Starting phenix.real_space_refine on Wed Feb 21 07:48:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py7_13715/02_2024/7py7_13715.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py7_13715/02_2024/7py7_13715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py7_13715/02_2024/7py7_13715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py7_13715/02_2024/7py7_13715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py7_13715/02_2024/7py7_13715.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7py7_13715/02_2024/7py7_13715.pdb" } resolution = 4.1 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= 0.009 sd= 0.063 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 113 5.16 5 C 18500 2.51 5 N 5380 2.21 5 O 5935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1020": "OE1" <-> "OE2" Residue "C ASP 1064": "OD1" <-> "OD2" Residue "C ASP 1088": "OD1" <-> "OD2" Residue "C ASP 1126": "OD1" <-> "OD2" Residue "C PHE 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1279": "OE1" <-> "OE2" Residue "C TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "G GLU 41": "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: 30000 Number of models: 1 Model: "" Number of chains: 11 Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "T" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 630 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 235 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 8} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1699 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'PTRANS': 55, 'TRANS': 1279} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "G" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 987 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 4, 'ASP:plan': 42, 'PHE:plan': 14, 'GLU:plan': 56, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 830 Chain: "D" 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 16061 SG CYS D 88 83.689 109.793 73.304 1.00206.22 S ATOM 21749 SG CYS D 814 92.870 42.365 76.295 1.00151.01 S ATOM 22314 SG CYS D 888 94.486 45.902 76.118 1.00134.73 S ATOM 22365 SG CYS D 895 93.360 44.565 79.349 1.00142.38 S ATOM 22386 SG CYS D 898 96.234 42.910 77.889 1.00135.85 S Time building chain proxies: 15.83, per 1000 atoms: 0.53 Number of scatterers: 30000 At special positions: 0 Unit cell: (187.48, 154.78, 168.95, 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 113 16.00 P 69 15.00 Mg 1 11.99 O 5935 8.00 N 5380 7.00 C 18500 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: 12.47 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " Number of angles added : 6 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7094 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 49 sheets defined 37.4% alpha, 14.0% beta 29 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 10.58 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.841A pdb=" N LEU A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.975A pdb=" N GLU A 162 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 3.533A pdb=" N ALA A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.843A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.703A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.672A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.775A pdb=" N ARG C 10 " --> pdb=" O GLU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.792A pdb=" N GLY C 45 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN C 46 " --> pdb=" O PRO C 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 42 through 46' Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.797A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.514A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.503A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 4.071A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 614 Processing helix chain 'C' and resid 657 through 661 removed outlier: 3.613A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.681A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.512A pdb=" N ALA C 679 " --> pdb=" O ASP C 675 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 3.824A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 907 removed outlier: 3.545A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 984 removed outlier: 3.732A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 984 " --> pdb=" O VAL C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 removed outlier: 3.574A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 999 Processing helix chain 'C' and resid 1005 through 1035 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 3.853A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.862A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.720A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP C1150 " --> pdb=" O GLN C1146 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1175 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.531A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.786A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 4.095A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C1310 " --> pdb=" O LYS C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.025A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.705A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.667A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 263 through 285 removed outlier: 4.289A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 405 through 416 removed outlier: 4.283A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.800A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.680A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 648 through 670 removed outlier: 4.619A pdb=" N GLU D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 658 " --> pdb=" O ILE D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 704 removed outlier: 4.013A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU D 704 " --> pdb=" O ASN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.116A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.556A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.545A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 3.683A pdb=" N ASP D1073 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1244 removed outlier: 3.921A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL D1226 " --> pdb=" O ARG D1222 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N HIS D1227 " --> pdb=" O LEU D1223 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.368A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1325 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.267A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.666A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.511A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 90 Processing helix chain 'G' and resid 18 through 34 Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.528A pdb=" N VAL G 108 " --> pdb=" O SER G 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 10 Processing helix chain 'F' and resid 19 through 39 removed outlier: 3.943A pdb=" N ALA F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 128 removed outlier: 4.007A pdb=" N GLN F 112 " --> pdb=" O GLN F 108 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL F 115 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU F 120 " --> pdb=" O GLN F 116 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 126 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 134 removed outlier: 3.873A pdb=" N GLU F 134 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 208 removed outlier: 4.357A pdb=" N LEU F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 266 removed outlier: 3.719A pdb=" N GLU F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 314 removed outlier: 3.670A pdb=" N LEU F 314 " --> pdb=" O ALA F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 329 Processing helix chain 'F' and resid 342 through 351 removed outlier: 4.556A pdb=" N HIS F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 362 removed outlier: 4.078A pdb=" N ALA F 355 " --> pdb=" O GLU F 351 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE F 359 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR F 360 " --> pdb=" O ILE F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 370 removed outlier: 3.711A pdb=" N PHE F 369 " --> pdb=" O ASP F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 removed outlier: 4.047A pdb=" N GLU F 404 " --> pdb=" O PRO F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 425 removed outlier: 4.033A pdb=" N SER F 424 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU F 425 " --> pdb=" O GLU F 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 421 through 425' Processing helix chain 'F' and resid 443 through 447 removed outlier: 3.918A pdb=" N PHE F 446 " --> pdb=" O ASP F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 459 removed outlier: 4.387A pdb=" N ASP F 458 " --> pdb=" O THR F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 479 removed outlier: 3.632A pdb=" N ALA F 478 " --> pdb=" O THR F 474 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY F 479 " --> pdb=" O ASP F 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 474 through 479' Processing helix chain 'F' and resid 479 through 487 removed outlier: 4.089A pdb=" N MET F 483 " --> pdb=" O GLY F 479 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA F 484 " --> pdb=" O ALA F 480 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 485 " --> pdb=" O LEU F 481 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG F 486 " --> pdb=" O ILE F 482 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN F 487 " --> pdb=" O MET F 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 479 through 487' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 4.159A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 104 removed outlier: 3.777A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.766A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 17 removed outlier: 6.911A pdb=" N THR B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE B 16 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS B 25 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 28 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 201 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 104 removed outlier: 7.892A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.629A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.864A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.807A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 284 through 285 removed outlier: 4.893A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.763A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 303 removed outlier: 6.775A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 599 through 606 removed outlier: 6.256A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC1, first strand: chain 'C' and resid 749 through 752 removed outlier: 4.098A pdb=" N ILE C 732 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C 722 " --> pdb=" O VAL C 777 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.702A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.464A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.738A pdb=" N GLY C 846 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.149A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AC9, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.728A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA D 467 " --> pdb=" O ASN D 424 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN D 424 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.728A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 4.032A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 112 removed outlier: 4.066A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.736A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 253 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.547A pdb=" N LYS D 566 " --> pdb=" O GLU D 554 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.687A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 849 through 850 removed outlier: 3.744A pdb=" N ASP D 855 " --> pdb=" O LYS D 850 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.928A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 991 through 996 removed outlier: 3.677A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1024 through 1028 removed outlier: 4.241A pdb=" N ALA D1122 " --> pdb=" O VAL D1027 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 4.270A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AE8, first strand: chain 'D' and resid 1187 through 1190 Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.803A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 42 through 43 removed outlier: 3.852A pdb=" N LEU G 70 " --> pdb=" O MET G 43 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY G 91 " --> pdb=" O GLN G 13 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 47 through 49 Processing sheet with id=AF3, first strand: chain 'F' and resid 138 through 141 removed outlier: 3.740A pdb=" N GLY F 181 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 152 through 154 removed outlier: 3.577A pdb=" N ALA F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL F 197 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL F 161 " --> pdb=" O VAL F 197 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 3060 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 15.94 Time building geometry restraints manager: 13.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9389 1.33 - 1.46: 4679 1.46 - 1.58: 16153 1.58 - 1.70: 134 1.70 - 1.82: 198 Bond restraints: 30553 Sorted by residual: bond pdb=" C ARG A 166 " pdb=" N PRO A 167 " ideal model delta sigma weight residual 1.330 1.382 -0.051 1.19e-02 7.06e+03 1.87e+01 bond pdb=" N PRO G 45 " pdb=" CA PRO G 45 " ideal model delta sigma weight residual 1.469 1.514 -0.045 1.22e-02 6.72e+03 1.37e+01 bond pdb=" C VAL G 44 " pdb=" N PRO G 45 " ideal model delta sigma weight residual 1.333 1.373 -0.040 1.17e-02 7.31e+03 1.16e+01 bond pdb=" N VAL D 357 " pdb=" CA VAL D 357 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.93e+00 bond pdb=" N TYR D 360 " pdb=" CA TYR D 360 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.01e+00 ... (remaining 30548 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.01: 744 105.01 - 112.28: 15534 112.28 - 119.54: 10496 119.54 - 126.80: 14472 126.80 - 134.06: 411 Bond angle restraints: 41657 Sorted by residual: angle pdb=" C VAL G 44 " pdb=" N PRO G 45 " pdb=" CA PRO G 45 " ideal model delta sigma weight residual 119.90 126.68 -6.78 1.05e+00 9.07e-01 4.17e+01 angle pdb=" CB MET C 239 " pdb=" CG MET C 239 " pdb=" SD MET C 239 " ideal model delta sigma weight residual 112.70 99.77 12.93 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C ALA C 910 " pdb=" N SER C 911 " pdb=" CA SER C 911 " ideal model delta sigma weight residual 121.70 128.96 -7.26 1.80e+00 3.09e-01 1.63e+01 angle pdb=" C LEU C 946 " pdb=" N GLU C 947 " pdb=" CA GLU C 947 " ideal model delta sigma weight residual 121.14 114.20 6.94 1.75e+00 3.27e-01 1.57e+01 angle pdb=" C LYS C1035 " pdb=" N ILE C1036 " pdb=" CA ILE C1036 " ideal model delta sigma weight residual 121.97 128.50 -6.53 1.80e+00 3.09e-01 1.32e+01 ... (remaining 41652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 18089 35.44 - 70.89: 466 70.89 - 106.33: 29 106.33 - 141.78: 2 141.78 - 177.22: 2 Dihedral angle restraints: 18588 sinusoidal: 7585 harmonic: 11003 Sorted by residual: dihedral pdb=" CA LYS C1035 " pdb=" C LYS C1035 " pdb=" N ILE C1036 " pdb=" CA ILE C1036 " ideal model delta harmonic sigma weight residual -180.00 -143.83 -36.17 0 5.00e+00 4.00e-02 5.23e+01 dihedral pdb=" CA LYS G 7 " pdb=" C LYS G 7 " pdb=" N ARG G 8 " pdb=" CA ARG G 8 " ideal model delta harmonic sigma weight residual -180.00 -155.30 -24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA GLU C 44 " pdb=" C GLU C 44 " pdb=" N GLY C 45 " pdb=" CA GLY C 45 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 18585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3295 0.039 - 0.077: 1077 0.077 - 0.116: 391 0.116 - 0.154: 55 0.154 - 0.193: 10 Chirality restraints: 4828 Sorted by residual: chirality pdb=" CB ILE C 572 " pdb=" CA ILE C 572 " pdb=" CG1 ILE C 572 " pdb=" CG2 ILE C 572 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CA MET C 488 " pdb=" N MET C 488 " pdb=" C MET C 488 " pdb=" CB MET C 488 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA ASP C 199 " pdb=" N ASP C 199 " pdb=" C ASP C 199 " pdb=" CB ASP C 199 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 4825 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C1229 " -0.021 2.00e-02 2.50e+03 2.31e-02 1.07e+01 pdb=" CG TYR C1229 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR C1229 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C1229 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C1229 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C1229 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C1229 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C1229 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 165 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C GLU A 165 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU A 165 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 166 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO C 552 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " 0.027 5.00e-02 4.00e+02 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 559 2.66 - 3.22: 28807 3.22 - 3.78: 46999 3.78 - 4.34: 59839 4.34 - 4.90: 93981 Nonbonded interactions: 230185 Sorted by model distance: nonbonded pdb=" OG1 THR C1286 " pdb=" OE2 GLU D 479 " model vdw 2.097 2.440 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1502 " model vdw 2.151 2.310 nonbonded pdb=" O LYS C 324 " pdb=" OG SER C 328 " model vdw 2.156 2.440 nonbonded pdb=" OE1 GLN C1268 " pdb=" OG SER D 350 " model vdw 2.162 2.440 nonbonded pdb=" OH TYR D1186 " pdb=" OE1 GLU D1188 " model vdw 2.181 2.440 ... (remaining 230180 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 'A' and (resid 7 through 158 or resid 170 through 234)) selection = (chain 'B' and resid 7 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.270 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 94.640 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.170 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:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 0.003 0.053 30553 Z= 0.205 Angle : 0.646 12.928 41657 Z= 0.342 Chirality : 0.044 0.193 4828 Planarity : 0.004 0.049 5268 Dihedral : 15.459 177.220 11494 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.23 % Rotamer: Outliers : 0.04 % Allowed : 0.28 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3812 helix: -0.02 (0.15), residues: 1219 sheet: -0.67 (0.24), residues: 436 loop : -1.67 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 115 HIS 0.004 0.001 HIS D 104 PHE 0.033 0.001 PHE C1025 TYR 0.056 0.001 TYR C1229 ARG 0.011 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7930 (p) cc_final: 0.7309 (p) REVERT: C 130 MET cc_start: 0.8735 (mmm) cc_final: 0.8414 (mmm) REVERT: C 239 MET cc_start: 0.8807 (mmm) cc_final: 0.8355 (mmm) REVERT: C 315 MET cc_start: 0.8633 (ttp) cc_final: 0.8276 (ptm) REVERT: C 403 MET cc_start: 0.9220 (tmm) cc_final: 0.8851 (tmm) REVERT: C 681 MET cc_start: 0.8803 (ttp) cc_final: 0.7697 (ptp) REVERT: C 685 MET cc_start: 0.8914 (ptp) cc_final: 0.8260 (ptp) REVERT: C 704 MET cc_start: 0.8787 (mmp) cc_final: 0.8577 (mmp) REVERT: C 760 ASN cc_start: 0.8165 (m110) cc_final: 0.7781 (m110) REVERT: C 1034 ARG cc_start: 0.9110 (tmm160) cc_final: 0.8815 (ttp80) REVERT: C 1151 LEU cc_start: 0.8633 (tp) cc_final: 0.8400 (tp) REVERT: D 343 LEU cc_start: 0.9523 (mt) cc_final: 0.9101 (mt) REVERT: D 484 MET cc_start: 0.7829 (mpp) cc_final: 0.7420 (mpp) REVERT: D 625 MET cc_start: 0.8640 (ttp) cc_final: 0.8350 (tmm) REVERT: D 644 MET cc_start: 0.8384 (mpp) cc_final: 0.7663 (mpp) REVERT: D 1156 LEU cc_start: 0.9199 (mp) cc_final: 0.8917 (mp) REVERT: D 1189 MET cc_start: 0.8974 (tpp) cc_final: 0.8639 (mmm) REVERT: E 43 ASN cc_start: 0.9146 (t0) cc_final: 0.8904 (t0) REVERT: E 62 GLN cc_start: 0.9753 (tt0) cc_final: 0.9099 (tm-30) REVERT: G 29 HIS cc_start: 0.8778 (m90) cc_final: 0.8475 (m90) REVERT: G 35 MET cc_start: 0.6600 (mpp) cc_final: 0.6159 (mpp) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.3670 time to fit residues: 161.8314 Evaluate side-chains 194 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 0.5980 chunk 293 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 197 optimal weight: 0.0980 chunk 156 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 184 optimal weight: 0.2980 chunk 225 optimal weight: 0.9990 chunk 351 optimal weight: 40.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 276 GLN C 573 ASN C 824 GLN C1288 GLN D 448 GLN D1326 GLN E 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30553 Z= 0.134 Angle : 0.524 9.267 41657 Z= 0.277 Chirality : 0.041 0.166 4828 Planarity : 0.003 0.045 5268 Dihedral : 13.401 178.805 4950 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.62 % Favored : 95.33 % Rotamer: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3812 helix: 0.39 (0.15), residues: 1284 sheet: -0.63 (0.23), residues: 473 loop : -1.67 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.004 0.001 HIS C1023 PHE 0.016 0.001 PHE C1164 TYR 0.041 0.001 TYR C1229 ARG 0.009 0.000 ARG C 275 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7997 (p) cc_final: 0.7464 (p) REVERT: C 47 TYR cc_start: 0.1802 (m-80) cc_final: 0.0817 (m-80) REVERT: C 239 MET cc_start: 0.8930 (mmm) cc_final: 0.8299 (mmm) REVERT: C 315 MET cc_start: 0.8608 (ttp) cc_final: 0.8272 (ptm) REVERT: C 403 MET cc_start: 0.9168 (tmm) cc_final: 0.8770 (tmm) REVERT: C 488 MET cc_start: 0.8917 (tpt) cc_final: 0.8557 (tpt) REVERT: C 681 MET cc_start: 0.8871 (ttp) cc_final: 0.7856 (ptp) REVERT: C 685 MET cc_start: 0.8885 (ptp) cc_final: 0.8409 (ptp) REVERT: C 704 MET cc_start: 0.8753 (mmp) cc_final: 0.8497 (mmp) REVERT: C 760 ASN cc_start: 0.8002 (m110) cc_final: 0.7668 (m110) REVERT: C 930 ASP cc_start: 0.7356 (t70) cc_final: 0.7077 (t0) REVERT: C 1034 ARG cc_start: 0.9131 (tmm160) cc_final: 0.8745 (ttp80) REVERT: C 1151 LEU cc_start: 0.8655 (tp) cc_final: 0.8420 (tp) REVERT: C 1230 MET cc_start: 0.8755 (ppp) cc_final: 0.8076 (ppp) REVERT: C 1232 MET cc_start: 0.7974 (mmm) cc_final: 0.7748 (mmt) REVERT: C 1274 GLU cc_start: 0.8917 (pm20) cc_final: 0.8670 (pm20) REVERT: C 1290 MET cc_start: 0.9223 (tpp) cc_final: 0.8750 (mmp) REVERT: C 1319 MET cc_start: 0.8674 (tmm) cc_final: 0.7829 (tmm) REVERT: D 180 MET cc_start: 0.7423 (tmm) cc_final: 0.6544 (ttp) REVERT: D 298 MET cc_start: 0.9269 (ttp) cc_final: 0.9026 (ttp) REVERT: D 484 MET cc_start: 0.8184 (mpp) cc_final: 0.7647 (mpp) REVERT: D 625 MET cc_start: 0.8688 (ttp) cc_final: 0.8203 (tmm) REVERT: D 644 MET cc_start: 0.8239 (mpp) cc_final: 0.7612 (mpp) REVERT: D 718 SER cc_start: 0.8660 (t) cc_final: 0.8393 (m) REVERT: D 743 MET cc_start: 0.8175 (ppp) cc_final: 0.7581 (ppp) REVERT: D 1260 MET cc_start: 0.8814 (mmm) cc_final: 0.8324 (tpp) REVERT: D 1349 GLU cc_start: 0.8209 (pm20) cc_final: 0.7491 (pm20) REVERT: E 43 ASN cc_start: 0.9141 (t0) cc_final: 0.8725 (t0) REVERT: G 29 HIS cc_start: 0.8821 (m90) cc_final: 0.8425 (m90) REVERT: G 35 MET cc_start: 0.6674 (mpp) cc_final: 0.6134 (mpp) REVERT: G 43 MET cc_start: 0.6473 (mmm) cc_final: 0.6031 (mmm) outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.3679 time to fit residues: 175.4139 Evaluate side-chains 207 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 292 optimal weight: 30.0000 chunk 239 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 352 optimal weight: 40.0000 chunk 380 optimal weight: 8.9990 chunk 313 optimal weight: 4.9990 chunk 349 optimal weight: 20.0000 chunk 120 optimal weight: 0.3980 chunk 282 optimal weight: 20.0000 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 628 HIS C 649 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS C1209 GLN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 30553 Z= 0.440 Angle : 0.723 16.188 41657 Z= 0.379 Chirality : 0.045 0.271 4828 Planarity : 0.005 0.061 5268 Dihedral : 13.779 174.320 4950 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.29 % Favored : 92.65 % Rotamer: Outliers : 0.14 % Allowed : 6.40 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3812 helix: 0.21 (0.14), residues: 1266 sheet: -1.00 (0.23), residues: 459 loop : -1.80 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 580 HIS 0.007 0.002 HIS C 551 PHE 0.018 0.002 PHE C 390 TYR 0.034 0.002 TYR C1229 ARG 0.015 0.001 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 238 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.9388 (m-10) cc_final: 0.9170 (m-10) REVERT: C 130 MET cc_start: 0.8748 (mmm) cc_final: 0.8401 (mmm) REVERT: C 239 MET cc_start: 0.9047 (mmm) cc_final: 0.8672 (mmm) REVERT: C 403 MET cc_start: 0.9260 (tmm) cc_final: 0.8740 (tmm) REVERT: C 488 MET cc_start: 0.9050 (tpt) cc_final: 0.8820 (tpt) REVERT: C 659 GLN cc_start: 0.9168 (pp30) cc_final: 0.8800 (pp30) REVERT: C 674 ASP cc_start: 0.9191 (m-30) cc_final: 0.8824 (m-30) REVERT: C 681 MET cc_start: 0.9071 (ttp) cc_final: 0.7950 (ptm) REVERT: C 685 MET cc_start: 0.8820 (ptp) cc_final: 0.8309 (ptp) REVERT: C 704 MET cc_start: 0.9090 (mmp) cc_final: 0.8776 (mmp) REVERT: C 760 ASN cc_start: 0.8567 (m110) cc_final: 0.8198 (m110) REVERT: C 785 ASP cc_start: 0.8967 (p0) cc_final: 0.8735 (p0) REVERT: C 1066 MET cc_start: 0.8782 (ppp) cc_final: 0.8486 (ppp) REVERT: C 1101 LEU cc_start: 0.9419 (mm) cc_final: 0.9120 (mm) REVERT: C 1107 MET cc_start: 0.8420 (mpp) cc_final: 0.8002 (mmt) REVERT: C 1151 LEU cc_start: 0.8790 (tp) cc_final: 0.8409 (tp) REVERT: C 1243 MET cc_start: 0.9334 (tmm) cc_final: 0.8754 (tmm) REVERT: C 1272 GLU cc_start: 0.7756 (tt0) cc_final: 0.7444 (tt0) REVERT: C 1275 VAL cc_start: 0.9397 (t) cc_final: 0.9106 (t) REVERT: D 298 MET cc_start: 0.9441 (ttp) cc_final: 0.9082 (ptm) REVERT: D 343 LEU cc_start: 0.9389 (mt) cc_final: 0.9132 (mt) REVERT: D 484 MET cc_start: 0.8228 (mpp) cc_final: 0.7772 (mtm) REVERT: D 485 MET cc_start: 0.8328 (mtt) cc_final: 0.8039 (mmm) REVERT: D 625 MET cc_start: 0.8838 (ttp) cc_final: 0.8436 (tmm) REVERT: D 1099 TYR cc_start: 0.8182 (m-80) cc_final: 0.7870 (m-10) REVERT: E 36 ASP cc_start: 0.9234 (t0) cc_final: 0.8977 (t0) REVERT: E 43 ASN cc_start: 0.9117 (t0) cc_final: 0.8730 (t0) REVERT: G 29 HIS cc_start: 0.8849 (m90) cc_final: 0.8486 (m90) REVERT: G 73 MET cc_start: 0.8290 (pmm) cc_final: 0.7999 (pmm) REVERT: G 77 ASP cc_start: 0.5390 (t0) cc_final: 0.4516 (t0) REVERT: G 81 HIS cc_start: 0.8626 (OUTLIER) cc_final: 0.8238 (m90) outliers start: 4 outliers final: 1 residues processed: 240 average time/residue: 0.3667 time to fit residues: 149.7596 Evaluate side-chains 190 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 0.0970 chunk 264 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 353 optimal weight: 50.0000 chunk 374 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 573 ASN C 649 GLN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30553 Z= 0.180 Angle : 0.551 11.581 41657 Z= 0.291 Chirality : 0.042 0.168 4828 Planarity : 0.004 0.052 5268 Dihedral : 13.707 172.341 4950 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -1.16 (0.13), residues: 3812 helix: 0.58 (0.15), residues: 1266 sheet: -0.73 (0.24), residues: 444 loop : -1.68 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 580 HIS 0.005 0.001 HIS D 104 PHE 0.018 0.001 PHE A 35 TYR 0.056 0.001 TYR C1229 ARG 0.004 0.000 ARG D 515 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 266 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7965 (p) cc_final: 0.7252 (t) REVERT: C 130 MET cc_start: 0.8704 (mmm) cc_final: 0.8142 (mmm) REVERT: C 239 MET cc_start: 0.8974 (mmm) cc_final: 0.8571 (tmm) REVERT: C 315 MET cc_start: 0.8595 (ttp) cc_final: 0.8212 (ptm) REVERT: C 403 MET cc_start: 0.9205 (tmm) cc_final: 0.8717 (tmm) REVERT: C 659 GLN cc_start: 0.8951 (pp30) cc_final: 0.8701 (pp30) REVERT: C 674 ASP cc_start: 0.9142 (m-30) cc_final: 0.8816 (m-30) REVERT: C 681 MET cc_start: 0.9028 (ttp) cc_final: 0.7810 (ptm) REVERT: C 685 MET cc_start: 0.8876 (ptp) cc_final: 0.8371 (ptp) REVERT: C 704 MET cc_start: 0.8916 (mmp) cc_final: 0.8586 (mmp) REVERT: C 760 ASN cc_start: 0.8369 (m110) cc_final: 0.8013 (m110) REVERT: C 764 CYS cc_start: 0.9413 (t) cc_final: 0.9130 (t) REVERT: C 1101 LEU cc_start: 0.9242 (mm) cc_final: 0.9007 (mm) REVERT: C 1107 MET cc_start: 0.8139 (mpp) cc_final: 0.7907 (mmt) REVERT: C 1151 LEU cc_start: 0.8667 (tp) cc_final: 0.8313 (tp) REVERT: C 1230 MET cc_start: 0.9076 (ppp) cc_final: 0.8642 (ppp) REVERT: C 1272 GLU cc_start: 0.7602 (tt0) cc_final: 0.7326 (tt0) REVERT: C 1278 LEU cc_start: 0.9543 (tp) cc_final: 0.9281 (tp) REVERT: D 237 MET cc_start: 0.9578 (mtm) cc_final: 0.9364 (mtm) REVERT: D 298 MET cc_start: 0.9415 (ttp) cc_final: 0.9052 (ptm) REVERT: D 484 MET cc_start: 0.7963 (mpp) cc_final: 0.7432 (mpp) REVERT: D 625 MET cc_start: 0.8744 (ttp) cc_final: 0.8507 (tmm) REVERT: D 743 MET cc_start: 0.8152 (ppp) cc_final: 0.7693 (ppp) REVERT: D 1349 GLU cc_start: 0.8378 (pm20) cc_final: 0.7992 (pm20) REVERT: G 29 HIS cc_start: 0.8875 (m90) cc_final: 0.8457 (m90) outliers start: 2 outliers final: 1 residues processed: 268 average time/residue: 0.3888 time to fit residues: 175.0547 Evaluate side-chains 198 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 278 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 191 optimal weight: 0.5980 chunk 335 optimal weight: 50.0000 chunk 94 optimal weight: 0.0070 overall best weight: 0.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 573 ASN C 649 GLN C 824 GLN ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30553 Z= 0.134 Angle : 0.531 9.393 41657 Z= 0.278 Chirality : 0.042 0.163 4828 Planarity : 0.003 0.052 5268 Dihedral : 13.630 172.123 4950 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -0.98 (0.14), residues: 3812 helix: 0.75 (0.15), residues: 1268 sheet: -0.61 (0.24), residues: 442 loop : -1.59 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 33 HIS 0.003 0.001 HIS D 104 PHE 0.015 0.001 PHE C1025 TYR 0.022 0.001 TYR C1229 ARG 0.004 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7853 (p) cc_final: 0.7058 (t) REVERT: A 95 LYS cc_start: 0.8767 (ptpp) cc_final: 0.8504 (ptpp) REVERT: C 130 MET cc_start: 0.8670 (mmm) cc_final: 0.8081 (mmm) REVERT: C 315 MET cc_start: 0.8543 (ttp) cc_final: 0.8282 (ptm) REVERT: C 403 MET cc_start: 0.9177 (tmm) cc_final: 0.8721 (tmm) REVERT: C 488 MET cc_start: 0.8852 (tpt) cc_final: 0.8591 (tpt) REVERT: C 659 GLN cc_start: 0.8694 (pp30) cc_final: 0.8259 (pp30) REVERT: C 674 ASP cc_start: 0.9146 (m-30) cc_final: 0.8755 (m-30) REVERT: C 681 MET cc_start: 0.9008 (ttp) cc_final: 0.7801 (ptm) REVERT: C 685 MET cc_start: 0.8845 (ptp) cc_final: 0.8370 (ptp) REVERT: C 704 MET cc_start: 0.8841 (mmp) cc_final: 0.8571 (mmp) REVERT: C 760 ASN cc_start: 0.8310 (m110) cc_final: 0.8036 (m110) REVERT: C 764 CYS cc_start: 0.9393 (t) cc_final: 0.9145 (t) REVERT: C 778 GLU cc_start: 0.8987 (tp30) cc_final: 0.8713 (mm-30) REVERT: C 930 ASP cc_start: 0.7486 (t70) cc_final: 0.7195 (t0) REVERT: C 1151 LEU cc_start: 0.8656 (tp) cc_final: 0.8319 (tp) REVERT: C 1230 MET cc_start: 0.8556 (ppp) cc_final: 0.7507 (ppp) REVERT: C 1272 GLU cc_start: 0.7641 (tt0) cc_final: 0.6973 (tt0) REVERT: C 1278 LEU cc_start: 0.9550 (tp) cc_final: 0.9308 (tp) REVERT: D 237 MET cc_start: 0.9570 (mtm) cc_final: 0.9328 (mtm) REVERT: D 298 MET cc_start: 0.9382 (ttp) cc_final: 0.9127 (ttp) REVERT: D 452 LEU cc_start: 0.9638 (mt) cc_final: 0.9402 (mp) REVERT: D 625 MET cc_start: 0.8780 (ttp) cc_final: 0.8456 (tmm) REVERT: D 718 SER cc_start: 0.8699 (t) cc_final: 0.8427 (m) REVERT: D 743 MET cc_start: 0.8070 (ppp) cc_final: 0.7621 (ppp) REVERT: D 788 LEU cc_start: 0.9545 (tp) cc_final: 0.9340 (tp) REVERT: D 1325 PHE cc_start: 0.8613 (t80) cc_final: 0.8114 (t80) REVERT: D 1326 GLN cc_start: 0.8141 (pp30) cc_final: 0.7920 (tt0) REVERT: E 30 MET cc_start: 0.9124 (tpp) cc_final: 0.8890 (tpp) REVERT: E 43 ASN cc_start: 0.9023 (t0) cc_final: 0.8587 (t0) REVERT: G 29 HIS cc_start: 0.8915 (m90) cc_final: 0.8501 (m90) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3671 time to fit residues: 176.8676 Evaluate side-chains 210 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 0.6980 chunk 336 optimal weight: 40.0000 chunk 73 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 374 optimal weight: 0.2980 chunk 310 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN C 649 GLN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30553 Z= 0.297 Angle : 0.607 13.971 41657 Z= 0.319 Chirality : 0.043 0.168 4828 Planarity : 0.004 0.053 5268 Dihedral : 13.728 169.866 4950 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -1.13 (0.14), residues: 3812 helix: 0.64 (0.15), residues: 1268 sheet: -0.92 (0.23), residues: 458 loop : -1.65 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 580 HIS 0.006 0.001 HIS C 554 PHE 0.017 0.002 PHE C1025 TYR 0.025 0.002 TYR C1229 ARG 0.013 0.000 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7995 (p) cc_final: 0.7406 (t) REVERT: A 68 TYR cc_start: 0.9244 (m-10) cc_final: 0.9005 (m-10) REVERT: A 95 LYS cc_start: 0.8797 (ptpp) cc_final: 0.8552 (ptpp) REVERT: B 51 MET cc_start: 0.8047 (mtp) cc_final: 0.7799 (mtp) REVERT: C 130 MET cc_start: 0.8684 (mmm) cc_final: 0.8260 (mmm) REVERT: C 315 MET cc_start: 0.8608 (ttp) cc_final: 0.8223 (ptm) REVERT: C 403 MET cc_start: 0.9225 (tmm) cc_final: 0.8724 (tmm) REVERT: C 659 GLN cc_start: 0.8904 (pp30) cc_final: 0.8518 (pp30) REVERT: C 681 MET cc_start: 0.9049 (ttp) cc_final: 0.8055 (ttp) REVERT: C 685 MET cc_start: 0.8884 (ptp) cc_final: 0.8337 (ptp) REVERT: C 704 MET cc_start: 0.9034 (mmp) cc_final: 0.8684 (mmp) REVERT: C 760 ASN cc_start: 0.8441 (m110) cc_final: 0.8000 (m110) REVERT: C 764 CYS cc_start: 0.9424 (t) cc_final: 0.9105 (t) REVERT: C 785 ASP cc_start: 0.8809 (p0) cc_final: 0.8543 (p0) REVERT: C 1107 MET cc_start: 0.8322 (mpp) cc_final: 0.8039 (mmt) REVERT: C 1151 LEU cc_start: 0.8742 (tp) cc_final: 0.8377 (tp) REVERT: C 1230 MET cc_start: 0.8834 (ppp) cc_final: 0.8425 (ppp) REVERT: C 1272 GLU cc_start: 0.7415 (tt0) cc_final: 0.6788 (tt0) REVERT: C 1319 MET cc_start: 0.8658 (tmm) cc_final: 0.7784 (tmm) REVERT: D 298 MET cc_start: 0.9388 (ttp) cc_final: 0.9090 (ptm) REVERT: D 479 GLU cc_start: 0.8718 (pp20) cc_final: 0.8113 (tm-30) REVERT: D 625 MET cc_start: 0.8835 (ttp) cc_final: 0.8368 (tmm) REVERT: D 1260 MET cc_start: 0.8832 (tpp) cc_final: 0.8512 (tpp) REVERT: D 1349 GLU cc_start: 0.8371 (pm20) cc_final: 0.8017 (pm20) REVERT: E 30 MET cc_start: 0.9070 (tpp) cc_final: 0.8827 (tpp) REVERT: G 29 HIS cc_start: 0.8951 (m90) cc_final: 0.8529 (m90) REVERT: G 73 MET cc_start: 0.8131 (pmm) cc_final: 0.7830 (pmm) REVERT: G 77 ASP cc_start: 0.6230 (t70) cc_final: 0.5511 (t0) REVERT: G 81 HIS cc_start: 0.8734 (OUTLIER) cc_final: 0.8305 (m90) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.3764 time to fit residues: 164.5621 Evaluate side-chains 196 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 273 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 315 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 373 optimal weight: 50.0000 chunk 233 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 172 optimal weight: 0.6980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN C 573 ASN C 649 GLN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30553 Z= 0.246 Angle : 0.587 13.031 41657 Z= 0.308 Chirality : 0.042 0.165 4828 Planarity : 0.004 0.054 5268 Dihedral : 13.746 168.961 4950 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.19 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -1.10 (0.14), residues: 3812 helix: 0.69 (0.15), residues: 1268 sheet: -0.92 (0.23), residues: 450 loop : -1.64 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 580 HIS 0.005 0.001 HIS C 554 PHE 0.017 0.001 PHE C1025 TYR 0.021 0.001 TYR C1229 ARG 0.005 0.000 ARG D 744 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7949 (p) cc_final: 0.7388 (t) REVERT: A 68 TYR cc_start: 0.9231 (m-10) cc_final: 0.9011 (m-10) REVERT: A 95 LYS cc_start: 0.8774 (ptpp) cc_final: 0.8532 (ptpp) REVERT: C 130 MET cc_start: 0.8640 (mmm) cc_final: 0.8219 (mmm) REVERT: C 315 MET cc_start: 0.8589 (ttp) cc_final: 0.8221 (ptm) REVERT: C 403 MET cc_start: 0.9222 (tmm) cc_final: 0.8725 (tmm) REVERT: C 674 ASP cc_start: 0.9084 (m-30) cc_final: 0.8652 (m-30) REVERT: C 681 MET cc_start: 0.9055 (ttp) cc_final: 0.7979 (ptm) REVERT: C 685 MET cc_start: 0.8891 (ptp) cc_final: 0.8439 (ptt) REVERT: C 704 MET cc_start: 0.8971 (mmp) cc_final: 0.8640 (mmp) REVERT: C 764 CYS cc_start: 0.9443 (t) cc_final: 0.9180 (t) REVERT: C 785 ASP cc_start: 0.8837 (p0) cc_final: 0.8560 (p0) REVERT: C 1101 LEU cc_start: 0.9327 (mm) cc_final: 0.9002 (mm) REVERT: C 1107 MET cc_start: 0.8196 (mpp) cc_final: 0.7883 (mmt) REVERT: C 1151 LEU cc_start: 0.8716 (tp) cc_final: 0.8336 (tp) REVERT: C 1230 MET cc_start: 0.8737 (ppp) cc_final: 0.8491 (ppp) REVERT: C 1272 GLU cc_start: 0.7441 (tt0) cc_final: 0.6903 (tt0) REVERT: C 1292 THR cc_start: 0.8819 (m) cc_final: 0.8486 (p) REVERT: C 1319 MET cc_start: 0.8625 (tmm) cc_final: 0.7862 (tmm) REVERT: D 298 MET cc_start: 0.9390 (ttp) cc_final: 0.9072 (ptm) REVERT: D 484 MET cc_start: 0.7737 (mpp) cc_final: 0.7495 (mpp) REVERT: D 625 MET cc_start: 0.8842 (ttp) cc_final: 0.8349 (tmm) REVERT: D 1349 GLU cc_start: 0.8343 (pm20) cc_final: 0.7986 (pm20) REVERT: E 30 MET cc_start: 0.9147 (tpp) cc_final: 0.8930 (tpp) REVERT: G 29 HIS cc_start: 0.8932 (m90) cc_final: 0.8511 (m90) REVERT: G 73 MET cc_start: 0.8113 (pmm) cc_final: 0.7781 (pmm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3877 time to fit residues: 165.3764 Evaluate side-chains 199 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 222 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 73 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 237 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 293 optimal weight: 30.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 573 ASN C 649 GLN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30553 Z= 0.142 Angle : 0.547 9.307 41657 Z= 0.283 Chirality : 0.042 0.188 4828 Planarity : 0.003 0.054 5268 Dihedral : 13.634 170.699 4950 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -0.89 (0.14), residues: 3812 helix: 0.86 (0.15), residues: 1263 sheet: -0.59 (0.24), residues: 427 loop : -1.55 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS D 104 PHE 0.016 0.001 PHE C1025 TYR 0.039 0.001 TYR C1229 ARG 0.008 0.000 ARG D1174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7880 (p) cc_final: 0.7193 (t) REVERT: A 95 LYS cc_start: 0.8828 (ptpp) cc_final: 0.8589 (ptpp) REVERT: C 130 MET cc_start: 0.8610 (mmm) cc_final: 0.8096 (mmm) REVERT: C 315 MET cc_start: 0.8505 (ttp) cc_final: 0.8240 (ptm) REVERT: C 403 MET cc_start: 0.9190 (tmm) cc_final: 0.8754 (tmm) REVERT: C 674 ASP cc_start: 0.9087 (m-30) cc_final: 0.8589 (m-30) REVERT: C 681 MET cc_start: 0.9010 (ttp) cc_final: 0.7888 (ptm) REVERT: C 685 MET cc_start: 0.8857 (ptp) cc_final: 0.8420 (ptt) REVERT: C 704 MET cc_start: 0.8903 (mmp) cc_final: 0.8613 (mmp) REVERT: C 788 SER cc_start: 0.8908 (m) cc_final: 0.8236 (t) REVERT: C 796 LEU cc_start: 0.9299 (mt) cc_final: 0.9096 (mt) REVERT: C 1101 LEU cc_start: 0.9222 (mm) cc_final: 0.9020 (mm) REVERT: C 1107 MET cc_start: 0.8113 (mpp) cc_final: 0.7814 (mmt) REVERT: C 1151 LEU cc_start: 0.8642 (tp) cc_final: 0.8270 (tp) REVERT: C 1272 GLU cc_start: 0.7398 (tt0) cc_final: 0.6762 (tt0) REVERT: C 1292 THR cc_start: 0.8641 (m) cc_final: 0.8372 (p) REVERT: C 1319 MET cc_start: 0.8555 (tmm) cc_final: 0.7858 (tmm) REVERT: D 180 MET cc_start: 0.7192 (tmm) cc_final: 0.6658 (ttp) REVERT: D 237 MET cc_start: 0.9579 (mtm) cc_final: 0.9376 (mtm) REVERT: D 298 MET cc_start: 0.9381 (ttp) cc_final: 0.8961 (ptm) REVERT: D 450 HIS cc_start: 0.8561 (t-90) cc_final: 0.8319 (t-90) REVERT: D 581 MET cc_start: 0.8384 (ttm) cc_final: 0.8149 (ttm) REVERT: D 625 MET cc_start: 0.8782 (ttp) cc_final: 0.8303 (tmm) REVERT: D 718 SER cc_start: 0.8669 (t) cc_final: 0.8414 (m) REVERT: D 743 MET cc_start: 0.8137 (ppp) cc_final: 0.7421 (ppp) REVERT: D 822 MET cc_start: 0.8320 (tpt) cc_final: 0.8118 (tpp) REVERT: D 884 SER cc_start: 0.7678 (p) cc_final: 0.7451 (p) REVERT: D 1254 GLU cc_start: 0.8655 (tt0) cc_final: 0.7865 (tp30) REVERT: D 1260 MET cc_start: 0.8722 (tpp) cc_final: 0.8389 (tpp) REVERT: D 1325 PHE cc_start: 0.8808 (t80) cc_final: 0.8314 (t80) REVERT: D 1349 GLU cc_start: 0.8303 (pm20) cc_final: 0.7934 (pm20) REVERT: E 30 MET cc_start: 0.9196 (tpp) cc_final: 0.8970 (tpp) REVERT: G 29 HIS cc_start: 0.8931 (m90) cc_final: 0.8504 (m90) REVERT: G 31 LYS cc_start: 0.6226 (pttp) cc_final: 0.6006 (pttm) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3614 time to fit residues: 163.7375 Evaluate side-chains 209 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 40.0000 chunk 357 optimal weight: 7.9990 chunk 326 optimal weight: 0.0980 chunk 347 optimal weight: 40.0000 chunk 209 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 314 optimal weight: 9.9990 chunk 328 optimal weight: 0.9990 chunk 346 optimal weight: 50.0000 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 573 ASN C 649 GLN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30553 Z= 0.186 Angle : 0.567 13.735 41657 Z= 0.293 Chirality : 0.042 0.185 4828 Planarity : 0.003 0.053 5268 Dihedral : 13.627 172.437 4950 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 0.04 % Allowed : 0.81 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -0.89 (0.14), residues: 3812 helix: 0.88 (0.15), residues: 1256 sheet: -0.70 (0.24), residues: 441 loop : -1.53 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 33 HIS 0.003 0.001 HIS C 554 PHE 0.017 0.001 PHE C 464 TYR 0.055 0.001 TYR C1229 ARG 0.008 0.000 ARG C1034 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7931 (p) cc_final: 0.7239 (t) REVERT: A 95 LYS cc_start: 0.8822 (ptpp) cc_final: 0.8574 (ptpp) REVERT: B 51 MET cc_start: 0.7983 (mtp) cc_final: 0.7690 (mtp) REVERT: C 130 MET cc_start: 0.8578 (mmm) cc_final: 0.8072 (mmm) REVERT: C 403 MET cc_start: 0.9207 (tmm) cc_final: 0.8742 (tmm) REVERT: C 488 MET cc_start: 0.8844 (tpt) cc_final: 0.8587 (tpt) REVERT: C 674 ASP cc_start: 0.9083 (m-30) cc_final: 0.8549 (m-30) REVERT: C 681 MET cc_start: 0.9019 (ttp) cc_final: 0.7893 (ptm) REVERT: C 685 MET cc_start: 0.8857 (ptp) cc_final: 0.8424 (ptt) REVERT: C 704 MET cc_start: 0.8970 (mmp) cc_final: 0.8670 (mmp) REVERT: C 764 CYS cc_start: 0.9428 (t) cc_final: 0.9175 (t) REVERT: C 788 SER cc_start: 0.8868 (m) cc_final: 0.8190 (t) REVERT: C 796 LEU cc_start: 0.9328 (mt) cc_final: 0.9121 (mt) REVERT: C 1101 LEU cc_start: 0.9281 (mm) cc_final: 0.8976 (mp) REVERT: C 1107 MET cc_start: 0.8154 (mpp) cc_final: 0.7794 (mmt) REVERT: C 1151 LEU cc_start: 0.8691 (tp) cc_final: 0.8323 (tp) REVERT: C 1230 MET cc_start: 0.8685 (ppp) cc_final: 0.8400 (ppp) REVERT: C 1272 GLU cc_start: 0.7382 (tt0) cc_final: 0.6437 (tt0) REVERT: C 1319 MET cc_start: 0.8633 (tmm) cc_final: 0.7934 (tmm) REVERT: D 298 MET cc_start: 0.9393 (ttp) cc_final: 0.8969 (ptm) REVERT: D 625 MET cc_start: 0.8786 (ttp) cc_final: 0.8225 (tmm) REVERT: D 718 SER cc_start: 0.8669 (t) cc_final: 0.8403 (m) REVERT: D 743 MET cc_start: 0.8257 (ppp) cc_final: 0.7662 (ppp) REVERT: D 822 MET cc_start: 0.8340 (tpt) cc_final: 0.8053 (tpp) REVERT: D 1260 MET cc_start: 0.8849 (tpp) cc_final: 0.8527 (tpp) REVERT: D 1349 GLU cc_start: 0.8294 (pm20) cc_final: 0.7942 (pm20) REVERT: E 30 MET cc_start: 0.9167 (tpp) cc_final: 0.8945 (tpp) REVERT: G 29 HIS cc_start: 0.8958 (m90) cc_final: 0.8543 (m90) REVERT: G 73 MET cc_start: 0.7921 (pmm) cc_final: 0.7588 (pmm) REVERT: G 77 ASP cc_start: 0.5738 (t0) cc_final: 0.4767 (t0) REVERT: G 81 HIS cc_start: 0.8691 (OUTLIER) cc_final: 0.8281 (m90) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.3592 time to fit residues: 159.5382 Evaluate side-chains 207 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 3.9990 chunk 367 optimal weight: 40.0000 chunk 224 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 385 optimal weight: 8.9990 chunk 354 optimal weight: 40.0000 chunk 307 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 chunk 237 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 573 ASN C 649 GLN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30553 Z= 0.184 Angle : 0.571 10.720 41657 Z= 0.296 Chirality : 0.042 0.186 4828 Planarity : 0.003 0.053 5268 Dihedral : 13.630 173.169 4950 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -0.91 (0.14), residues: 3812 helix: 0.80 (0.15), residues: 1263 sheet: -0.69 (0.24), residues: 443 loop : -1.52 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 33 HIS 0.016 0.001 HIS C1023 PHE 0.017 0.001 PHE C1025 TYR 0.057 0.001 TYR C1229 ARG 0.008 0.000 ARG C1034 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7624 Ramachandran restraints generated. 3812 Oldfield, 0 Emsley, 3812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 CYS cc_start: 0.7863 (p) cc_final: 0.7170 (t) REVERT: B 51 MET cc_start: 0.7987 (mtp) cc_final: 0.7686 (mtp) REVERT: C 130 MET cc_start: 0.8568 (mmm) cc_final: 0.8043 (mmm) REVERT: C 403 MET cc_start: 0.9205 (tmm) cc_final: 0.8737 (tmm) REVERT: C 674 ASP cc_start: 0.9053 (m-30) cc_final: 0.8528 (m-30) REVERT: C 681 MET cc_start: 0.9014 (ttp) cc_final: 0.7880 (ptm) REVERT: C 685 MET cc_start: 0.8863 (ptp) cc_final: 0.8426 (ptt) REVERT: C 704 MET cc_start: 0.8974 (mmp) cc_final: 0.8681 (mmp) REVERT: C 764 CYS cc_start: 0.9434 (t) cc_final: 0.9168 (t) REVERT: C 788 SER cc_start: 0.8868 (m) cc_final: 0.8160 (t) REVERT: C 1107 MET cc_start: 0.8104 (mpp) cc_final: 0.7741 (mmt) REVERT: C 1151 LEU cc_start: 0.8686 (tp) cc_final: 0.8323 (tp) REVERT: C 1230 MET cc_start: 0.8645 (ppp) cc_final: 0.8391 (ppp) REVERT: C 1272 GLU cc_start: 0.7461 (tt0) cc_final: 0.6522 (tt0) REVERT: C 1293 VAL cc_start: 0.9041 (p) cc_final: 0.8610 (p) REVERT: C 1319 MET cc_start: 0.8556 (tmm) cc_final: 0.7900 (tmm) REVERT: D 180 MET cc_start: 0.7280 (tmm) cc_final: 0.6692 (ttp) REVERT: D 298 MET cc_start: 0.9412 (ttp) cc_final: 0.9152 (ttp) REVERT: D 625 MET cc_start: 0.8754 (ttp) cc_final: 0.8251 (tmm) REVERT: D 718 SER cc_start: 0.8649 (t) cc_final: 0.8421 (m) REVERT: D 743 MET cc_start: 0.8265 (ppp) cc_final: 0.7674 (ppp) REVERT: D 788 LEU cc_start: 0.9612 (tp) cc_final: 0.9379 (tt) REVERT: D 1260 MET cc_start: 0.8866 (tpp) cc_final: 0.8514 (tpp) REVERT: D 1349 GLU cc_start: 0.8295 (pm20) cc_final: 0.7933 (pm20) REVERT: E 30 MET cc_start: 0.9163 (tpp) cc_final: 0.8948 (tpp) REVERT: G 29 HIS cc_start: 0.8948 (m90) cc_final: 0.8535 (m90) REVERT: G 73 MET cc_start: 0.7891 (pmm) cc_final: 0.7573 (pmm) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.3477 time to fit residues: 151.7839 Evaluate side-chains 200 residues out of total 3251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 4.9990 chunk 327 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 307 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 315 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 573 ASN C 649 GLN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.089928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.061487 restraints weight = 137830.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.063280 restraints weight = 70611.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.064487 restraints weight = 45175.792| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30553 Z= 0.179 Angle : 0.568 10.676 41657 Z= 0.294 Chirality : 0.042 0.184 4828 Planarity : 0.003 0.053 5268 Dihedral : 13.628 173.770 4950 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.88 % Favored : 94.07 % Rotamer: Outliers : 0.07 % Allowed : 0.39 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.05 % 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: -0.88 (0.14), residues: 3812 helix: 0.81 (0.15), residues: 1269 sheet: -0.67 (0.24), residues: 443 loop : -1.49 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.010 0.001 HIS D 450 PHE 0.017 0.001 PHE C 464 TYR 0.047 0.001 TYR C1229 ARG 0.008 0.000 ARG C1034 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5002.52 seconds wall clock time: 92 minutes 51.74 seconds (5571.74 seconds total)