160) REVERT: U 80 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7720 (ttp-110) REVERT: V 77 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7695 (t0) REVERT: V 358 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6466 (mm-40) REVERT: V 396 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: V 398 GLU cc_start: 0.6200 (OUTLIER) cc_final: 0.5876 (mt-10) REVERT: W 83 MET cc_start: 0.8804 (mtt) cc_final: 0.8512 (mtt) REVERT: Y 351 MET cc_start: 0.7148 (mmm) cc_final: 0.6765 (mmm) REVERT: Z 21 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6224 (mm-30) REVERT: Z 32 LYS cc_start: 0.7265 (mmmm) cc_final: 0.6950 (tppt) REVERT: a 266 MET cc_start: 0.3315 (mmm) cc_final: 0.2929 (mmm) REVERT: a 267 ARG cc_start: 0.4881 (OUTLIER) cc_final: 0.4172 (ppt170) outliers start: 116 outliers final: 73 residues processed: 737 average time/residue: 1.6479 time to fit residues: 1564.7452 Evaluate side-chains 747 residues out of total 5530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 651 time to evaluate : 5.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 LEU Chi-restraints excluded: chain 0 residue 65 LEU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 62 VAL Chi-restraints excluded: chain 1 residue 72 VAL Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 268 GLN Chi-restraints excluded: chain 1 residue 288 GLU Chi-restraints excluded: chain 4 residue 58 VAL Chi-restraints excluded: chain 4 residue 67 LYS Chi-restraints excluded: chain 4 residue 149 ILE Chi-restraints excluded: chain 4 residue 293 THR Chi-restraints excluded: chain 4 residue 297 LEU Chi-restraints excluded: chain 4 residue 322 HIS Chi-restraints excluded: chain 4 residue 401 MET Chi-restraints excluded: chain 4 residue 507 GLU Chi-restraints excluded: chain 4 residue 562 GLN Chi-restraints excluded: chain 4 residue 599 PHE Chi-restraints excluded: chain 4 residue 632 GLU Chi-restraints excluded: chain 4 residue 655 ILE Chi-restraints excluded: chain 5 residue 70 THR Chi-restraints excluded: chain 5 residue 96 MET Chi-restraints excluded: chain 5 residue 202 TYR Chi-restraints excluded: chain 5 residue 275 GLU Chi-restraints excluded: chain 5 residue 326 LEU Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 322 LEU Chi-restraints excluded: chain 7 residue 343 THR Chi-restraints excluded: chain 7 residue 440 LEU Chi-restraints excluded: chain 7 residue 441 THR Chi-restraints excluded: chain 8 residue 90 LEU Chi-restraints excluded: chain 8 residue 105 LEU Chi-restraints excluded: chain 8 residue 210 GLU Chi-restraints excluded: chain 8 residue 224 VAL Chi-restraints excluded: chain 8 residue 265 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain K residue 51 ARG Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 113 LYS Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain O residue 63 GLU Chi-restraints excluded: chain O residue 92 LYS Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 53 SER Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 153 THR Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain T residue 9 ILE Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain U residue 128 GLU Chi-restraints excluded: chain U residue 168 ILE Chi-restraints excluded: chain V residue 77 ASP Chi-restraints excluded: chain V residue 358 GLN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 396 GLN Chi-restraints excluded: chain V residue 398 GLU Chi-restraints excluded: chain W residue 82 SER Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 81 HIS Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 182 LEU Chi-restraints excluded: chain X residue 233 VAL Chi-restraints excluded: chain Y residue 252 THR Chi-restraints excluded: chain Y residue 258 ILE Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 21 GLU Chi-restraints excluded: chain Z residue 40 LEU Chi-restraints excluded: chain a residue 164 ILE Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 267 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 436 optimal weight: 0.6980 chunk 584 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 506 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 549 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 564 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN 0 32 GLN 0 179 GLN 1 321 ASN ** 4 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 285 ASN 4 562 GLN 5 208 HIS 8 83 ASN ** 8 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 266 GLN K 113 HIS O 65 GLN R 277 ASN S 47 GLN S 91 ASN S 107 GLN T 14 GLN T 20 ASN X 81 HIS ** Y 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 301 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.152778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118388 restraints weight = 95966.334| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.47 r_work: 0.3355 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 70822 Z= 0.242 Angle : 0.775 50.530 99567 Z= 0.466 Chirality : 0.122 6.337 11638 Planarity : 0.004 0.073 9784 Dihedral : 19.236 176.067 19022 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.91 % Favored : 98.07 % Rotamer: Outliers : 1.62 % Allowed : 15.35 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.11), residues: 6167 helix: 2.06 (0.10), residues: 2936 sheet: 0.63 (0.20), residues: 644 loop : 0.39 (0.13), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP a 191 HIS 0.009 0.001 HIS 7 52 PHE 0.027 0.001 PHE 7 43 TYR 0.016 0.001 TYR 5 202 ARG 0.012 0.000 ARG a 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26608.08 seconds wall clock time: 454 minutes 22.40 seconds (27262.40 seconds total)