Starting phenix.real_space_refine on Sun Feb 18 22:30:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsh_34997/02_2024/8hsh_34997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsh_34997/02_2024/8hsh_34997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsh_34997/02_2024/8hsh_34997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsh_34997/02_2024/8hsh_34997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsh_34997/02_2024/8hsh_34997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsh_34997/02_2024/8hsh_34997.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 62 5.16 5 C 14625 2.51 5 N 4081 2.21 5 O 4301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 481": "OD1" <-> "OD2" Residue "I GLU 527": "OE1" <-> "OE2" Residue "I GLU 622": "OE1" <-> "OE2" Residue "I GLU 693": "OE1" <-> "OE2" Residue "I GLU 940": "OE1" <-> "OE2" Residue "I TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 1091": "OE1" <-> "OE2" Residue "I ASP 1110": "OD1" <-> "OD2" Residue "J GLU 16": "OE1" <-> "OE2" Residue "J TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 979": "OE1" <-> "OE2" Residue "J TYR 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1090": "OD1" <-> "OD2" Residue "J GLU 1285": "OE1" <-> "OE2" Residue "J GLU 1464": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K GLU 77": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23072 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "H" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1806 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 214} Chain: "I" Number of atoms: 8644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8644 Classifications: {'peptide': 1096} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1025} Chain breaks: 1 Chain: "J" Number of atoms: 10078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 10078 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 62, 'TRANS': 1215} Chain breaks: 3 Chain: "K" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19413 SG CYS J1112 72.061 87.192 31.746 1.00132.11 S ATOM 20057 SG CYS J1194 71.350 87.254 35.503 1.00128.57 S ATOM 20113 SG CYS J1201 69.505 84.871 33.258 1.00129.94 S ATOM 20137 SG CYS J1204 72.882 84.054 33.956 1.00132.51 S Time building chain proxies: 12.61, per 1000 atoms: 0.55 Number of scatterers: 23072 At special positions: 0 Unit cell: (125.08, 184.44, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 62 16.00 Mg 1 11.99 O 4301 8.00 N 4081 7.00 C 14625 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: 9.27 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1602 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1201 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1204 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1194 " pdb="ZN ZN J1602 " - pdb=" SG CYS J1112 " Number of angles added : 6 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5396 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 40 sheets defined 39.0% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'G' and resid 31 through 47 removed outlier: 3.826A pdb=" N THR G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Proline residue: G 39 - end of helix Processing helix chain 'G' and resid 74 through 84 removed outlier: 3.887A pdb=" N GLU G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 114 removed outlier: 3.532A pdb=" N ASP G 113 " --> pdb=" O LYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 157 removed outlier: 3.935A pdb=" N HIS G 156 " --> pdb=" O PRO G 152 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY G 157 " --> pdb=" O ALA G 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 152 through 157' Processing helix chain 'G' and resid 206 through 223 Processing helix chain 'G' and resid 224 through 227 removed outlier: 3.866A pdb=" N ASN G 227 " --> pdb=" O TYR G 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 224 through 227' Processing helix chain 'H' and resid 31 through 47 removed outlier: 3.627A pdb=" N THR H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Proline residue: H 39 - end of helix Processing helix chain 'H' and resid 74 through 84 removed outlier: 4.110A pdb=" N GLU H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 152 through 157 removed outlier: 4.158A pdb=" N HIS H 156 " --> pdb=" O PRO H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 223 Processing helix chain 'H' and resid 224 through 226 No H-bonds generated for 'chain 'H' and resid 224 through 226' Processing helix chain 'I' and resid 19 through 30 removed outlier: 3.593A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 79 through 86 Processing helix chain 'I' and resid 193 through 200 Processing helix chain 'I' and resid 203 through 211 Processing helix chain 'I' and resid 215 through 217 No H-bonds generated for 'chain 'I' and resid 215 through 217' Processing helix chain 'I' and resid 218 through 223 Processing helix chain 'I' and resid 232 through 242 removed outlier: 3.576A pdb=" N ILE I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 279 removed outlier: 3.668A pdb=" N GLU I 279 " --> pdb=" O TYR I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 316 Processing helix chain 'I' and resid 327 through 329 No H-bonds generated for 'chain 'I' and resid 327 through 329' Processing helix chain 'I' and resid 335 through 362 Processing helix chain 'I' and resid 375 through 389 removed outlier: 3.741A pdb=" N SER I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 424 through 429 removed outlier: 4.454A pdb=" N ASP I 429 " --> pdb=" O PHE I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 435 removed outlier: 3.907A pdb=" N TYR I 435 " --> pdb=" O ARG I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 492 Processing helix chain 'I' and resid 525 through 529 Processing helix chain 'I' and resid 535 through 540 Processing helix chain 'I' and resid 543 through 547 removed outlier: 3.596A pdb=" N LEU I 546 " --> pdb=" O ASN I 543 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 567 removed outlier: 3.501A pdb=" N THR I 566 " --> pdb=" O SER I 562 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN I 567 " --> pdb=" O ASN I 563 " (cutoff:3.500A) Processing helix chain 'I' and resid 583 through 591 Processing helix chain 'I' and resid 692 through 697 Processing helix chain 'I' and resid 732 through 737 removed outlier: 3.593A pdb=" N ARG I 735 " --> pdb=" O ALA I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 874 through 879 removed outlier: 3.814A pdb=" N SER I 878 " --> pdb=" O LEU I 874 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG I 879 " --> pdb=" O GLY I 875 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 874 through 879' Processing helix chain 'I' and resid 882 through 898 removed outlier: 3.605A pdb=" N PHE I 896 " --> pdb=" O LEU I 892 " (cutoff:3.500A) Processing helix chain 'I' and resid 910 through 932 removed outlier: 3.635A pdb=" N GLU I 932 " --> pdb=" O LYS I 928 " (cutoff:3.500A) Processing helix chain 'I' and resid 937 through 950 Processing helix chain 'I' and resid 958 through 969 Processing helix chain 'I' and resid 1034 through 1043 removed outlier: 3.517A pdb=" N TYR I1043 " --> pdb=" O ALA I1039 " (cutoff:3.500A) Processing helix chain 'I' and resid 1046 through 1054 Processing helix chain 'I' and resid 1059 through 1073 Processing helix chain 'I' and resid 1082 through 1095 removed outlier: 3.506A pdb=" N LEU I1095 " --> pdb=" O GLU I1091 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 22 Processing helix chain 'J' and resid 46 through 51 removed outlier: 3.513A pdb=" N PHE J 50 " --> pdb=" O ASP J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'J' and resid 102 through 107 Processing helix chain 'J' and resid 110 through 116 Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 155 through 163 removed outlier: 3.757A pdb=" N TYR J 163 " --> pdb=" O ARG J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 423 through 426 Processing helix chain 'J' and resid 456 through 468 removed outlier: 3.891A pdb=" N ALA J 460 " --> pdb=" O MET J 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 469 through 483 Processing helix chain 'J' and resid 485 through 505 removed outlier: 3.576A pdb=" N ARG J 489 " --> pdb=" O SER J 485 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS J 491 " --> pdb=" O ALA J 487 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL J 498 " --> pdb=" O LYS J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 508 through 511 removed outlier: 3.738A pdb=" N TRP J 511 " --> pdb=" O ARG J 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 508 through 511' Processing helix chain 'J' and resid 521 through 525 Processing helix chain 'J' and resid 538 through 561 removed outlier: 3.964A pdb=" N ASP J 542 " --> pdb=" O SER J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 563 through 583 Processing helix chain 'J' and resid 602 through 608 Processing helix chain 'J' and resid 612 through 618 removed outlier: 3.907A pdb=" N ASN J 617 " --> pdb=" O ARG J 613 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 618 " --> pdb=" O PHE J 614 " (cutoff:3.500A) Processing helix chain 'J' and resid 646 through 653 removed outlier: 3.522A pdb=" N PHE J 653 " --> pdb=" O ALA J 649 " (cutoff:3.500A) Processing helix chain 'J' and resid 653 through 664 removed outlier: 3.569A pdb=" N LYS J 664 " --> pdb=" O LYS J 660 " (cutoff:3.500A) Processing helix chain 'J' and resid 669 through 678 Processing helix chain 'J' and resid 679 through 683 removed outlier: 3.621A pdb=" N ASP J 682 " --> pdb=" O ARG J 679 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE J 683 " --> pdb=" O GLN J 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 679 through 683' Processing helix chain 'J' and resid 684 through 695 Processing helix chain 'J' and resid 709 through 711 No H-bonds generated for 'chain 'J' and resid 709 through 711' Processing helix chain 'J' and resid 729 through 734 removed outlier: 4.243A pdb=" N GLU J 734 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing helix chain 'J' and resid 752 through 763 Processing helix chain 'J' and resid 782 through 793 Processing helix chain 'J' and resid 810 through 822 removed outlier: 4.460A pdb=" N ALA J 814 " --> pdb=" O GLU J 810 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 841 Processing helix chain 'J' and resid 845 through 855 Processing helix chain 'J' and resid 876 through 890 Processing helix chain 'J' and resid 893 through 899 Processing helix chain 'J' and resid 907 through 923 Processing helix chain 'J' and resid 924 through 946 removed outlier: 3.650A pdb=" N GLY J 946 " --> pdb=" O SER J 942 " (cutoff:3.500A) Processing helix chain 'J' and resid 959 through 980 Processing helix chain 'J' and resid 984 through 1015 removed outlier: 3.588A pdb=" N GLU J1001 " --> pdb=" O THR J 997 " (cutoff:3.500A) Processing helix chain 'J' and resid 1018 through 1026 Processing helix chain 'J' and resid 1031 through 1040 Processing helix chain 'J' and resid 1066 through 1102 removed outlier: 3.956A pdb=" N HIS J1075 " --> pdb=" O PHE J1071 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY J1076 " --> pdb=" O ILE J1072 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA J1089 " --> pdb=" O ALA J1085 " (cutoff:3.500A) Processing helix chain 'J' and resid 1136 through 1145 Processing helix chain 'J' and resid 1167 through 1181 Processing helix chain 'J' and resid 1190 through 1194 Processing helix chain 'J' and resid 1201 through 1206 Processing helix chain 'J' and resid 1220 through 1231 removed outlier: 3.658A pdb=" N VAL J1224 " --> pdb=" O ALA J1220 " (cutoff:3.500A) Processing helix chain 'J' and resid 1232 through 1236 Processing helix chain 'J' and resid 1256 through 1264 Processing helix chain 'J' and resid 1331 through 1339 Processing helix chain 'J' and resid 1340 through 1359 removed outlier: 3.724A pdb=" N VAL J1355 " --> pdb=" O GLU J1351 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR J1356 " --> pdb=" O ILE J1352 " (cutoff:3.500A) Processing helix chain 'J' and resid 1364 through 1376 removed outlier: 4.549A pdb=" N ILE J1368 " --> pdb=" O HIS J1364 " (cutoff:3.500A) Processing helix chain 'J' and resid 1395 through 1407 Processing helix chain 'J' and resid 1423 through 1430 Processing helix chain 'J' and resid 1433 through 1441 removed outlier: 4.089A pdb=" N ALA J1437 " --> pdb=" O SER J1433 " (cutoff:3.500A) Processing helix chain 'J' and resid 1442 through 1453 removed outlier: 3.567A pdb=" N VAL J1446 " --> pdb=" O ASN J1442 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA J1453 " --> pdb=" O GLU J1449 " (cutoff:3.500A) Processing helix chain 'J' and resid 1461 through 1469 removed outlier: 4.080A pdb=" N ASN J1465 " --> pdb=" O GLY J1461 " (cutoff:3.500A) Processing helix chain 'J' and resid 1474 through 1477 Processing helix chain 'J' and resid 1478 through 1483 removed outlier: 4.640A pdb=" N PHE J1483 " --> pdb=" O ASP J1479 " (cutoff:3.500A) Processing helix chain 'J' and resid 1489 through 1503 Processing helix chain 'K' and resid 5 through 12 removed outlier: 3.525A pdb=" N MET K 12 " --> pdb=" O LYS K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 33 Processing helix chain 'K' and resid 52 through 56 Processing helix chain 'K' and resid 59 through 70 removed outlier: 4.047A pdb=" N THR K 70 " --> pdb=" O LYS K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 90 removed outlier: 4.019A pdb=" N LEU K 85 " --> pdb=" O PRO K 81 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU K 90 " --> pdb=" O GLN K 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 10 through 16 removed outlier: 3.513A pdb=" N TYR G 20 " --> pdb=" O GLN G 16 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR G 20 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR G 201 " --> pdb=" O TYR G 20 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLU G 22 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE G 199 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL G 24 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU G 197 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU G 26 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU G 195 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 96 through 103 removed outlier: 7.636A pdb=" N ASN G 139 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE G 58 " --> pdb=" O ASN G 139 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU G 141 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL G 56 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG G 143 " --> pdb=" O THR G 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 16 removed outlier: 3.608A pdb=" N TYR H 20 " --> pdb=" O GLN H 16 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR H 20 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR H 201 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU H 22 " --> pdb=" O ILE H 199 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE H 199 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL H 24 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU H 197 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU H 26 " --> pdb=" O LEU H 195 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU H 195 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU H 192 " --> pdb=" O THR H 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 96 through 103 removed outlier: 7.588A pdb=" N ASN H 139 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE H 58 " --> pdb=" O ASN H 139 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU H 141 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL H 56 " --> pdb=" O GLU H 141 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG H 143 " --> pdb=" O THR H 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA8, first strand: chain 'H' and resid 108 through 110 Processing sheet with id=AA9, first strand: chain 'H' and resid 150 through 151 Processing sheet with id=AB1, first strand: chain 'I' and resid 2 through 5 removed outlier: 6.208A pdb=" N GLU I 2 " --> pdb=" O ARG I 900 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE I 902 " --> pdb=" O GLU I 2 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS I 4 " --> pdb=" O ILE I 902 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 65 through 72 removed outlier: 5.146A pdb=" N LEU I 66 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE I 101 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE I 68 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN I 99 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU I 70 " --> pdb=" O ARG I 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 65 through 72 removed outlier: 5.146A pdb=" N LEU I 66 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE I 101 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N PHE I 68 " --> pdb=" O GLN I 99 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN I 99 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU I 70 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY I 116 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA I 96 " --> pdb=" O PHE I 114 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE I 114 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AB5, first strand: chain 'I' and resid 331 through 334 removed outlier: 6.588A pdb=" N SER I 138 " --> pdb=" O SER I 411 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 145 through 150 removed outlier: 6.125A pdb=" N TYR I 158 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL I 176 " --> pdb=" O TYR I 158 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP I 173 " --> pdb=" O LYS I 185 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS I 185 " --> pdb=" O ASP I 173 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 460 through 461 removed outlier: 5.544A pdb=" N GLU I 482 " --> pdb=" O ARG I 473 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL I 475 " --> pdb=" O THR I 480 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR I 480 " --> pdb=" O VAL I 475 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 460 through 461 Processing sheet with id=AB9, first strand: chain 'I' and resid 513 through 516 Processing sheet with id=AC1, first strand: chain 'I' and resid 595 through 596 removed outlier: 6.488A pdb=" N LEU I 595 " --> pdb=" O LEU I 655 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 620 through 624 removed outlier: 5.760A pdb=" N ARG I 614 " --> pdb=" O VAL I 603 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL I 603 " --> pdb=" O ARG I 614 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 629 through 630 Processing sheet with id=AC4, first strand: chain 'I' and resid 971 through 972 removed outlier: 7.330A pdb=" N ILE I 688 " --> pdb=" O ALA I 850 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE I 852 " --> pdb=" O ILE I 688 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE I 690 " --> pdb=" O ILE I 852 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N VAL I 869 " --> pdb=" O ASN I 671 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU I 673 " --> pdb=" O VAL I 869 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU I 871 " --> pdb=" O LEU I 673 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA I 675 " --> pdb=" O LEU I 871 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL I 988 " --> pdb=" O ILE I 676 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 701 through 713 removed outlier: 7.611A pdb=" N ARG I 820 " --> pdb=" O ARG I 807 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG I 807 " --> pdb=" O ARG I 820 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL I 822 " --> pdb=" O ARG I 805 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG I 805 " --> pdb=" O VAL I 822 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG I 824 " --> pdb=" O THR I 803 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR I 803 " --> pdb=" O ARG I 824 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR I 826 " --> pdb=" O VAL I 801 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 721 through 722 Processing sheet with id=AC7, first strand: chain 'I' and resid 754 through 756 removed outlier: 6.827A pdb=" N LEU I 790 " --> pdb=" O LEU I 755 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 1108 through 1109 removed outlier: 4.170A pdb=" N THR I1101 " --> pdb=" O VAL I1109 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN I1100 " --> pdb=" O ARG J 9 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS J 7 " --> pdb=" O LEU I1102 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE J 10 " --> pdb=" O LYS J1455 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 91 through 100 removed outlier: 3.566A pdb=" N LEU J 95 " --> pdb=" O GLU J 515 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU J 515 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 11.403A pdb=" N THR J 97 " --> pdb=" O ILE J 513 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N ILE J 513 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 132 through 134 removed outlier: 3.539A pdb=" N LEU J 153 " --> pdb=" O ILE J 133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 167 through 170 removed outlier: 3.642A pdb=" N GLU J 183 " --> pdb=" O ALA J 203 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 399 through 402 Processing sheet with id=AD4, first strand: chain 'J' and resid 420 through 422 removed outlier: 7.598A pdb=" N VAL J 427 " --> pdb=" O LEU J 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 528 through 529 Processing sheet with id=AD6, first strand: chain 'J' and resid 626 through 633 removed outlier: 7.661A pdb=" N ILE J 726 " --> pdb=" O ARG J 628 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL J 630 " --> pdb=" O ILE J 726 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU J 728 " --> pdb=" O VAL J 630 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL J 632 " --> pdb=" O LEU J 728 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 842 through 843 removed outlier: 7.183A pdb=" N PHE J 843 " --> pdb=" O ARG J 867 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 1118 through 1121 Processing sheet with id=AD9, first strand: chain 'J' and resid 1123 through 1124 removed outlier: 3.811A pdb=" N ARG J1133 " --> pdb=" O GLN J1124 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 1153 through 1154 Processing sheet with id=AE2, first strand: chain 'J' and resid 1300 through 1305 Processing sheet with id=AE3, first strand: chain 'J' and resid 1392 through 1394 removed outlier: 4.580A pdb=" N TYR J1378 " --> pdb=" O LEU J1420 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1485 through 1488 939 hydrogen bonds defined for protein. 2631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.72 Time building geometry restraints manager: 9.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7616 1.34 - 1.46: 2951 1.46 - 1.58: 12793 1.58 - 1.70: 2 1.70 - 1.82: 115 Bond restraints: 23477 Sorted by residual: bond pdb=" CB PRO J 39 " pdb=" CG PRO J 39 " ideal model delta sigma weight residual 1.492 1.609 -0.117 5.00e-02 4.00e+02 5.47e+00 bond pdb=" CB PRO G 9 " pdb=" CG PRO G 9 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.03e+00 bond pdb=" CG GLN K 29 " pdb=" CD GLN K 29 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.58e+00 bond pdb=" C ASP I 857 " pdb=" N MET I 858 " ideal model delta sigma weight residual 1.339 1.262 0.077 5.57e-02 3.22e+02 1.92e+00 bond pdb=" C ILE I 852 " pdb=" N LEU I 853 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.83e-02 1.25e+03 1.54e+00 ... (remaining 23472 not shown) Histogram of bond angle deviations from ideal: 97.30 - 104.66: 453 104.66 - 112.01: 11440 112.01 - 119.37: 8389 119.37 - 126.73: 11227 126.73 - 134.09: 246 Bond angle restraints: 31755 Sorted by residual: angle pdb=" CA PRO J 39 " pdb=" N PRO J 39 " pdb=" CD PRO J 39 " ideal model delta sigma weight residual 112.00 104.87 7.13 1.40e+00 5.10e-01 2.60e+01 angle pdb=" N VAL I 254 " pdb=" CA VAL I 254 " pdb=" C VAL I 254 " ideal model delta sigma weight residual 113.53 108.55 4.98 9.80e-01 1.04e+00 2.58e+01 angle pdb=" C HIS I 117 " pdb=" N ILE I 118 " pdb=" CA ILE I 118 " ideal model delta sigma weight residual 123.43 118.45 4.98 1.10e+00 8.26e-01 2.05e+01 angle pdb=" CA PRO G 9 " pdb=" N PRO G 9 " pdb=" CD PRO G 9 " ideal model delta sigma weight residual 112.00 105.97 6.03 1.40e+00 5.10e-01 1.85e+01 angle pdb=" N GLN K 29 " pdb=" CA GLN K 29 " pdb=" CB GLN K 29 " ideal model delta sigma weight residual 110.16 116.23 -6.07 1.48e+00 4.57e-01 1.68e+01 ... (remaining 31750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 13199 17.82 - 35.64: 1065 35.64 - 53.45: 145 53.45 - 71.27: 37 71.27 - 89.09: 14 Dihedral angle restraints: 14460 sinusoidal: 6068 harmonic: 8392 Sorted by residual: dihedral pdb=" CA GLU J1109 " pdb=" C GLU J1109 " pdb=" N ALA J1110 " pdb=" CA ALA J1110 " ideal model delta harmonic sigma weight residual 180.00 142.36 37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA ASP J 136 " pdb=" C ASP J 136 " pdb=" N PRO J 137 " pdb=" CA PRO J 137 " ideal model delta harmonic sigma weight residual -180.00 -149.93 -30.07 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA VAL I1081 " pdb=" C VAL I1081 " pdb=" N PRO I1082 " pdb=" CA PRO I1082 " ideal model delta harmonic sigma weight residual 180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 14457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2871 0.056 - 0.113: 644 0.113 - 0.169: 74 0.169 - 0.226: 0 0.226 - 0.282: 1 Chirality restraints: 3590 Sorted by residual: chirality pdb=" CB ILE I 163 " pdb=" CA ILE I 163 " pdb=" CG1 ILE I 163 " pdb=" CG2 ILE I 163 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE I 21 " pdb=" CA ILE I 21 " pdb=" CG1 ILE I 21 " pdb=" CG2 ILE I 21 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA ILE G 58 " pdb=" N ILE G 58 " pdb=" C ILE G 58 " pdb=" CB ILE G 58 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 3587 not shown) Planarity restraints: 4170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS J 38 " 0.081 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO J 39 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO J 39 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO J 39 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 8 " -0.056 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO G 9 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO G 9 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 9 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 309 " 0.027 2.00e-02 2.50e+03 1.97e-02 7.78e+00 pdb=" CG TYR I 309 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR I 309 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR I 309 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR I 309 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR I 309 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR I 309 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR I 309 " 0.003 2.00e-02 2.50e+03 ... (remaining 4167 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 331 2.62 - 3.19: 21194 3.19 - 3.76: 36116 3.76 - 4.33: 49649 4.33 - 4.90: 80215 Nonbonded interactions: 187505 Sorted by model distance: nonbonded pdb=" OD1 ASP J 741 " pdb="MG MG J1603 " model vdw 2.046 2.170 nonbonded pdb=" OD1 ASP J 739 " pdb="MG MG J1603 " model vdw 2.072 2.170 nonbonded pdb=" OH TYR J1378 " pdb=" O SER J1430 " model vdw 2.099 2.440 nonbonded pdb=" O ALA I1116 " pdb=" OH TYR J 23 " model vdw 2.107 2.440 nonbonded pdb=" OG SER I 525 " pdb=" OE1 GLU I 528 " model vdw 2.112 2.440 ... (remaining 187500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.190 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 66.930 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 23477 Z= 0.273 Angle : 0.696 11.000 31755 Z= 0.365 Chirality : 0.046 0.282 3590 Planarity : 0.005 0.118 4170 Dihedral : 13.144 89.088 9064 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.08 % Allowed : 0.24 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.61 % Twisted General : 0.04 % 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: -0.86 (0.16), residues: 2905 helix: 0.34 (0.17), residues: 959 sheet: -0.53 (0.25), residues: 424 loop : -1.16 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 21 HIS 0.014 0.001 HIS K 33 PHE 0.035 0.002 PHE J 754 TYR 0.047 0.002 TYR I 309 ARG 0.005 0.000 ARG I1031 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 123 MET cc_start: 0.8658 (mpp) cc_final: 0.8167 (mpp) REVERT: I 580 MET cc_start: 0.8804 (mtm) cc_final: 0.8476 (mtm) REVERT: I 880 MET cc_start: 0.7716 (mpp) cc_final: 0.7434 (mpp) REVERT: I 1041 GLU cc_start: 0.8717 (tt0) cc_final: 0.8411 (tp30) REVERT: I 1052 MET cc_start: 0.8698 (ttm) cc_final: 0.8451 (ttm) REVERT: I 1067 TYR cc_start: 0.9144 (t80) cc_final: 0.8925 (t80) REVERT: I 1111 ILE cc_start: 0.9092 (mp) cc_final: 0.8561 (tt) REVERT: J 21 TRP cc_start: 0.7918 (m-10) cc_final: 0.7144 (m-10) REVERT: J 41 ARG cc_start: 0.8695 (tpm170) cc_final: 0.8332 (ptp-170) REVERT: J 456 MET cc_start: 0.6130 (mmm) cc_final: 0.5410 (tpt) REVERT: J 573 MET cc_start: 0.5980 (ttp) cc_final: 0.5469 (tpp) REVERT: J 661 MET cc_start: 0.8420 (ppp) cc_final: 0.8033 (ppp) REVERT: K 52 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7623 (mm-30) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.3452 time to fit residues: 90.9244 Evaluate side-chains 117 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 5.9990 chunk 219 optimal weight: 30.0000 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 212 ASN ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 632 ASN J 617 ASN ** J1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 23477 Z= 0.273 Angle : 0.648 15.119 31755 Z= 0.322 Chirality : 0.045 0.186 3590 Planarity : 0.005 0.077 4170 Dihedral : 5.229 37.249 3237 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.56 % Allowed : 7.97 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.66 (0.16), residues: 2905 helix: 0.52 (0.17), residues: 971 sheet: -0.59 (0.26), residues: 415 loop : -1.00 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J1398 HIS 0.009 0.001 HIS K 33 PHE 0.030 0.002 PHE J 806 TYR 0.029 0.002 TYR J1207 ARG 0.004 0.000 ARG K 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 2.703 Fit side-chains revert: symmetry clash REVERT: G 123 MET cc_start: 0.8594 (mpp) cc_final: 0.8207 (mpp) REVERT: I 880 MET cc_start: 0.7888 (mpp) cc_final: 0.7648 (mpp) REVERT: I 1041 GLU cc_start: 0.8715 (tt0) cc_final: 0.8330 (tp30) REVERT: I 1111 ILE cc_start: 0.9036 (mp) cc_final: 0.8603 (tt) REVERT: J 41 ARG cc_start: 0.8895 (tpm170) cc_final: 0.8476 (ptp-170) REVERT: J 512 MET cc_start: 0.8772 (tmm) cc_final: 0.8503 (tmm) REVERT: K 44 GLU cc_start: 0.8970 (tp30) cc_final: 0.8095 (pm20) outliers start: 14 outliers final: 6 residues processed: 128 average time/residue: 0.3113 time to fit residues: 68.0248 Evaluate side-chains 112 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain I residue 202 TYR Chi-restraints excluded: chain I residue 227 PHE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 1479 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 218 optimal weight: 0.9980 chunk 178 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 262 optimal weight: 20.0000 chunk 284 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 260 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 728 HIS I1093 GLN ** J1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23477 Z= 0.197 Angle : 0.589 14.669 31755 Z= 0.291 Chirality : 0.043 0.159 3590 Planarity : 0.004 0.065 4170 Dihedral : 5.047 37.792 3237 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.01 % Allowed : 11.35 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2905 helix: 0.65 (0.17), residues: 986 sheet: -0.46 (0.26), residues: 410 loop : -0.97 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP J 21 HIS 0.006 0.001 HIS I 999 PHE 0.016 0.001 PHE I 227 TYR 0.027 0.001 TYR J1207 ARG 0.004 0.000 ARG K 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 2.773 Fit side-chains REVERT: G 123 MET cc_start: 0.8557 (mpp) cc_final: 0.8170 (mpp) REVERT: I 158 TYR cc_start: 0.5554 (OUTLIER) cc_final: 0.4580 (p90) REVERT: I 275 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7956 (m-10) REVERT: I 340 MET cc_start: 0.8501 (tmm) cc_final: 0.8299 (tmm) REVERT: I 880 MET cc_start: 0.7829 (mpp) cc_final: 0.7607 (mpp) REVERT: I 1005 MET cc_start: 0.7235 (mtt) cc_final: 0.7022 (mtm) REVERT: I 1041 GLU cc_start: 0.8681 (tt0) cc_final: 0.8319 (tp30) REVERT: I 1052 MET cc_start: 0.8219 (ttm) cc_final: 0.7946 (ttm) REVERT: I 1083 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6049 (tp30) REVERT: I 1111 ILE cc_start: 0.9040 (mp) cc_final: 0.8566 (tt) REVERT: J 21 TRP cc_start: 0.8084 (m-10) cc_final: 0.7395 (m-10) REVERT: J 41 ARG cc_start: 0.8884 (tpm170) cc_final: 0.8477 (ptp-170) REVERT: J 512 MET cc_start: 0.8649 (tmm) cc_final: 0.8394 (tmm) REVERT: J 924 MET cc_start: 0.9111 (mmm) cc_final: 0.8875 (mmp) REVERT: K 29 GLN cc_start: 0.9475 (mp10) cc_final: 0.9087 (mp10) REVERT: K 74 VAL cc_start: 0.9147 (t) cc_final: 0.8736 (m) outliers start: 25 outliers final: 5 residues processed: 147 average time/residue: 0.3077 time to fit residues: 77.2318 Evaluate side-chains 123 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1479 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 263 optimal weight: 1.9990 chunk 279 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 ASN ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 728 HIS ** J1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1227 GLN ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 23477 Z= 0.264 Angle : 0.607 15.257 31755 Z= 0.301 Chirality : 0.044 0.189 3590 Planarity : 0.004 0.067 4170 Dihedral : 5.039 38.280 3237 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.41 % Allowed : 14.05 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.49 (0.16), residues: 2905 helix: 0.78 (0.17), residues: 980 sheet: -0.49 (0.26), residues: 422 loop : -1.00 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J1398 HIS 0.006 0.001 HIS I 889 PHE 0.020 0.002 PHE J1440 TYR 0.028 0.002 TYR J1207 ARG 0.004 0.000 ARG I 879 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 123 MET cc_start: 0.8502 (mpp) cc_final: 0.8146 (mpp) REVERT: H 1 MET cc_start: 0.8652 (ppp) cc_final: 0.7827 (ppp) REVERT: I 158 TYR cc_start: 0.5610 (OUTLIER) cc_final: 0.4703 (p90) REVERT: I 275 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.8259 (m-10) REVERT: I 340 MET cc_start: 0.8533 (tmm) cc_final: 0.8286 (tmm) REVERT: I 880 MET cc_start: 0.7952 (mpp) cc_final: 0.7638 (mpp) REVERT: I 1041 GLU cc_start: 0.8730 (tt0) cc_final: 0.8351 (tp30) REVERT: I 1052 MET cc_start: 0.8242 (ttm) cc_final: 0.7950 (ttm) REVERT: I 1083 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6109 (tp30) REVERT: I 1111 ILE cc_start: 0.9049 (mp) cc_final: 0.8623 (tt) REVERT: J 21 TRP cc_start: 0.8125 (m-10) cc_final: 0.7460 (m-10) REVERT: J 41 ARG cc_start: 0.8854 (tpm170) cc_final: 0.8437 (ptp-170) REVERT: J 512 MET cc_start: 0.8718 (tmm) cc_final: 0.8382 (tmm) REVERT: J 625 TYR cc_start: 0.8317 (m-80) cc_final: 0.8031 (m-80) REVERT: J 657 LEU cc_start: 0.9480 (mm) cc_final: 0.9231 (mm) REVERT: J 661 MET cc_start: 0.9476 (ptt) cc_final: 0.9137 (ptt) REVERT: K 44 GLU cc_start: 0.8898 (tp30) cc_final: 0.7980 (pm20) REVERT: K 74 VAL cc_start: 0.9156 (t) cc_final: 0.8758 (m) outliers start: 35 outliers final: 16 residues processed: 148 average time/residue: 0.2982 time to fit residues: 75.9529 Evaluate side-chains 132 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain J residue 829 VAL Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1479 ASP Chi-restraints excluded: chain J residue 1483 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1374 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 23477 Z= 0.399 Angle : 0.686 13.232 31755 Z= 0.343 Chirality : 0.046 0.313 3590 Planarity : 0.005 0.066 4170 Dihedral : 5.284 39.803 3237 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.13 % Allowed : 15.58 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.73 (0.16), residues: 2905 helix: 0.61 (0.17), residues: 984 sheet: -0.61 (0.25), residues: 427 loop : -1.18 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J1398 HIS 0.009 0.001 HIS I 889 PHE 0.020 0.002 PHE G 32 TYR 0.031 0.002 TYR J1207 ARG 0.005 0.000 ARG I 879 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 122 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 123 MET cc_start: 0.8553 (mpp) cc_final: 0.8154 (mpp) REVERT: H 1 MET cc_start: 0.8661 (ppp) cc_final: 0.8339 (ppp) REVERT: I 1 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7272 (tmm) REVERT: I 158 TYR cc_start: 0.5897 (OUTLIER) cc_final: 0.4951 (p90) REVERT: I 275 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8304 (m-10) REVERT: I 340 MET cc_start: 0.8655 (tmm) cc_final: 0.8412 (tmm) REVERT: I 880 MET cc_start: 0.7897 (mpp) cc_final: 0.7414 (mpp) REVERT: I 881 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7627 (p0) REVERT: I 1041 GLU cc_start: 0.8853 (tt0) cc_final: 0.8446 (tp30) REVERT: I 1052 MET cc_start: 0.8336 (ttm) cc_final: 0.8043 (ttm) REVERT: I 1081 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7453 (m) REVERT: I 1111 ILE cc_start: 0.9054 (mp) cc_final: 0.8724 (tp) REVERT: J 21 TRP cc_start: 0.8114 (m-10) cc_final: 0.7450 (m-10) REVERT: J 41 ARG cc_start: 0.8831 (tpm170) cc_final: 0.8423 (ptp-170) REVERT: J 512 MET cc_start: 0.8744 (tmm) cc_final: 0.8394 (tmm) REVERT: J 657 LEU cc_start: 0.9466 (mm) cc_final: 0.9186 (mm) REVERT: J 924 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8927 (mmp) REVERT: K 29 GLN cc_start: 0.9440 (mt0) cc_final: 0.9003 (mt0) REVERT: K 44 GLU cc_start: 0.8896 (tp30) cc_final: 0.7994 (pm20) REVERT: K 74 VAL cc_start: 0.9143 (t) cc_final: 0.8794 (m) outliers start: 53 outliers final: 32 residues processed: 167 average time/residue: 0.3156 time to fit residues: 88.7637 Evaluate side-chains 148 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 110 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 183 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 275 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 533 ASP Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 881 ASN Chi-restraints excluded: chain I residue 963 LEU Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1081 VAL Chi-restraints excluded: chain J residue 637 LEU Chi-restraints excluded: chain J residue 648 MET Chi-restraints excluded: chain J residue 747 VAL Chi-restraints excluded: chain J residue 827 ILE Chi-restraints excluded: chain J residue 836 VAL Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 873 LEU Chi-restraints excluded: chain J residue 924 MET Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain K residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 0.6980 chunk 251 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 279 optimal weight: 20.0000 chunk 232 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 91 GLN I 102 HIS I 543 ASN I 632 ASN ** J1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23477 Z= 0.170 Angle : 0.581 13.447 31755 Z= 0.286 Chirality : 0.043 0.226 3590 Planarity : 0.004 0.069 4170 Dihedral : 4.951 39.145 3237 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.73 % Allowed : 16.87 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.48 (0.16), residues: 2905 helix: 0.85 (0.17), residues: 985 sheet: -0.58 (0.26), residues: 425 loop : -1.02 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J1398 HIS 0.004 0.001 HIS J1364 PHE 0.026 0.001 PHE J1440 TYR 0.027 0.001 TYR J1207 ARG 0.008 0.000 ARG K 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 123 MET cc_start: 0.8528 (mpp) cc_final: 0.8119 (mpp) REVERT: H 1 MET cc_start: 0.8610 (ppp) cc_final: 0.7305 (ppp) REVERT: I 1 MET cc_start: 0.7663 (tmm) cc_final: 0.7436 (tmm) REVERT: I 158 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.5227 (p90) REVERT: I 340 MET cc_start: 0.8541 (tmm) cc_final: 0.8267 (tmm) REVERT: I 880 MET cc_start: 0.8014 (mpp) cc_final: 0.7570 (mpp) REVERT: I 881 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7383 (p0) REVERT: I 1041 GLU cc_start: 0.8731 (tt0) cc_final: 0.8446 (tp30) REVERT: I 1052 MET cc_start: 0.8219 (ttm) cc_final: 0.7813 (ttm) REVERT: I 1059 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7204 (t0) REVERT: I 1081 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7447 (m) REVERT: I 1111 ILE cc_start: 0.9057 (mp) cc_final: 0.8702 (tp) REVERT: J 21 TRP cc_start: 0.8097 (m-10) cc_final: 0.7481 (m-10) REVERT: J 41 ARG cc_start: 0.8753 (tpm170) cc_final: 0.8345 (ptp-170) REVERT: J 512 MET cc_start: 0.8750 (tmm) cc_final: 0.8380 (tmm) REVERT: J 625 TYR cc_start: 0.8286 (m-80) cc_final: 0.8054 (m-80) REVERT: J 657 LEU cc_start: 0.9372 (mm) cc_final: 0.9107 (mm) REVERT: J 796 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8400 (ptp-170) REVERT: J 1278 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8885 (m-30) REVERT: J 1488 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7513 (p0) REVERT: K 29 GLN cc_start: 0.9397 (mt0) cc_final: 0.8845 (mp10) REVERT: K 31 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9216 (mm) REVERT: K 44 GLU cc_start: 0.8837 (tp30) cc_final: 0.7956 (pm20) REVERT: K 74 VAL cc_start: 0.9136 (t) cc_final: 0.8799 (m) outliers start: 43 outliers final: 21 residues processed: 165 average time/residue: 0.3198 time to fit residues: 88.1520 Evaluate side-chains 148 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 569 VAL Chi-restraints excluded: chain I residue 881 ASN Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1081 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain J residue 648 MET Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 796 ARG Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1211 MET Chi-restraints excluded: chain J residue 1278 ASP Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain J residue 1488 ASP Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 156 optimal weight: 0.5980 chunk 278 optimal weight: 7.9990 chunk 174 optimal weight: 40.0000 chunk 169 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 23477 Z= 0.275 Angle : 0.615 13.285 31755 Z= 0.304 Chirality : 0.044 0.326 3590 Planarity : 0.004 0.072 4170 Dihedral : 4.976 38.752 3237 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.09 % Allowed : 17.23 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.52 (0.16), residues: 2905 helix: 0.81 (0.17), residues: 989 sheet: -0.53 (0.26), residues: 431 loop : -1.07 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J1434 HIS 0.006 0.001 HIS I 889 PHE 0.017 0.002 PHE J1440 TYR 0.028 0.002 TYR J 128 ARG 0.006 0.000 ARG K 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 122 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 123 MET cc_start: 0.8553 (mpp) cc_final: 0.8182 (mpp) REVERT: H 1 MET cc_start: 0.8670 (ppp) cc_final: 0.7259 (ppp) REVERT: I 1 MET cc_start: 0.7593 (tmm) cc_final: 0.7372 (tmm) REVERT: I 158 TYR cc_start: 0.6314 (OUTLIER) cc_final: 0.5582 (p90) REVERT: I 340 MET cc_start: 0.8595 (tmm) cc_final: 0.8255 (tmm) REVERT: I 880 MET cc_start: 0.7981 (mpp) cc_final: 0.7455 (mpp) REVERT: I 881 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7520 (p0) REVERT: I 944 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8891 (mm) REVERT: I 1052 MET cc_start: 0.8303 (ttm) cc_final: 0.7939 (ttm) REVERT: I 1059 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7210 (t0) REVERT: I 1111 ILE cc_start: 0.9105 (mp) cc_final: 0.8640 (tt) REVERT: J 21 TRP cc_start: 0.8143 (m-10) cc_final: 0.7549 (m-10) REVERT: J 41 ARG cc_start: 0.8765 (tpm170) cc_final: 0.8370 (ptp-170) REVERT: J 512 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8340 (tmm) REVERT: J 625 TYR cc_start: 0.8309 (m-80) cc_final: 0.8092 (m-80) REVERT: J 657 LEU cc_start: 0.9403 (mm) cc_final: 0.9108 (mm) REVERT: J 796 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8596 (ptp-170) REVERT: J 911 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9212 (mm) REVERT: J 1488 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7538 (p0) REVERT: K 29 GLN cc_start: 0.9422 (mt0) cc_final: 0.8871 (mp10) REVERT: K 31 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9228 (mm) REVERT: K 44 GLU cc_start: 0.8878 (tp30) cc_final: 0.8057 (pm20) REVERT: K 74 VAL cc_start: 0.9142 (t) cc_final: 0.8798 (m) outliers start: 52 outliers final: 33 residues processed: 166 average time/residue: 0.3182 time to fit residues: 89.8443 Evaluate side-chains 158 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 183 ASP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 175 GLU Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 321 GLU Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 533 ASP Chi-restraints excluded: chain I residue 569 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 881 ASN Chi-restraints excluded: chain I residue 944 LEU Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 512 MET Chi-restraints excluded: chain J residue 648 MET Chi-restraints excluded: chain J residue 751 LEU Chi-restraints excluded: chain J residue 796 ARG Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 895 VAL Chi-restraints excluded: chain J residue 911 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1219 GLU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1435 LEU Chi-restraints excluded: chain J residue 1459 LEU Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain J residue 1488 ASP Chi-restraints excluded: chain K residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 229 GLN ** J1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23477 Z= 0.206 Angle : 0.585 13.240 31755 Z= 0.289 Chirality : 0.044 0.632 3590 Planarity : 0.004 0.073 4170 Dihedral : 4.871 38.203 3237 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.21 % Allowed : 17.11 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.46 (0.16), residues: 2905 helix: 0.85 (0.17), residues: 991 sheet: -0.54 (0.26), residues: 424 loop : -1.02 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J1398 HIS 0.005 0.001 HIS I 999 PHE 0.013 0.001 PHE I 227 TYR 0.027 0.001 TYR J1207 ARG 0.005 0.000 ARG K 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 126 time to evaluate : 2.735 Fit side-chains revert: symmetry clash REVERT: G 1 MET cc_start: 0.7564 (tmm) cc_final: 0.7353 (tmm) REVERT: G 123 MET cc_start: 0.8562 (mpp) cc_final: 0.8137 (mpp) REVERT: H 1 MET cc_start: 0.8512 (ppp) cc_final: 0.7834 (ppp) REVERT: I 1 MET cc_start: 0.7559 (tmm) cc_final: 0.7352 (tmm) REVERT: I 158 TYR cc_start: 0.6515 (OUTLIER) cc_final: 0.5788 (p90) REVERT: I 340 MET cc_start: 0.8568 (tmm) cc_final: 0.8281 (tmm) REVERT: I 880 MET cc_start: 0.8000 (mpp) cc_final: 0.7570 (mpp) REVERT: I 881 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7427 (p0) REVERT: I 1005 MET cc_start: 0.7467 (mtt) cc_final: 0.7144 (mtm) REVERT: I 1052 MET cc_start: 0.8244 (ttm) cc_final: 0.7794 (ttm) REVERT: I 1059 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7218 (t0) REVERT: I 1081 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7696 (m) REVERT: I 1097 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8120 (mm) REVERT: I 1111 ILE cc_start: 0.9115 (mp) cc_final: 0.8773 (tp) REVERT: J 21 TRP cc_start: 0.8155 (m-10) cc_final: 0.7573 (m-10) REVERT: J 41 ARG cc_start: 0.8733 (tpm170) cc_final: 0.8327 (ptp-170) REVERT: J 512 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8313 (tmm) REVERT: J 625 TYR cc_start: 0.8287 (m-80) cc_final: 0.8083 (m-80) REVERT: J 657 LEU cc_start: 0.9359 (mm) cc_final: 0.9037 (mm) REVERT: J 796 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8448 (ptp-170) REVERT: J 911 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9205 (mm) REVERT: J 1398 TRP cc_start: 0.7222 (m-90) cc_final: 0.7001 (m-10) REVERT: J 1488 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7554 (p0) REVERT: K 29 GLN cc_start: 0.9393 (mt0) cc_final: 0.8832 (mp10) REVERT: K 31 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9216 (mm) REVERT: K 44 GLU cc_start: 0.8742 (tp30) cc_final: 0.7940 (pm20) REVERT: K 74 VAL cc_start: 0.9146 (t) cc_final: 0.8806 (m) outliers start: 55 outliers final: 35 residues processed: 174 average time/residue: 0.3054 time to fit residues: 89.9535 Evaluate side-chains 164 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 119 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 321 GLU Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 533 ASP Chi-restraints excluded: chain I residue 569 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 881 ASN Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1081 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 512 MET Chi-restraints excluded: chain J residue 648 MET Chi-restraints excluded: chain J residue 796 ARG Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 895 VAL Chi-restraints excluded: chain J residue 911 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1219 GLU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1459 LEU Chi-restraints excluded: chain J residue 1471 LEU Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain J residue 1488 ASP Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 0.2980 chunk 266 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 259 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 234 optimal weight: 0.8980 chunk 245 optimal weight: 0.0070 chunk 258 optimal weight: 7.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23477 Z= 0.160 Angle : 0.580 13.375 31755 Z= 0.285 Chirality : 0.044 0.378 3590 Planarity : 0.004 0.074 4170 Dihedral : 4.733 36.786 3237 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.89 % Allowed : 17.67 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2905 helix: 0.90 (0.17), residues: 994 sheet: -0.41 (0.26), residues: 430 loop : -0.97 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J1398 HIS 0.003 0.001 HIS J1364 PHE 0.014 0.001 PHE J 919 TYR 0.024 0.001 TYR J1207 ARG 0.004 0.000 ARG K 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 3.021 Fit side-chains revert: symmetry clash REVERT: G 1 MET cc_start: 0.7607 (tmm) cc_final: 0.7379 (tmm) REVERT: G 123 MET cc_start: 0.8522 (mpp) cc_final: 0.8152 (mpp) REVERT: H 1 MET cc_start: 0.8410 (ppp) cc_final: 0.7714 (ppp) REVERT: I 158 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.5970 (p90) REVERT: I 340 MET cc_start: 0.8527 (tmm) cc_final: 0.8134 (tmm) REVERT: I 880 MET cc_start: 0.7894 (mpp) cc_final: 0.7551 (mpp) REVERT: I 881 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7243 (p0) REVERT: I 1005 MET cc_start: 0.7410 (mtt) cc_final: 0.7098 (mtm) REVERT: I 1052 MET cc_start: 0.8286 (ttm) cc_final: 0.7812 (ttm) REVERT: I 1059 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7197 (t0) REVERT: I 1081 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7731 (m) REVERT: I 1097 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8060 (mm) REVERT: I 1111 ILE cc_start: 0.9167 (mp) cc_final: 0.8811 (tp) REVERT: J 21 TRP cc_start: 0.8176 (m-10) cc_final: 0.7622 (m-10) REVERT: J 41 ARG cc_start: 0.8740 (tpm170) cc_final: 0.8344 (ptp-170) REVERT: J 512 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8243 (tmm) REVERT: J 657 LEU cc_start: 0.9332 (mm) cc_final: 0.8992 (mm) REVERT: J 796 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8365 (ptt-90) REVERT: J 1488 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7532 (p0) REVERT: K 29 GLN cc_start: 0.9382 (mt0) cc_final: 0.8811 (mt0) REVERT: K 31 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9210 (mm) REVERT: K 66 LYS cc_start: 0.8746 (ptpt) cc_final: 0.8493 (pttt) REVERT: K 74 VAL cc_start: 0.9132 (t) cc_final: 0.8790 (m) outliers start: 47 outliers final: 30 residues processed: 169 average time/residue: 0.3597 time to fit residues: 102.7815 Evaluate side-chains 155 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 116 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 881 ASN Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1081 VAL Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 512 MET Chi-restraints excluded: chain J residue 648 MET Chi-restraints excluded: chain J residue 796 ARG Chi-restraints excluded: chain J residue 853 VAL Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1211 MET Chi-restraints excluded: chain J residue 1219 GLU Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain J residue 1488 ASP Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 40.0000 chunk 274 optimal weight: 6.9990 chunk 167 optimal weight: 0.0030 chunk 130 optimal weight: 0.9980 chunk 190 optimal weight: 0.0020 chunk 287 optimal weight: 6.9990 chunk 264 optimal weight: 8.9990 chunk 229 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 177 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 999 HIS I1018 GLN ** J 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 23477 Z= 0.160 Angle : 0.581 13.673 31755 Z= 0.283 Chirality : 0.044 0.446 3590 Planarity : 0.004 0.075 4170 Dihedral : 4.631 35.832 3237 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.69 % Allowed : 18.00 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2905 helix: 0.92 (0.17), residues: 994 sheet: -0.32 (0.26), residues: 427 loop : -0.92 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP J1398 HIS 0.004 0.001 HIS I 999 PHE 0.041 0.001 PHE I1085 TYR 0.023 0.001 TYR J1207 ARG 0.005 0.000 ARG K 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5810 Ramachandran restraints generated. 2905 Oldfield, 0 Emsley, 2905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 123 MET cc_start: 0.8495 (mpp) cc_final: 0.8124 (mpp) REVERT: H 1 MET cc_start: 0.8427 (ppp) cc_final: 0.6877 (ppp) REVERT: I 158 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.6340 (p90) REVERT: I 340 MET cc_start: 0.8500 (tmm) cc_final: 0.8110 (tmm) REVERT: I 699 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8766 (t80) REVERT: I 880 MET cc_start: 0.7820 (mpp) cc_final: 0.7537 (mpp) REVERT: I 881 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7290 (p0) REVERT: I 1005 MET cc_start: 0.7444 (mtt) cc_final: 0.7201 (mtm) REVERT: I 1052 MET cc_start: 0.8258 (ttm) cc_final: 0.7800 (ttm) REVERT: I 1059 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7277 (t0) REVERT: I 1081 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7729 (m) REVERT: I 1097 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8062 (mm) REVERT: I 1111 ILE cc_start: 0.9197 (mp) cc_final: 0.8811 (tp) REVERT: J 21 TRP cc_start: 0.8203 (m-10) cc_final: 0.7636 (m-10) REVERT: J 41 ARG cc_start: 0.8737 (tpm170) cc_final: 0.8336 (ptp-170) REVERT: J 512 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8242 (tmm) REVERT: J 657 LEU cc_start: 0.9361 (mm) cc_final: 0.9020 (mm) REVERT: J 911 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9194 (mm) REVERT: J 985 ASP cc_start: 0.8699 (p0) cc_final: 0.8381 (t0) REVERT: J 1488 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7494 (p0) REVERT: K 29 GLN cc_start: 0.9375 (mt0) cc_final: 0.8800 (mt0) REVERT: K 31 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9198 (mm) REVERT: K 74 VAL cc_start: 0.9145 (t) cc_final: 0.8812 (m) outliers start: 42 outliers final: 25 residues processed: 167 average time/residue: 0.3064 time to fit residues: 87.3923 Evaluate side-chains 159 residues out of total 2484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 114 PHE Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 158 TYR Chi-restraints excluded: chain I residue 461 VAL Chi-restraints excluded: chain I residue 464 LEU Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 513 VAL Chi-restraints excluded: chain I residue 569 VAL Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain I residue 668 LEU Chi-restraints excluded: chain I residue 699 PHE Chi-restraints excluded: chain I residue 800 VAL Chi-restraints excluded: chain I residue 865 THR Chi-restraints excluded: chain I residue 881 ASN Chi-restraints excluded: chain I residue 997 LEU Chi-restraints excluded: chain I residue 1059 ASP Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1081 VAL Chi-restraints excluded: chain I residue 1097 LEU Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 512 MET Chi-restraints excluded: chain J residue 911 LEU Chi-restraints excluded: chain J residue 1158 VAL Chi-restraints excluded: chain J residue 1211 MET Chi-restraints excluded: chain J residue 1415 VAL Chi-restraints excluded: chain J residue 1466 VAL Chi-restraints excluded: chain J residue 1483 PHE Chi-restraints excluded: chain J residue 1488 ASP Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 9.9990 chunk 244 optimal weight: 0.0370 chunk 70 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 235 optimal weight: 0.0470 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1075 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.078258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053745 restraints weight = 88057.916| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.61 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23477 Z= 0.189 Angle : 0.588 13.482 31755 Z= 0.287 Chirality : 0.044 0.358 3590 Planarity : 0.004 0.076 4170 Dihedral : 4.630 36.130 3237 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.61 % Allowed : 18.08 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.30 (0.16), residues: 2905 helix: 0.89 (0.17), residues: 1006 sheet: -0.30 (0.26), residues: 427 loop : -0.92 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J1398 HIS 0.004 0.001 HIS I 999 PHE 0.045 0.001 PHE I1085 TYR 0.023 0.001 TYR J1207 ARG 0.005 0.000 ARG K 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3965.76 seconds wall clock time: 74 minutes 0.15 seconds (4440.15 seconds total)