Starting phenix.real_space_refine on Tue Feb 20 01:35:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egb_28113/02_2024/8egb_28113_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egb_28113/02_2024/8egb_28113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egb_28113/02_2024/8egb_28113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egb_28113/02_2024/8egb_28113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egb_28113/02_2024/8egb_28113_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8egb_28113/02_2024/8egb_28113_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 69 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 16356 2.51 5 N 4653 2.21 5 O 5233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 136": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 67": "OE1" <-> "OE2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I GLU 386": "OE1" <-> "OE2" Residue "I GLU 546": "OE1" <-> "OE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I GLU 825": "OE1" <-> "OE2" Residue "I GLU 947": "OE1" <-> "OE2" Residue "I GLU 1089": "OE1" <-> "OE2" Residue "I GLU 1194": "OE1" <-> "OE2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 443": "OE1" <-> "OE2" Residue "J GLU 556": "OE1" <-> "OE2" Residue "J GLU 658": "OE1" <-> "OE2" Residue "J GLU 660": "OE1" <-> "OE2" Residue "J GLU 993": "OE1" <-> "OE2" Residue "J GLU 1334": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26419 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 548 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "B" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 9} Chain: "G" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1684 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10555 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 10360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10360 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1278} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 79} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'1N7': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 2} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15796 SG CYS J 70 111.274 60.694 69.590 1.00 94.03 S ATOM 15810 SG CYS J 72 112.697 57.286 69.070 1.00 98.26 S ATOM 15918 SG CYS J 85 113.603 60.145 66.663 1.00 97.17 S ATOM 15942 SG CYS J 88 110.111 58.865 66.547 1.00 95.31 S ATOM 21618 SG CYS J 814 85.843 121.267 78.728 1.00 66.05 S ATOM 22183 SG CYS J 888 85.083 117.612 77.772 1.00 61.83 S ATOM 22234 SG CYS J 895 85.780 118.577 81.374 1.00 58.10 S ATOM 22255 SG CYS J 898 82.613 119.711 79.946 1.00 57.60 S Time building chain proxies: 14.24, per 1000 atoms: 0.54 Number of scatterers: 26419 At special positions: 0 Unit cell: (143, 159.9, 166.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 105 16.00 P 69 15.00 Mg 1 11.99 O 5233 8.00 N 4653 7.00 C 16356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.99 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " Number of angles added : 12 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5900 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 30 sheets defined 32.3% alpha, 11.4% beta 30 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 13.49 Creating SS restraints... Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 86 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 231 removed outlier: 4.217A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 228 removed outlier: 3.526A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 39 removed outlier: 3.638A pdb=" N PHE I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 Processing helix chain 'I' and resid 271 through 280 Processing helix chain 'I' and resid 291 through 294 removed outlier: 3.716A pdb=" N GLY I 294 " --> pdb=" O TYR I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 291 through 294' Processing helix chain 'I' and resid 319 through 326 Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.831A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 448 through 450 No H-bonds generated for 'chain 'I' and resid 448 through 450' Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.670A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 507 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 552 through 554 No H-bonds generated for 'chain 'I' and resid 552 through 554' Processing helix chain 'I' and resid 608 through 613 removed outlier: 3.643A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 613' Processing helix chain 'I' and resid 665 through 667 No H-bonds generated for 'chain 'I' and resid 665 through 667' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 676 through 688 removed outlier: 3.947A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 943 through 980 Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1104 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1168 through 1176 Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1239 through 1241 No H-bonds generated for 'chain 'I' and resid 1239 through 1241' Processing helix chain 'I' and resid 1272 through 1280 Processing helix chain 'I' and resid 1285 through 1291 Processing helix chain 'I' and resid 1298 through 1310 Processing helix chain 'I' and resid 1321 through 1332 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 181 through 190 Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 212 through 229 removed outlier: 3.589A pdb=" N LYS J 222 " --> pdb=" O THR J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 247 through 250 Processing helix chain 'J' and resid 264 through 284 Processing helix chain 'J' and resid 289 through 306 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 337 through 341 Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 406 through 416 removed outlier: 4.367A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 452 through 457 Processing helix chain 'J' and resid 474 through 483 Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 580 Processing helix chain 'J' and resid 589 through 592 Processing helix chain 'J' and resid 598 through 611 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 648 through 669 removed outlier: 3.887A pdb=" N HIS J 651 " --> pdb=" O GLU J 648 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU J 652 " --> pdb=" O LYS J 649 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE J 654 " --> pdb=" O HIS J 651 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN J 669 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 741 Processing helix chain 'J' and resid 769 through 803 removed outlier: 4.594A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 866 through 874 Processing helix chain 'J' and resid 896 through 899 No H-bonds generated for 'chain 'J' and resid 896 through 899' Processing helix chain 'J' and resid 916 through 929 Proline residue: J 926 - end of helix removed outlier: 3.564A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1138 through 1146 Processing helix chain 'J' and resid 1217 through 1223 Processing helix chain 'J' and resid 1226 through 1243 removed outlier: 3.522A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1260 Processing helix chain 'J' and resid 1282 through 1294 Processing helix chain 'J' and resid 1309 through 1314 Processing helix chain 'J' and resid 1319 through 1324 Processing helix chain 'J' and resid 1328 through 1338 Processing helix chain 'J' and resid 1348 through 1353 Processing helix chain 'J' and resid 1362 through 1372 Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 61 through 83 Processing sheet with id= A, first strand: chain 'G' and resid 12 through 16 removed outlier: 7.156A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.547A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 151 through 153 removed outlier: 3.580A pdb=" N VAL G 153 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.953A pdb=" N GLY G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 12 through 18 removed outlier: 7.524A pdb=" N THR H 27 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE H 16 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS H 25 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN H 18 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS H 23 " --> pdb=" O GLN H 18 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU H 198 " --> pdb=" O ALA H 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 97 through 104 removed outlier: 3.712A pdb=" N ARG H 143 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.781A pdb=" N GLY H 108 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU H 133 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= I, first strand: chain 'I' and resid 117 through 123 removed outlier: 3.763A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= K, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.633A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= M, first strand: chain 'I' and resid 603 through 607 removed outlier: 3.524A pdb=" N THR I 589 " --> pdb=" O LEU I 606 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= O, first strand: chain 'I' and resid 749 through 751 removed outlier: 3.835A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.322A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET I1230 " --> pdb=" O MET I 800 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET I 800 " --> pdb=" O MET I1230 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 830 through 839 removed outlier: 3.799A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.370A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.529A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 145 through 147 removed outlier: 3.655A pdb=" N VAL J 145 " --> pdb=" O LYS J 179 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= V, first strand: chain 'J' and resid 547 through 553 Processing sheet with id= W, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= X, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.691A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= Z, first strand: chain 'J' and resid 1024 through 1026 Processing sheet with id= AA, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.573A pdb=" N VAL J1081 " --> pdb=" O PHE J1034 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 1046 through 1050 removed outlier: 3.708A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AD, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.623A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 11.52 Time building geometry restraints manager: 11.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4461 1.29 - 1.43: 6499 1.43 - 1.56: 15655 1.56 - 1.69: 153 1.69 - 1.83: 188 Bond restraints: 26956 Sorted by residual: bond pdb=" C19 1N7 I1402 " pdb=" C3 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.827 -0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.822 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C3 1N7 I1401 " pdb=" C4 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.728 -0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C3 1N7 I1402 " pdb=" C4 1N7 I1402 " ideal model delta sigma weight residual 1.532 1.728 -0.196 2.00e-02 2.50e+03 9.59e+01 bond pdb=" C7 1N7 I1401 " pdb=" C8 1N7 I1401 " ideal model delta sigma weight residual 1.542 1.702 -0.160 2.00e-02 2.50e+03 6.41e+01 ... (remaining 26951 not shown) Histogram of bond angle deviations from ideal: 97.08 - 104.46: 624 104.46 - 111.84: 12943 111.84 - 119.21: 9779 119.21 - 126.59: 12971 126.59 - 133.97: 410 Bond angle restraints: 36727 Sorted by residual: angle pdb=" CA PRO I 897 " pdb=" N PRO I 897 " pdb=" CD PRO I 897 " ideal model delta sigma weight residual 112.00 103.37 8.63 1.40e+00 5.10e-01 3.80e+01 angle pdb=" N ASP I 915 " pdb=" CA ASP I 915 " pdb=" C ASP I 915 " ideal model delta sigma weight residual 108.23 117.37 -9.14 1.72e+00 3.38e-01 2.82e+01 angle pdb=" C3' DC A 5 " pdb=" O3' DC A 5 " pdb=" P DC A 6 " ideal model delta sigma weight residual 120.20 128.03 -7.83 1.50e+00 4.44e-01 2.72e+01 angle pdb=" N ALA J 315 " pdb=" CA ALA J 315 " pdb=" C ALA J 315 " ideal model delta sigma weight residual 109.59 102.29 7.30 1.47e+00 4.63e-01 2.47e+01 angle pdb=" C4' DG A 7 " pdb=" C3' DG A 7 " pdb=" O3' DG A 7 " ideal model delta sigma weight residual 110.00 116.58 -6.58 1.50e+00 4.44e-01 1.92e+01 ... (remaining 36722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 16164 35.86 - 71.72: 350 71.72 - 107.57: 22 107.57 - 143.43: 0 143.43 - 179.29: 2 Dihedral angle restraints: 16538 sinusoidal: 7365 harmonic: 9173 Sorted by residual: dihedral pdb=" N ASN J 309 " pdb=" C ASN J 309 " pdb=" CA ASN J 309 " pdb=" CB ASN J 309 " ideal model delta harmonic sigma weight residual 122.80 111.70 11.10 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" CA SER H 20 " pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta harmonic sigma weight residual -180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" C PRO I 897 " pdb=" N PRO I 897 " pdb=" CA PRO I 897 " pdb=" CB PRO I 897 " ideal model delta harmonic sigma weight residual -120.70 -130.91 10.21 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 16535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3949 0.094 - 0.187: 262 0.187 - 0.281: 8 0.281 - 0.374: 2 0.374 - 0.468: 1 Chirality restraints: 4222 Sorted by residual: chirality pdb=" CA PRO I 897 " pdb=" N PRO I 897 " pdb=" C PRO I 897 " pdb=" CB PRO I 897 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.85 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C19 1N7 I1402 " pdb=" C18 1N7 I1402 " pdb=" C2 1N7 I1402 " pdb=" C3 1N7 I1402 " both_signs ideal model delta sigma weight residual False -2.53 -2.85 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 4219 not shown) Planarity restraints: 4556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 896 " 0.097 5.00e-02 4.00e+02 1.44e-01 3.30e+01 pdb=" N PRO I 897 " -0.248 5.00e-02 4.00e+02 pdb=" CA PRO I 897 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO I 897 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 892 " -0.026 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C GLU I 892 " 0.088 2.00e-02 2.50e+03 pdb=" O GLU I 892 " -0.033 2.00e-02 2.50e+03 pdb=" N THR I 893 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 515 " -0.384 9.50e-02 1.11e+02 1.73e-01 1.94e+01 pdb=" NE ARG J 515 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG J 515 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG J 515 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG J 515 " -0.007 2.00e-02 2.50e+03 ... (remaining 4553 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 290 2.58 - 3.16: 22845 3.16 - 3.74: 40179 3.74 - 4.32: 55039 4.32 - 4.90: 91549 Nonbonded interactions: 209902 Sorted by model distance: nonbonded pdb=" O LEU J 930 " pdb=" OG1 THR J 931 " model vdw 2.001 2.440 nonbonded pdb=" O GLN I1288 " pdb=" OG1 THR I1292 " model vdw 2.011 2.440 nonbonded pdb=" O3' G R 16 " pdb="MG MG J1501 " model vdw 2.014 2.170 nonbonded pdb=" OE1 GLU I 50 " pdb=" OH TYR I 70 " model vdw 2.027 2.440 nonbonded pdb=" O ASP I 516 " pdb=" OG SER I 522 " model vdw 2.038 2.440 ... (remaining 209897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.280 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 84.610 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 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 : 0.006 0.295 26956 Z= 0.378 Angle : 0.625 10.884 36727 Z= 0.345 Chirality : 0.045 0.468 4222 Planarity : 0.005 0.173 4556 Dihedral : 14.583 179.289 10638 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.72 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 0.18 % Favored : 99.70 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3179 helix: 1.47 (0.16), residues: 1086 sheet: -0.38 (0.28), residues: 364 loop : -1.42 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 115 HIS 0.011 0.001 HIS I1023 PHE 0.015 0.001 PHE J 719 TYR 0.015 0.001 TYR I1281 ARG 0.024 0.001 ARG J 311 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 352 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.7933 (m110) cc_final: 0.7373 (m110) REVERT: I 286 GLU cc_start: 0.6824 (mt-10) cc_final: 0.5475 (pm20) REVERT: I 337 PHE cc_start: 0.8182 (t80) cc_final: 0.7973 (t80) REVERT: I 403 MET cc_start: 0.8097 (ttt) cc_final: 0.7896 (ttp) REVERT: I 515 MET cc_start: 0.8131 (ttp) cc_final: 0.7771 (ttt) REVERT: J 869 CYS cc_start: 0.8264 (m) cc_final: 0.7901 (m) REVERT: J 870 ASP cc_start: 0.7505 (m-30) cc_final: 0.7274 (m-30) outliers start: 3 outliers final: 1 residues processed: 355 average time/residue: 0.3433 time to fit residues: 199.8794 Evaluate side-chains 266 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 917 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 3.9990 chunk 245 optimal weight: 8.9990 chunk 136 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 253 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 294 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 147 GLN H 37 HIS H 66 HIS H 75 GLN H 132 HIS H 194 GLN I 69 GLN I 150 HIS I 165 HIS I 620 ASN I 799 ASN ** J 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 545 HIS J1244 GLN K 61 ASN K 73 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 26956 Z= 0.208 Angle : 0.539 9.197 36727 Z= 0.280 Chirality : 0.042 0.215 4222 Planarity : 0.004 0.141 4556 Dihedral : 13.551 174.824 4432 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.09 % Rotamer: Outliers : 1.03 % Allowed : 7.27 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3179 helix: 1.54 (0.16), residues: 1083 sheet: -0.50 (0.27), residues: 377 loop : -1.33 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 115 HIS 0.023 0.001 HIS I 165 PHE 0.011 0.001 PHE I1221 TYR 0.018 0.001 TYR J1365 ARG 0.005 0.000 ARG I 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 297 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 188 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7501 (pt0) REVERT: H 66 HIS cc_start: 0.6892 (OUTLIER) cc_final: 0.6477 (m-70) REVERT: H 84 ASN cc_start: 0.8052 (m110) cc_final: 0.7352 (m110) REVERT: I 70 TYR cc_start: 0.7569 (t80) cc_final: 0.6978 (t80) REVERT: I 115 LYS cc_start: 0.6301 (mtmt) cc_final: 0.5590 (mtmm) REVERT: I 202 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7573 (ttp-110) REVERT: I 286 GLU cc_start: 0.7047 (mt-10) cc_final: 0.5559 (pm20) REVERT: I 370 MET cc_start: 0.7637 (mmm) cc_final: 0.7153 (mmm) REVERT: I 427 ASP cc_start: 0.7896 (m-30) cc_final: 0.7481 (m-30) REVERT: I 545 PHE cc_start: 0.7274 (m-80) cc_final: 0.7062 (m-80) REVERT: I 1170 MET cc_start: 0.8190 (tpt) cc_final: 0.7967 (tpp) REVERT: J 21 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7470 (tttm) REVERT: J 198 CYS cc_start: 0.7953 (t) cc_final: 0.7583 (t) REVERT: J 484 MET cc_start: 0.8604 (mtt) cc_final: 0.8078 (mtt) REVERT: J 869 CYS cc_start: 0.8411 (m) cc_final: 0.7965 (m) REVERT: J 870 ASP cc_start: 0.7402 (m-30) cc_final: 0.7164 (m-30) REVERT: K 60 ASN cc_start: 0.8308 (p0) cc_final: 0.7907 (p0) outliers start: 28 outliers final: 15 residues processed: 310 average time/residue: 0.3707 time to fit residues: 187.2173 Evaluate side-chains 280 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 264 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 66 HIS Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 777 HIS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 81 optimal weight: 40.0000 chunk 294 optimal weight: 7.9990 chunk 318 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 292 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 chunk 236 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS H 66 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 GLN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS J1023 HIS K 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 26956 Z= 0.324 Angle : 0.581 9.999 36727 Z= 0.301 Chirality : 0.043 0.234 4222 Planarity : 0.004 0.137 4556 Dihedral : 13.735 173.952 4431 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.34 % Rotamer: Outliers : 1.85 % Allowed : 9.78 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3179 helix: 1.27 (0.16), residues: 1098 sheet: -0.60 (0.28), residues: 363 loop : -1.39 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 686 HIS 0.020 0.001 HIS I 165 PHE 0.017 0.002 PHE J 620 TYR 0.021 0.001 TYR J1365 ARG 0.004 0.000 ARG K 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 272 time to evaluate : 3.404 Fit side-chains revert: symmetry clash REVERT: G 227 GLN cc_start: 0.8731 (mm110) cc_final: 0.8515 (mm110) REVERT: H 84 ASN cc_start: 0.8229 (m110) cc_final: 0.7486 (m110) REVERT: I 119 GLU cc_start: 0.7283 (pm20) cc_final: 0.7053 (pm20) REVERT: I 202 ARG cc_start: 0.8287 (ttp-110) cc_final: 0.7685 (ttp-110) REVERT: I 286 GLU cc_start: 0.7048 (mt-10) cc_final: 0.5438 (pm20) REVERT: I 351 LEU cc_start: 0.8214 (mt) cc_final: 0.7972 (mt) REVERT: I 369 MET cc_start: 0.7278 (tmm) cc_final: 0.7020 (tmm) REVERT: I 370 MET cc_start: 0.7514 (mmm) cc_final: 0.6757 (mmm) REVERT: I 488 MET cc_start: 0.3040 (mmt) cc_final: 0.2820 (mmt) REVERT: I 962 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: I 1170 MET cc_start: 0.8251 (tpt) cc_final: 0.7999 (tpp) REVERT: J 21 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7691 (tttm) REVERT: J 52 GLU cc_start: 0.5830 (mm-30) cc_final: 0.5496 (mm-30) REVERT: J 100 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7863 (tm-30) REVERT: J 198 CYS cc_start: 0.8021 (t) cc_final: 0.7654 (t) REVERT: J 660 GLU cc_start: 0.6682 (mm-30) cc_final: 0.6434 (mm-30) REVERT: J 869 CYS cc_start: 0.8428 (m) cc_final: 0.7950 (m) REVERT: J 870 ASP cc_start: 0.7504 (m-30) cc_final: 0.7234 (m-30) REVERT: K 62 GLN cc_start: 0.7366 (tm-30) cc_final: 0.6963 (tp40) outliers start: 50 outliers final: 28 residues processed: 301 average time/residue: 0.3669 time to fit residues: 181.3161 Evaluate side-chains 285 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 256 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 313 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS H 66 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 649 GLN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 26956 Z= 0.276 Angle : 0.547 9.888 36727 Z= 0.284 Chirality : 0.042 0.191 4222 Planarity : 0.004 0.133 4556 Dihedral : 13.786 173.828 4431 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 1.99 % Allowed : 12.33 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3179 helix: 1.29 (0.16), residues: 1085 sheet: -0.57 (0.28), residues: 352 loop : -1.31 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 686 HIS 0.018 0.001 HIS I 165 PHE 0.016 0.001 PHE J 668 TYR 0.021 0.001 TYR J1365 ARG 0.004 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 271 time to evaluate : 2.920 Fit side-chains revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8271 (m110) cc_final: 0.7461 (m110) REVERT: I 70 TYR cc_start: 0.7828 (t80) cc_final: 0.7532 (t80) REVERT: I 119 GLU cc_start: 0.7404 (pm20) cc_final: 0.7123 (pm20) REVERT: I 202 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7578 (ttp-110) REVERT: I 286 GLU cc_start: 0.7061 (mt-10) cc_final: 0.5416 (pm20) REVERT: I 351 LEU cc_start: 0.8195 (mt) cc_final: 0.7781 (mt) REVERT: I 370 MET cc_start: 0.7545 (mmm) cc_final: 0.7196 (mmm) REVERT: I 419 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8791 (mt) REVERT: I 962 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: I 1170 MET cc_start: 0.8218 (tpt) cc_final: 0.8017 (tpp) REVERT: J 52 GLU cc_start: 0.5700 (mm-30) cc_final: 0.5260 (mm-30) REVERT: J 100 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7775 (tm-30) REVERT: J 198 CYS cc_start: 0.8046 (t) cc_final: 0.7690 (t) REVERT: J 264 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8338 (t70) REVERT: J 298 MET cc_start: 0.7569 (mmp) cc_final: 0.7362 (mmt) REVERT: J 576 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7920 (mtt180) REVERT: J 777 HIS cc_start: 0.8234 (m-70) cc_final: 0.7753 (t-90) REVERT: J 869 CYS cc_start: 0.8413 (m) cc_final: 0.7926 (m) REVERT: J 870 ASP cc_start: 0.7358 (m-30) cc_final: 0.7073 (m-30) outliers start: 54 outliers final: 32 residues processed: 303 average time/residue: 0.3637 time to fit residues: 178.6940 Evaluate side-chains 295 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 260 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 264 ASP Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 233 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS H 75 GLN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1218 HIS K 61 ASN K 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 26956 Z= 0.225 Angle : 0.530 10.350 36727 Z= 0.272 Chirality : 0.041 0.196 4222 Planarity : 0.004 0.128 4556 Dihedral : 13.754 173.752 4431 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 2.18 % Allowed : 13.51 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3179 helix: 1.38 (0.16), residues: 1088 sheet: -0.39 (0.28), residues: 351 loop : -1.35 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 686 HIS 0.017 0.001 HIS I 165 PHE 0.023 0.001 PHE J 668 TYR 0.024 0.001 TYR J1365 ARG 0.004 0.000 ARG J1174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 283 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 84 ASN cc_start: 0.8253 (m110) cc_final: 0.7403 (m110) REVERT: I 129 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9005 (mm) REVERT: I 202 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.7564 (ttp-110) REVERT: I 286 GLU cc_start: 0.6947 (mt-10) cc_final: 0.5252 (pm20) REVERT: I 351 LEU cc_start: 0.8261 (mt) cc_final: 0.7846 (mt) REVERT: I 419 ILE cc_start: 0.9038 (pt) cc_final: 0.8831 (mt) REVERT: I 962 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: I 1170 MET cc_start: 0.8240 (tpt) cc_final: 0.7997 (tpp) REVERT: J 21 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7624 (tttm) REVERT: J 52 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5496 (mm-30) REVERT: J 100 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7953 (tm-30) REVERT: J 198 CYS cc_start: 0.8034 (t) cc_final: 0.7673 (t) REVERT: J 270 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8073 (ttp80) REVERT: J 298 MET cc_start: 0.7553 (mmp) cc_final: 0.7352 (mmt) REVERT: J 484 MET cc_start: 0.8734 (mtt) cc_final: 0.8246 (mtt) REVERT: J 576 ARG cc_start: 0.8373 (mtt90) cc_final: 0.8029 (mtt180) REVERT: J 777 HIS cc_start: 0.8261 (m-70) cc_final: 0.7762 (t-90) REVERT: J 869 CYS cc_start: 0.8427 (m) cc_final: 0.7919 (m) REVERT: J 870 ASP cc_start: 0.7358 (m-30) cc_final: 0.7060 (m-30) REVERT: K 55 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7556 (tm-30) outliers start: 59 outliers final: 35 residues processed: 320 average time/residue: 0.3671 time to fit residues: 191.4901 Evaluate side-chains 293 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 256 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 714 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 1.9990 chunk 282 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 313 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 103 optimal weight: 0.0010 chunk 164 optimal weight: 0.1980 overall best weight: 0.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 GLN H 75 GLN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 73 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.094 26956 Z= 0.144 Angle : 0.497 10.839 36727 Z= 0.254 Chirality : 0.040 0.214 4222 Planarity : 0.004 0.128 4556 Dihedral : 13.677 173.689 4431 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 1.59 % Allowed : 14.95 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3179 helix: 1.68 (0.16), residues: 1083 sheet: -0.28 (0.29), residues: 341 loop : -1.24 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I1276 HIS 0.015 0.001 HIS I 165 PHE 0.022 0.001 PHE J 668 TYR 0.020 0.001 TYR J1365 ARG 0.005 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 306 time to evaluate : 3.135 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8256 (mttt) cc_final: 0.8055 (mtmt) REVERT: H 84 ASN cc_start: 0.8249 (m110) cc_final: 0.7586 (m-40) REVERT: H 208 ASN cc_start: 0.8125 (p0) cc_final: 0.7921 (p0) REVERT: I 286 GLU cc_start: 0.7257 (mt-10) cc_final: 0.5459 (pm20) REVERT: I 351 LEU cc_start: 0.8303 (mt) cc_final: 0.7811 (mt) REVERT: I 419 ILE cc_start: 0.8994 (pt) cc_final: 0.8751 (mt) REVERT: I 427 ASP cc_start: 0.7808 (m-30) cc_final: 0.7343 (m-30) REVERT: I 488 MET cc_start: 0.2897 (mmt) cc_final: 0.2496 (mmt) REVERT: I 545 PHE cc_start: 0.7077 (m-80) cc_final: 0.6864 (m-80) REVERT: I 688 GLN cc_start: 0.7943 (mt0) cc_final: 0.7730 (mt0) REVERT: I 781 ASP cc_start: 0.7444 (t0) cc_final: 0.7200 (t70) REVERT: I 947 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: I 962 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: I 1170 MET cc_start: 0.8161 (tpt) cc_final: 0.7716 (tpp) REVERT: J 21 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7754 (tttm) REVERT: J 100 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7918 (tm-30) REVERT: J 198 CYS cc_start: 0.8023 (t) cc_final: 0.7668 (t) REVERT: J 236 TRP cc_start: 0.8971 (m-10) cc_final: 0.8452 (m-10) REVERT: J 270 ARG cc_start: 0.8656 (ttm110) cc_final: 0.8122 (ttp80) REVERT: J 412 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8533 (tt) REVERT: J 484 MET cc_start: 0.8498 (mtt) cc_final: 0.7928 (mtt) REVERT: J 576 ARG cc_start: 0.8294 (mtt90) cc_final: 0.8048 (mtt180) REVERT: J 697 MET cc_start: 0.8159 (tmm) cc_final: 0.7790 (tmm) REVERT: J 777 HIS cc_start: 0.8127 (m-70) cc_final: 0.7713 (t-90) REVERT: J 869 CYS cc_start: 0.8533 (m) cc_final: 0.8012 (m) REVERT: J 870 ASP cc_start: 0.7309 (m-30) cc_final: 0.6997 (m-30) REVERT: J 1349 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7111 (mt-10) REVERT: K 3 ARG cc_start: 0.6295 (mmm-85) cc_final: 0.6092 (mmm160) REVERT: K 55 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7310 (tm-30) outliers start: 43 outliers final: 24 residues processed: 331 average time/residue: 0.3790 time to fit residues: 202.2845 Evaluate side-chains 293 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 947 GLU Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 372 MET Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 263 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 ASN K 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 26956 Z= 0.284 Angle : 0.554 12.317 36727 Z= 0.282 Chirality : 0.042 0.208 4222 Planarity : 0.004 0.121 4556 Dihedral : 13.780 173.561 4431 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.02 % Rotamer: Outliers : 1.81 % Allowed : 15.98 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3179 helix: 1.44 (0.16), residues: 1103 sheet: -0.49 (0.28), residues: 366 loop : -1.32 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 686 HIS 0.013 0.001 HIS I 165 PHE 0.027 0.001 PHE J 668 TYR 0.023 0.001 TYR J1365 ARG 0.007 0.000 ARG J 744 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 269 time to evaluate : 3.070 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8300 (mttt) cc_final: 0.8098 (mtmt) REVERT: H 84 ASN cc_start: 0.8271 (m110) cc_final: 0.7584 (m-40) REVERT: H 145 LYS cc_start: 0.8246 (tptp) cc_final: 0.7884 (tptt) REVERT: I 286 GLU cc_start: 0.7029 (mt-10) cc_final: 0.5128 (pm20) REVERT: I 351 LEU cc_start: 0.8284 (mt) cc_final: 0.7828 (mt) REVERT: I 369 MET cc_start: 0.7346 (ppp) cc_final: 0.7045 (ppp) REVERT: I 370 MET cc_start: 0.7526 (mmm) cc_final: 0.6785 (mmm) REVERT: I 419 ILE cc_start: 0.9046 (pt) cc_final: 0.8792 (mt) REVERT: I 488 MET cc_start: 0.2994 (mmt) cc_final: 0.2565 (mmt) REVERT: I 962 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: I 1170 MET cc_start: 0.8160 (tpt) cc_final: 0.7908 (tpp) REVERT: J 21 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7767 (tttm) REVERT: J 100 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7903 (tm-30) REVERT: J 198 CYS cc_start: 0.8046 (t) cc_final: 0.7700 (t) REVERT: J 218 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7913 (p) REVERT: J 270 ARG cc_start: 0.8612 (ttm110) cc_final: 0.8094 (ttp80) REVERT: J 412 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8543 (tt) REVERT: J 479 GLU cc_start: 0.7839 (tp30) cc_final: 0.7385 (tp30) REVERT: J 777 HIS cc_start: 0.8083 (m-70) cc_final: 0.7779 (t-90) REVERT: J 869 CYS cc_start: 0.8557 (m) cc_final: 0.8054 (m) REVERT: J 870 ASP cc_start: 0.7380 (m-30) cc_final: 0.7079 (m-30) REVERT: J 1349 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6771 (mt-10) outliers start: 49 outliers final: 35 residues processed: 303 average time/residue: 0.3807 time to fit residues: 186.3531 Evaluate side-chains 297 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 259 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1061 GLN Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 245 optimal weight: 0.3980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 ASN K 61 ASN K 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 26956 Z= 0.203 Angle : 0.526 11.360 36727 Z= 0.266 Chirality : 0.041 0.197 4222 Planarity : 0.004 0.117 4556 Dihedral : 13.752 173.137 4431 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 1.66 % Allowed : 16.91 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3179 helix: 1.49 (0.16), residues: 1094 sheet: -0.52 (0.28), residues: 351 loop : -1.24 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I1276 HIS 0.012 0.001 HIS I 165 PHE 0.030 0.001 PHE I 337 TYR 0.022 0.001 TYR J1365 ARG 0.003 0.000 ARG J 744 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 269 time to evaluate : 3.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8244 (mttt) cc_final: 0.8034 (mtmt) REVERT: H 84 ASN cc_start: 0.8221 (m110) cc_final: 0.7534 (m-40) REVERT: H 145 LYS cc_start: 0.8239 (tptp) cc_final: 0.7873 (tptt) REVERT: H 208 ASN cc_start: 0.8148 (p0) cc_final: 0.7948 (p0) REVERT: I 286 GLU cc_start: 0.7061 (mt-10) cc_final: 0.5172 (pm20) REVERT: I 351 LEU cc_start: 0.8281 (mt) cc_final: 0.7822 (mt) REVERT: I 419 ILE cc_start: 0.9014 (pt) cc_final: 0.8745 (mt) REVERT: I 427 ASP cc_start: 0.7890 (m-30) cc_final: 0.7485 (m-30) REVERT: I 488 MET cc_start: 0.2981 (mmt) cc_final: 0.2602 (mmt) REVERT: I 562 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8329 (tm-30) REVERT: I 947 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: I 962 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: I 1170 MET cc_start: 0.8134 (tpt) cc_final: 0.7895 (tpp) REVERT: J 100 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7882 (tm-30) REVERT: J 198 CYS cc_start: 0.8047 (t) cc_final: 0.7723 (t) REVERT: J 270 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8117 (ttp80) REVERT: J 412 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8533 (tt) REVERT: J 479 GLU cc_start: 0.7725 (tp30) cc_final: 0.7303 (tp30) REVERT: J 484 MET cc_start: 0.8645 (mtt) cc_final: 0.8154 (mtt) REVERT: J 697 MET cc_start: 0.8165 (tmm) cc_final: 0.7825 (tmm) REVERT: J 777 HIS cc_start: 0.8243 (m-70) cc_final: 0.7772 (t-90) REVERT: J 869 CYS cc_start: 0.8555 (m) cc_final: 0.8037 (m) REVERT: J 870 ASP cc_start: 0.7372 (m-30) cc_final: 0.7055 (m-30) REVERT: J 1349 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6759 (mt-10) outliers start: 45 outliers final: 35 residues processed: 299 average time/residue: 0.3744 time to fit residues: 181.6270 Evaluate side-chains 297 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 259 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 739 ASP Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 947 GLU Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1061 GLN Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 273 ILE Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 958 ILE Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 5.9990 chunk 299 optimal weight: 8.9990 chunk 272 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 175 optimal weight: 7.9990 chunk 126 optimal weight: 0.0770 chunk 228 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 275 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 ASN K 61 ASN K 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 26956 Z= 0.345 Angle : 0.606 13.680 36727 Z= 0.309 Chirality : 0.043 0.206 4222 Planarity : 0.004 0.115 4556 Dihedral : 13.910 172.754 4431 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.61 % Favored : 93.36 % Rotamer: Outliers : 2.10 % Allowed : 16.69 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3179 helix: 1.23 (0.16), residues: 1090 sheet: -0.62 (0.28), residues: 349 loop : -1.38 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 686 HIS 0.012 0.001 HIS I 165 PHE 0.033 0.002 PHE I 337 TYR 0.026 0.002 TYR J1365 ARG 0.004 0.000 ARG I 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 267 time to evaluate : 2.991 Fit side-chains revert: symmetry clash REVERT: G 95 LYS cc_start: 0.8316 (mttt) cc_final: 0.8110 (mtmt) REVERT: I 351 LEU cc_start: 0.8269 (mt) cc_final: 0.7813 (mt) REVERT: I 419 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8847 (mt) REVERT: I 455 SER cc_start: 0.9025 (m) cc_final: 0.8800 (t) REVERT: I 562 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8340 (tm-30) REVERT: I 947 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: I 962 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: J 100 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7928 (tm-30) REVERT: J 198 CYS cc_start: 0.8138 (t) cc_final: 0.7786 (t) REVERT: J 412 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8535 (tt) REVERT: J 668 PHE cc_start: 0.3659 (t80) cc_final: 0.3252 (t80) REVERT: J 762 ASN cc_start: 0.8936 (p0) cc_final: 0.8696 (p0) REVERT: J 777 HIS cc_start: 0.8140 (m-70) cc_final: 0.7815 (t-90) REVERT: J 869 CYS cc_start: 0.8554 (m) cc_final: 0.8057 (m) REVERT: J 870 ASP cc_start: 0.7379 (m-30) cc_final: 0.7060 (m-30) REVERT: J 1349 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6782 (mt-10) outliers start: 57 outliers final: 47 residues processed: 308 average time/residue: 0.3720 time to fit residues: 189.2392 Evaluate side-chains 313 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 262 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 234 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 947 GLU Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1061 GLN Chi-restraints excluded: chain I residue 1072 ASN Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 273 ILE Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 578 ILE Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 6.9990 chunk 307 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 322 optimal weight: 1.9990 chunk 297 optimal weight: 8.9990 chunk 257 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 198 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 26956 Z= 0.164 Angle : 0.520 11.492 36727 Z= 0.265 Chirality : 0.041 0.221 4222 Planarity : 0.004 0.111 4556 Dihedral : 13.745 171.784 4431 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 1.73 % Allowed : 17.31 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3179 helix: 1.49 (0.16), residues: 1086 sheet: -0.48 (0.28), residues: 356 loop : -1.32 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I1276 HIS 0.012 0.001 HIS I 165 PHE 0.031 0.001 PHE I 337 TYR 0.021 0.001 TYR J1365 ARG 0.010 0.000 ARG J1173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6358 Ramachandran restraints generated. 3179 Oldfield, 0 Emsley, 3179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 282 time to evaluate : 3.199 Fit side-chains REVERT: G 8 PHE cc_start: 0.7274 (m-80) cc_final: 0.7059 (m-10) REVERT: G 95 LYS cc_start: 0.8274 (mttt) cc_final: 0.8010 (mtmt) REVERT: H 84 ASN cc_start: 0.8212 (m110) cc_final: 0.7586 (m-40) REVERT: I 351 LEU cc_start: 0.8260 (mt) cc_final: 0.7800 (mt) REVERT: I 419 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8692 (mt) REVERT: I 427 ASP cc_start: 0.7837 (m-30) cc_final: 0.7418 (m-30) REVERT: I 488 MET cc_start: 0.3036 (mmt) cc_final: 0.2560 (mmt) REVERT: I 562 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8273 (tm-30) REVERT: I 781 ASP cc_start: 0.7498 (t0) cc_final: 0.7247 (t70) REVERT: I 947 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: I 962 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: I 1170 MET cc_start: 0.8225 (tpt) cc_final: 0.7968 (tpp) REVERT: J 21 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7748 (tttm) REVERT: J 100 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7879 (tm-30) REVERT: J 198 CYS cc_start: 0.8111 (t) cc_final: 0.7757 (t) REVERT: J 270 ARG cc_start: 0.8632 (ttm110) cc_final: 0.8142 (ttp80) REVERT: J 412 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8521 (tt) REVERT: J 479 GLU cc_start: 0.7574 (tp30) cc_final: 0.7062 (tp30) REVERT: J 668 PHE cc_start: 0.3860 (t80) cc_final: 0.3474 (t80) REVERT: J 697 MET cc_start: 0.8294 (tmm) cc_final: 0.7931 (tmm) REVERT: J 744 ARG cc_start: 0.8132 (ptm-80) cc_final: 0.7840 (ptm160) REVERT: J 777 HIS cc_start: 0.8185 (m-70) cc_final: 0.7732 (t-90) REVERT: J 869 CYS cc_start: 0.8550 (m) cc_final: 0.8030 (m) REVERT: J 870 ASP cc_start: 0.7372 (m-30) cc_final: 0.7047 (m-30) REVERT: J 1349 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6856 (mt-10) outliers start: 47 outliers final: 32 residues processed: 314 average time/residue: 0.3639 time to fit residues: 185.6133 Evaluate side-chains 306 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 270 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 215 TYR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 947 GLU Chi-restraints excluded: chain I residue 962 GLU Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1163 THR Chi-restraints excluded: chain I residue 1199 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain J residue 85 CYS Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 151 MET Chi-restraints excluded: chain J residue 154 LEU Chi-restraints excluded: chain J residue 412 LEU Chi-restraints excluded: chain J residue 466 MET Chi-restraints excluded: chain J residue 513 MET Chi-restraints excluded: chain J residue 604 MET Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 66 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 5.9990 chunk 273 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 237 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 257 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 HIS H 103 ASN J 762 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.139318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103730 restraints weight = 42992.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.105234 restraints weight = 25413.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105272 restraints weight = 19069.351| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 26956 Z= 0.201 Angle : 0.532 11.358 36727 Z= 0.270 Chirality : 0.041 0.212 4222 Planarity : 0.004 0.108 4556 Dihedral : 13.759 171.812 4431 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 1.81 % Allowed : 17.39 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3179 helix: 1.51 (0.16), residues: 1093 sheet: -0.57 (0.28), residues: 356 loop : -1.32 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 686 HIS 0.012 0.001 HIS I 165 PHE 0.028 0.001 PHE I 337 TYR 0.022 0.001 TYR J1365 ARG 0.003 0.000 ARG G 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4725.21 seconds wall clock time: 87 minutes 33.41 seconds (5253.41 seconds total)