Starting phenix.real_space_refine on Sun Jun 30 02:02:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2j_38012/06_2024/8x2j_38012_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2j_38012/06_2024/8x2j_38012.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2j_38012/06_2024/8x2j_38012_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2j_38012/06_2024/8x2j_38012_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2j_38012/06_2024/8x2j_38012_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2j_38012/06_2024/8x2j_38012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2j_38012/06_2024/8x2j_38012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2j_38012/06_2024/8x2j_38012_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x2j_38012/06_2024/8x2j_38012_updated.pdb" } resolution = 2.7 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= 0.004 sd= 0.072 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 Fe 21 7.16 5 P 2 5.49 5 S 115 5.16 5 C 12975 2.51 5 N 3303 2.21 5 O 3502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 19918 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1763 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "B" Number of atoms: 7350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7350 Classifications: {'peptide': 951} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 892} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3655 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 23, 'TRANS': 425} Chain: "D" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1350 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 15, 'TRANS': 159} Chain: "E" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1292 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 153} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3128 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 20, 'TRANS': 376} Chain: "G" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 623 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 6, 'TRANS': 73} Chain: "I" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'HEC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {'F3S': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 163 Unusual residues: {'HQO': 1, 'JL3': 1, 'JLQ': 1, 'JM9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7333 SG CYS B 797 52.971 42.479 98.627 1.00 54.19 S ATOM 8689 SG CYS B 972 58.593 44.572 97.472 1.00 46.49 S ATOM 7352 SG CYS B 800 53.549 46.749 93.858 1.00 40.41 S ATOM 7315 SG CYS B 794 55.983 40.836 92.991 1.00 54.61 S ATOM 8420 SG CYS B 934 57.104 57.106 93.824 1.00 41.75 S ATOM 8395 SG CYS B 931 56.645 54.279 87.535 1.00 45.38 S ATOM 7377 SG CYS B 804 52.080 54.392 91.611 1.00 53.52 S ATOM 8660 SG CYS B 968 57.812 51.547 93.169 1.00 37.46 S ATOM 7749 SG CYS B 850 57.652 54.887 82.065 1.00 48.46 S ATOM 7808 SG CYS B 858 56.630 57.333 76.258 1.00 35.36 S ATOM 8067 SG CYS B 892 53.945 52.082 77.292 1.00 29.72 S ATOM 7772 SG CYS B 853 60.601 52.044 77.597 1.00 27.77 S ATOM 8039 SG CYS B 888 50.053 59.553 75.179 1.00 40.82 S ATOM 7994 SG CYS B 882 48.012 64.117 77.835 1.00 35.82 S ATOM 7837 SG CYS B 862 52.953 64.122 73.376 1.00 29.08 S Time building chain proxies: 10.57, per 1000 atoms: 0.53 Number of scatterers: 19918 At special positions: 0 Unit cell: (100.44, 119.97, 150.66, 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) Fe 21 26.01 S 115 16.00 P 2 15.00 O 3502 8.00 N 3303 7.00 C 12975 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=23, symmetry=0 Number of additional bonds: simple=23, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.80 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1104 " pdb="FE1 F3S B1104 " - pdb=" SG CYS B 888 " pdb="FE4 F3S B1104 " - pdb=" SG CYS B 862 " pdb="FE3 F3S B1104 " - pdb=" SG CYS B 882 " pdb=" SF4 B1101 " pdb="FE3 SF4 B1101 " - pdb=" SG CYS B 800 " pdb="FE2 SF4 B1101 " - pdb=" SG CYS B 972 " pdb="FE1 SF4 B1101 " - pdb=" SG CYS B 797 " pdb="FE4 SF4 B1101 " - pdb=" SG CYS B 794 " pdb=" SF4 B1102 " pdb="FE2 SF4 B1102 " - pdb=" SG CYS B 931 " pdb="FE3 SF4 B1102 " - pdb=" SG CYS B 804 " pdb="FE4 SF4 B1102 " - pdb=" SG CYS B 968 " pdb="FE1 SF4 B1102 " - pdb=" SG CYS B 934 " pdb=" SF4 B1103 " pdb="FE1 SF4 B1103 " - pdb=" SG CYS B 850 " pdb="FE2 SF4 B1103 " - pdb=" SG CYS B 858 " pdb="FE3 SF4 B1103 " - pdb=" SG CYS B 892 " pdb="FE4 SF4 B1103 " - pdb=" SG CYS B 853 " Number of angles added : 45 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 103 helices and 12 sheets defined 49.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 7 through 36 removed outlier: 4.095A pdb=" N ASN A 10 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 11 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 14 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 22 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 84 through 91 removed outlier: 4.296A pdb=" N CYS A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 141 through 144 No H-bonds generated for 'chain 'A' and resid 141 through 144' Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.733A pdb=" N CYS A 167 " --> pdb=" O TRP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 214 through 217 No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'B' and resid 142 through 151 removed outlier: 4.706A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU B 149 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'B' and resid 201 through 213 Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 268 through 279 Processing helix chain 'B' and resid 300 through 303 No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 316 through 327 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 368 through 380 Processing helix chain 'B' and resid 401 through 414 Processing helix chain 'B' and resid 427 through 430 No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 456 through 460 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 528 through 537 Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 584 through 587 removed outlier: 4.600A pdb=" N ASN B 587 " --> pdb=" O PHE B 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 584 through 587' Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 611 through 618 Processing helix chain 'B' and resid 634 through 644 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 753 through 763 Processing helix chain 'B' and resid 791 through 793 No H-bonds generated for 'chain 'B' and resid 791 through 793' Processing helix chain 'B' and resid 799 through 808 Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 857 through 860 No H-bonds generated for 'chain 'B' and resid 857 through 860' Processing helix chain 'B' and resid 910 through 915 Processing helix chain 'B' and resid 935 through 952 Processing helix chain 'B' and resid 967 through 971 Processing helix chain 'B' and resid 988 through 993 Processing helix chain 'C' and resid 25 through 33 Processing helix chain 'C' and resid 40 through 42 No H-bonds generated for 'chain 'C' and resid 40 through 42' Processing helix chain 'C' and resid 45 through 71 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 86 through 111 removed outlier: 4.038A pdb=" N GLY C 98 " --> pdb=" O TRP C 94 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 120 through 141 removed outlier: 3.882A pdb=" N LEU C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.657A pdb=" N PHE C 148 " --> pdb=" O PRO C 145 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR C 149 " --> pdb=" O TRP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 200 Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 204 through 214 removed outlier: 4.061A pdb=" N ARG C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 254 removed outlier: 3.625A pdb=" N ARG C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 4.472A pdb=" N PHE C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 292 Proline residue: C 288 - end of helix Processing helix chain 'C' and resid 301 through 331 Processing helix chain 'C' and resid 335 through 346 Processing helix chain 'C' and resid 350 through 360 Processing helix chain 'C' and resid 362 through 368 Proline residue: C 366 - end of helix No H-bonds generated for 'chain 'C' and resid 362 through 368' Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 376 through 403 removed outlier: 3.871A pdb=" N ILE C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 418 through 441 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'D' and resid 15 through 27 Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 55 through 79 removed outlier: 3.611A pdb=" N GLN D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 136 through 142 removed outlier: 4.084A pdb=" N GLN D 139 " --> pdb=" O PRO D 136 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR D 140 " --> pdb=" O ARG D 137 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER D 142 " --> pdb=" O GLN D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 168 Processing helix chain 'E' and resid 68 through 71 No H-bonds generated for 'chain 'E' and resid 68 through 71' Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 138 through 146 Processing helix chain 'E' and resid 171 through 187 Processing helix chain 'F' and resid 12 through 38 removed outlier: 3.641A pdb=" N PHE F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU F 38 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 70 removed outlier: 3.609A pdb=" N PHE F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR F 49 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR F 56 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Proline residue: F 58 - end of helix Processing helix chain 'F' and resid 74 through 96 removed outlier: 5.336A pdb=" N ARG F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N MET F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR F 89 " --> pdb=" O ALA F 85 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU F 90 " --> pdb=" O GLY F 86 " (cutoff:3.500A) Proline residue: F 91 - end of helix Processing helix chain 'F' and resid 98 through 104 Processing helix chain 'F' and resid 106 through 111 removed outlier: 4.410A pdb=" N LYS F 109 " --> pdb=" O ASP F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 121 No H-bonds generated for 'chain 'F' and resid 119 through 121' Processing helix chain 'F' and resid 123 through 126 No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 146 through 176 Processing helix chain 'F' and resid 182 through 210 removed outlier: 3.796A pdb=" N ARG F 186 " --> pdb=" O LYS F 182 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N MET F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 244 Processing helix chain 'F' and resid 251 through 254 No H-bonds generated for 'chain 'F' and resid 251 through 254' Processing helix chain 'F' and resid 257 through 287 removed outlier: 3.729A pdb=" N GLN F 281 " --> pdb=" O MET F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 Processing helix chain 'F' and resid 305 through 315 Processing helix chain 'F' and resid 318 through 323 removed outlier: 3.591A pdb=" N PHE F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 331 No H-bonds generated for 'chain 'F' and resid 328 through 331' Processing helix chain 'F' and resid 333 through 358 Proline residue: F 357 - end of helix Processing helix chain 'F' and resid 369 through 391 Proline residue: F 374 - end of helix removed outlier: 3.803A pdb=" N GLN F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 405 removed outlier: 3.942A pdb=" N GLU F 403 " --> pdb=" O PRO F 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 54 Processing helix chain 'G' and resid 70 through 80 Processing helix chain 'G' and resid 99 through 106 Processing helix chain 'I' and resid 10 through 34 Processing sheet with id= A, first strand: chain 'B' and resid 100 through 107 removed outlier: 3.815A pdb=" N LYS B 126 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 191 through 194 removed outlier: 6.619A pdb=" N THR B 419 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU B 194 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE B 421 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 446 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N MET B 422 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 448 " --> pdb=" O MET B 422 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 242 through 246 Processing sheet with id= D, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.257A pdb=" N VAL B 253 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE B 361 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL B 255 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG B 290 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER B 256 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR B 292 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS B 307 " --> pdb=" O VAL B 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 475 through 477 Processing sheet with id= F, first strand: chain 'B' and resid 571 through 576 Processing sheet with id= G, first strand: chain 'B' and resid 607 through 609 Processing sheet with id= H, first strand: chain 'B' and resid 652 through 655 Processing sheet with id= I, first strand: chain 'B' and resid 741 through 743 removed outlier: 6.379A pdb=" N ARG B1016 " --> pdb=" O GLY B 742 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 977 through 981 Processing sheet with id= K, first strand: chain 'B' and resid 867 through 869 Processing sheet with id= L, first strand: chain 'D' and resid 173 through 177 removed outlier: 3.806A pdb=" N GLN D 173 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY D 7 " --> pdb=" O VAL D 177 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2274 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: 5.89 Time building geometry restraints manager: 8.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.75: 20283 1.75 - 2.32: 230 2.32 - 2.90: 1 2.90 - 3.47: 0 3.47 - 4.04: 3 Bond restraints: 20517 Sorted by residual: bond pdb=" S2 F3S B1104 " pdb="FE3 F3S B1104 " ideal model delta sigma weight residual 2.300 4.041 -1.741 2.00e-02 2.50e+03 7.58e+03 bond pdb=" S4 F3S B1104 " pdb="FE1 F3S B1104 " ideal model delta sigma weight residual 2.233 3.875 -1.642 2.00e-02 2.50e+03 6.74e+03 bond pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " ideal model delta sigma weight residual 2.258 3.784 -1.526 2.00e-02 2.50e+03 5.82e+03 bond pdb=" CA HIS C 141 " pdb=" C HIS C 141 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.41e-02 5.03e+03 2.00e+01 bond pdb=" CA SER B 889 " pdb=" CB SER B 889 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.63e-02 3.76e+03 1.63e+01 ... (remaining 20512 not shown) Histogram of bond angle deviations from ideal: 38.41 - 66.61: 6 66.61 - 94.80: 66 94.80 - 123.00: 26359 123.00 - 151.20: 1625 151.20 - 179.40: 12 Bond angle restraints: 28068 Sorted by residual: angle pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " pdb=" S3 F3S B1104 " ideal model delta sigma weight residual 114.75 65.69 49.06 3.00e+00 1.11e-01 2.67e+02 angle pdb=" S3 F3S B1104 " pdb="FE1 F3S B1104 " pdb=" S4 F3S B1104 " ideal model delta sigma weight residual 112.59 65.94 46.65 3.00e+00 1.11e-01 2.42e+02 angle pdb=" S2 F3S B1104 " pdb="FE3 F3S B1104 " pdb=" S4 F3S B1104 " ideal model delta sigma weight residual 103.26 69.17 34.09 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 F3S B1104 " pdb="FE3 F3S B1104 " pdb=" S2 F3S B1104 " ideal model delta sigma weight residual 103.25 69.37 33.88 3.00e+00 1.11e-01 1.28e+02 angle pdb="FE3 F3S B1104 " pdb=" S2 F3S B1104 " pdb="FE4 F3S B1104 " ideal model delta sigma weight residual 71.75 38.41 33.34 3.00e+00 1.11e-01 1.24e+02 ... (remaining 28063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.84: 11411 29.84 - 59.69: 369 59.69 - 89.53: 55 89.53 - 119.38: 4 119.38 - 149.22: 4 Dihedral angle restraints: 11843 sinusoidal: 4705 harmonic: 7138 Sorted by residual: dihedral pdb=" CA VAL C 35 " pdb=" C VAL C 35 " pdb=" N PRO C 36 " pdb=" CA PRO C 36 " ideal model delta harmonic sigma weight residual 180.00 155.41 24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ASP C 252 " pdb=" C ASP C 252 " pdb=" N PHE C 253 " pdb=" CA PHE C 253 " ideal model delta harmonic sigma weight residual 180.00 156.22 23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ALA B 461 " pdb=" C ALA B 461 " pdb=" N THR B 462 " pdb=" CA THR B 462 " ideal model delta harmonic sigma weight residual 180.00 156.41 23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 11840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.445: 3043 3.445 - 6.891: 0 6.891 - 10.336: 0 10.336 - 13.782: 0 13.782 - 17.227: 1 Chirality restraints: 3044 Sorted by residual: chirality pdb=" S2 F3S B1104 " pdb="FE1 F3S B1104 " pdb="FE3 F3S B1104 " pdb="FE4 F3S B1104 " both_signs ideal model delta sigma weight residual False 10.77 -6.46 17.23 2.00e-01 2.50e+01 7.42e+03 chirality pdb=" CG LEU D 79 " pdb=" CB LEU D 79 " pdb=" CD1 LEU D 79 " pdb=" CD2 LEU D 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL C 265 " pdb=" CA VAL C 265 " pdb=" CG1 VAL C 265 " pdb=" CG2 VAL C 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 3041 not shown) Planarity restraints: 3537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 192 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C GLN A 192 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN A 192 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 193 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 12 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO I 13 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO I 13 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 13 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 356 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO F 357 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 357 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 357 " 0.041 5.00e-02 4.00e+02 ... (remaining 3534 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 140 2.50 - 3.10: 13531 3.10 - 3.70: 33476 3.70 - 4.30: 50294 4.30 - 4.90: 81331 Nonbonded interactions: 178772 Sorted by model distance: nonbonded pdb=" CE1 HIS A 133 " pdb="FE HEC A 302 " model vdw 1.902 3.220 nonbonded pdb=" NE2 HIS A 70 " pdb="FE HEC A 304 " model vdw 2.084 3.080 nonbonded pdb=" NE2 HIS A 58 " pdb="FE HEC A 305 " model vdw 2.085 3.080 nonbonded pdb=" NE2 HIS A 130 " pdb="FE HEC A 303 " model vdw 2.119 3.080 nonbonded pdb=" NE2 HIS A 133 " pdb="FE HEC A 302 " model vdw 2.156 3.080 ... (remaining 178767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.930 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: 2.850 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 56.430 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.021 1.741 20517 Z= 1.454 Angle : 1.165 49.057 28068 Z= 0.547 Chirality : 0.317 17.227 3044 Planarity : 0.008 0.077 3537 Dihedral : 15.539 149.224 7279 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 0.39 % Allowed : 0.64 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 2455 helix: -0.93 (0.12), residues: 1252 sheet: -0.91 (0.39), residues: 176 loop : -1.53 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 115 HIS 0.011 0.002 HIS C 141 PHE 0.046 0.002 PHE C 266 TYR 0.035 0.002 TYR B 933 ARG 0.009 0.001 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 361 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8868 (t70) cc_final: 0.8406 (t70) REVERT: A 88 MET cc_start: 0.7322 (mmm) cc_final: 0.7103 (mmm) REVERT: A 121 ASP cc_start: 0.7436 (t0) cc_final: 0.7224 (t70) REVERT: A 202 GLU cc_start: 0.8531 (tt0) cc_final: 0.8209 (tt0) REVERT: B 83 TYR cc_start: 0.8122 (m-80) cc_final: 0.7390 (m-80) REVERT: B 113 THR cc_start: 0.8142 (t) cc_final: 0.7704 (m) REVERT: B 162 ARG cc_start: 0.6959 (ttt-90) cc_final: 0.6732 (ttt-90) REVERT: B 218 ARG cc_start: 0.6968 (mmt-90) cc_final: 0.6649 (mmp80) REVERT: B 342 GLU cc_start: 0.6908 (tt0) cc_final: 0.6261 (mm-30) REVERT: B 406 VAL cc_start: 0.6894 (t) cc_final: 0.6510 (m) REVERT: B 460 ARG cc_start: 0.7208 (ttm110) cc_final: 0.6914 (mtp-110) REVERT: B 530 THR cc_start: 0.8001 (t) cc_final: 0.7688 (m) REVERT: B 743 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7582 (mp0) REVERT: B 762 GLU cc_start: 0.7185 (tp30) cc_final: 0.6840 (tt0) REVERT: C 193 ASP cc_start: 0.7434 (m-30) cc_final: 0.6940 (m-30) REVERT: C 228 GLU cc_start: 0.6857 (mm-30) cc_final: 0.6578 (tt0) REVERT: C 337 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7153 (mm-30) REVERT: C 424 TYR cc_start: 0.8185 (t80) cc_final: 0.7407 (t80) REVERT: D 16 GLU cc_start: 0.7236 (mp0) cc_final: 0.7012 (mp0) REVERT: D 139 GLN cc_start: 0.7333 (tt0) cc_final: 0.7072 (pt0) REVERT: F 93 MET cc_start: 0.6155 (mmp) cc_final: 0.5587 (mmp) REVERT: F 119 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7135 (mt-10) REVERT: F 208 ASP cc_start: 0.7450 (m-30) cc_final: 0.7204 (m-30) REVERT: F 253 GLU cc_start: 0.5556 (mp0) cc_final: 0.5355 (tp30) REVERT: F 401 ASN cc_start: 0.8380 (m-40) cc_final: 0.8100 (m110) REVERT: I 23 MET cc_start: 0.6429 (ppp) cc_final: 0.5932 (mtt) outliers start: 8 outliers final: 3 residues processed: 368 average time/residue: 1.2267 time to fit residues: 511.9697 Evaluate side-chains 246 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 243 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 888 CYS Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain C residue 141 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.3980 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 212 GLN B 252 GLN B 501 ASN B 533 GLN B 587 ASN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 GLN B 798 ASN B 875 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN D 95 ASN F 139 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 20517 Z= 0.321 Angle : 0.970 49.041 28068 Z= 0.392 Chirality : 0.063 2.532 3044 Planarity : 0.006 0.066 3537 Dihedral : 11.163 138.745 2878 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.10 % Allowed : 10.02 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2455 helix: 0.24 (0.14), residues: 1269 sheet: -0.81 (0.40), residues: 174 loop : -1.15 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 274 HIS 0.007 0.002 HIS E 27 PHE 0.030 0.002 PHE C 266 TYR 0.020 0.002 TYR C 269 ARG 0.007 0.001 ARG B 881 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 279 time to evaluate : 2.074 Fit side-chains REVERT: A 105 ARG cc_start: 0.6127 (mtm-85) cc_final: 0.5881 (mtp180) REVERT: B 83 TYR cc_start: 0.8169 (m-80) cc_final: 0.7349 (m-80) REVERT: B 113 THR cc_start: 0.8350 (t) cc_final: 0.7859 (m) REVERT: B 151 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7303 (ttt) REVERT: B 212 GLN cc_start: 0.7378 (mm-40) cc_final: 0.6921 (mm-40) REVERT: B 218 ARG cc_start: 0.7106 (mmt-90) cc_final: 0.6895 (mmp80) REVERT: B 235 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7419 (mtt180) REVERT: B 297 SER cc_start: 0.8398 (p) cc_final: 0.7946 (t) REVERT: B 325 ASN cc_start: 0.7190 (t0) cc_final: 0.6901 (t0) REVERT: B 342 GLU cc_start: 0.6947 (tt0) cc_final: 0.6249 (mm-30) REVERT: B 460 ARG cc_start: 0.7279 (ttm110) cc_final: 0.6779 (mmm160) REVERT: B 530 THR cc_start: 0.7921 (t) cc_final: 0.7593 (m) REVERT: B 696 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7451 (mt) REVERT: B 743 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7608 (mp0) REVERT: B 748 LYS cc_start: 0.7519 (mtpt) cc_final: 0.7309 (mtpp) REVERT: B 752 LYS cc_start: 0.7106 (mttm) cc_final: 0.6472 (tttp) REVERT: B 757 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6866 (mt-10) REVERT: B 762 GLU cc_start: 0.7296 (tp30) cc_final: 0.6919 (tt0) REVERT: C 193 ASP cc_start: 0.7359 (m-30) cc_final: 0.7102 (m-30) REVERT: C 203 ASN cc_start: 0.7020 (t0) cc_final: 0.6812 (t0) REVERT: C 228 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6612 (tt0) REVERT: C 337 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7152 (mm-30) REVERT: C 356 LEU cc_start: 0.7384 (tp) cc_final: 0.7155 (tt) REVERT: D 16 GLU cc_start: 0.7050 (mp0) cc_final: 0.6818 (mp0) REVERT: D 52 ASP cc_start: 0.7563 (t70) cc_final: 0.7321 (t70) REVERT: D 94 THR cc_start: 0.8472 (m) cc_final: 0.8189 (p) REVERT: D 172 MET cc_start: 0.7596 (mtp) cc_final: 0.7299 (mtp) REVERT: F 41 THR cc_start: 0.7398 (m) cc_final: 0.7167 (m) REVERT: F 119 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7191 (mt-10) REVERT: F 181 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6901 (mmtt) REVERT: F 342 TRP cc_start: 0.7518 (t-100) cc_final: 0.6851 (t-100) REVERT: F 401 ASN cc_start: 0.8376 (m-40) cc_final: 0.7948 (m110) REVERT: G 80 LEU cc_start: 0.7406 (tm) cc_final: 0.5962 (mp) outliers start: 43 outliers final: 19 residues processed: 304 average time/residue: 1.2421 time to fit residues: 429.5407 Evaluate side-chains 268 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 246 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 888 CYS Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1010 ARG Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain G residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 150 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 238 optimal weight: 40.0000 chunk 196 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN B 533 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 HIS ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN D 95 ASN F 69 HIS F 261 HIS F 362 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 20517 Z= 0.329 Angle : 0.899 87.216 28068 Z= 0.374 Chirality : 0.052 1.398 3044 Planarity : 0.006 0.064 3537 Dihedral : 10.893 144.771 2875 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.08 % Allowed : 12.52 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2455 helix: 0.46 (0.14), residues: 1269 sheet: -0.93 (0.39), residues: 173 loop : -1.09 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 115 HIS 0.010 0.002 HIS E 27 PHE 0.022 0.002 PHE C 266 TYR 0.020 0.002 TYR C 269 ARG 0.007 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 259 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: B 113 THR cc_start: 0.8189 (t) cc_final: 0.7738 (m) REVERT: B 151 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7286 (ttt) REVERT: B 203 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7070 (tt) REVERT: B 212 GLN cc_start: 0.7174 (mm-40) cc_final: 0.6832 (mp10) REVERT: B 235 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7535 (mtt180) REVERT: B 325 ASN cc_start: 0.7324 (t0) cc_final: 0.7054 (t0) REVERT: B 342 GLU cc_start: 0.6960 (tt0) cc_final: 0.6261 (mm-30) REVERT: B 349 ARG cc_start: 0.6777 (mmt180) cc_final: 0.6378 (mmm-85) REVERT: B 460 ARG cc_start: 0.7259 (ttm110) cc_final: 0.6833 (mtp-110) REVERT: B 530 THR cc_start: 0.7633 (t) cc_final: 0.7326 (m) REVERT: B 616 LYS cc_start: 0.7959 (ttmm) cc_final: 0.6981 (tptt) REVERT: B 696 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7704 (mt) REVERT: B 743 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7543 (mp0) REVERT: B 752 LYS cc_start: 0.7122 (mttm) cc_final: 0.6241 (tptp) REVERT: B 757 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6898 (mt-10) REVERT: B 762 GLU cc_start: 0.7259 (tp30) cc_final: 0.6879 (tt0) REVERT: B 837 ASP cc_start: 0.7312 (p0) cc_final: 0.7025 (p0) REVERT: C 193 ASP cc_start: 0.7417 (m-30) cc_final: 0.7201 (m-30) REVERT: C 228 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6612 (tt0) REVERT: C 393 GLU cc_start: 0.7574 (tt0) cc_final: 0.7205 (tt0) REVERT: D 52 ASP cc_start: 0.7629 (t70) cc_final: 0.7405 (t70) REVERT: D 94 THR cc_start: 0.8527 (m) cc_final: 0.8304 (p) REVERT: D 156 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6906 (pp) REVERT: E 162 MET cc_start: 0.7550 (tpt) cc_final: 0.5988 (tmt) REVERT: F 252 ARG cc_start: 0.6651 (mmm160) cc_final: 0.6450 (mtm110) REVERT: F 342 TRP cc_start: 0.7538 (t-100) cc_final: 0.6846 (t-100) REVERT: F 365 ASP cc_start: 0.6687 (t0) cc_final: 0.6317 (t0) REVERT: F 398 ARG cc_start: 0.7246 (mtp-110) cc_final: 0.6933 (mtm110) REVERT: F 401 ASN cc_start: 0.8832 (m-40) cc_final: 0.8479 (m110) outliers start: 63 outliers final: 27 residues processed: 296 average time/residue: 1.2934 time to fit residues: 432.1852 Evaluate side-chains 274 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1010 ARG Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 395 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 210 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN B 229 ASN B 533 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN D 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 20517 Z= 0.187 Angle : 0.786 81.260 28068 Z= 0.322 Chirality : 0.050 1.594 3044 Planarity : 0.005 0.061 3537 Dihedral : 10.243 146.538 2874 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.64 % Allowed : 13.69 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2455 helix: 0.82 (0.14), residues: 1267 sheet: -1.01 (0.39), residues: 173 loop : -0.93 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 115 HIS 0.006 0.001 HIS A 133 PHE 0.013 0.001 PHE F 198 TYR 0.016 0.001 TYR F 104 ARG 0.005 0.000 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 256 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: B 83 TYR cc_start: 0.8172 (m-80) cc_final: 0.7259 (m-80) REVERT: B 151 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7451 (ttt) REVERT: B 203 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.6842 (tt) REVERT: B 212 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6841 (mp10) REVERT: B 235 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7372 (mtt180) REVERT: B 325 ASN cc_start: 0.7177 (OUTLIER) cc_final: 0.6913 (t0) REVERT: B 342 GLU cc_start: 0.6969 (tt0) cc_final: 0.6291 (mm-30) REVERT: B 349 ARG cc_start: 0.6763 (mmt180) cc_final: 0.6408 (mmm-85) REVERT: B 460 ARG cc_start: 0.7195 (ttm110) cc_final: 0.6826 (mmm160) REVERT: B 530 THR cc_start: 0.7630 (t) cc_final: 0.7332 (m) REVERT: B 616 LYS cc_start: 0.7960 (ttmm) cc_final: 0.6997 (tptt) REVERT: B 644 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7884 (tt) REVERT: B 743 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7626 (mp0) REVERT: B 752 LYS cc_start: 0.7111 (mttm) cc_final: 0.6288 (tptp) REVERT: B 757 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6889 (mt-10) REVERT: B 762 GLU cc_start: 0.7246 (tp30) cc_final: 0.6818 (tt0) REVERT: B 1024 LEU cc_start: 0.7086 (tp) cc_final: 0.6816 (tp) REVERT: C 124 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6484 (mt-10) REVERT: C 228 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6854 (mt-10) REVERT: C 296 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: C 381 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8036 (mt) REVERT: C 393 GLU cc_start: 0.7488 (tt0) cc_final: 0.7027 (tt0) REVERT: D 9 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7248 (ttp) REVERT: D 52 ASP cc_start: 0.7586 (t70) cc_final: 0.7362 (t70) REVERT: D 94 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8220 (p) REVERT: D 156 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6827 (pp) REVERT: E 83 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7926 (ttp) REVERT: E 162 MET cc_start: 0.7546 (tpt) cc_final: 0.6384 (tmt) REVERT: F 106 ASP cc_start: 0.7479 (t0) cc_final: 0.7268 (t0) REVERT: F 119 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6877 (mt-10) REVERT: F 211 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7057 (ttp) REVERT: F 342 TRP cc_start: 0.7474 (t-100) cc_final: 0.6800 (t-100) REVERT: F 365 ASP cc_start: 0.6783 (t0) cc_final: 0.6414 (t0) REVERT: F 395 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6327 (mt) REVERT: F 401 ASN cc_start: 0.8778 (m-40) cc_final: 0.8451 (m110) outliers start: 54 outliers final: 15 residues processed: 285 average time/residue: 1.2796 time to fit residues: 412.1753 Evaluate side-chains 272 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 244 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 888 CYS Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 395 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 162 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN B 533 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN D 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 20517 Z= 0.341 Angle : 0.868 80.505 28068 Z= 0.363 Chirality : 0.054 1.630 3044 Planarity : 0.005 0.064 3537 Dihedral : 10.451 147.690 2874 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.28 % Allowed : 14.28 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2455 helix: 0.69 (0.14), residues: 1266 sheet: -0.92 (0.40), residues: 173 loop : -0.94 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 219 HIS 0.010 0.002 HIS E 27 PHE 0.016 0.002 PHE A 40 TYR 0.018 0.002 TYR C 269 ARG 0.007 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 252 time to evaluate : 1.703 Fit side-chains revert: symmetry clash REVERT: A 121 ASP cc_start: 0.7535 (t0) cc_final: 0.7307 (t0) REVERT: B 151 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7268 (ttt) REVERT: B 171 GLU cc_start: 0.6700 (tt0) cc_final: 0.5554 (tp30) REVERT: B 203 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7017 (tt) REVERT: B 235 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7398 (mtt180) REVERT: B 325 ASN cc_start: 0.7279 (t0) cc_final: 0.7023 (t0) REVERT: B 342 GLU cc_start: 0.7008 (tt0) cc_final: 0.6256 (mm-30) REVERT: B 352 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7164 (pm20) REVERT: B 436 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7431 (mtm110) REVERT: B 460 ARG cc_start: 0.7182 (ttm110) cc_final: 0.6806 (mtp-110) REVERT: B 510 GLN cc_start: 0.7104 (mt0) cc_final: 0.6436 (mm-40) REVERT: B 530 THR cc_start: 0.7565 (t) cc_final: 0.7278 (m) REVERT: B 616 LYS cc_start: 0.8050 (ttmm) cc_final: 0.7197 (tptt) REVERT: B 743 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7663 (mp0) REVERT: B 752 LYS cc_start: 0.7170 (mttm) cc_final: 0.6458 (tttp) REVERT: B 757 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6910 (mt-10) REVERT: B 762 GLU cc_start: 0.7278 (tp30) cc_final: 0.6870 (tt0) REVERT: B 1025 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: C 228 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6889 (mt-10) REVERT: C 338 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7907 (mt-10) REVERT: C 381 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.8018 (mt) REVERT: C 393 GLU cc_start: 0.7551 (tt0) cc_final: 0.7109 (tt0) REVERT: C 448 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.5509 (p90) REVERT: D 9 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7303 (ttp) REVERT: D 52 ASP cc_start: 0.7652 (t70) cc_final: 0.7416 (t70) REVERT: D 156 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6880 (pp) REVERT: E 83 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8037 (ttp) REVERT: E 162 MET cc_start: 0.7556 (tpt) cc_final: 0.7260 (tmm) REVERT: F 93 MET cc_start: 0.6450 (mmp) cc_final: 0.5949 (mmp) REVERT: F 106 ASP cc_start: 0.7455 (t70) cc_final: 0.7234 (t0) REVERT: F 119 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7038 (mt-10) REVERT: F 342 TRP cc_start: 0.7557 (t-100) cc_final: 0.6888 (t-100) REVERT: F 365 ASP cc_start: 0.6774 (t0) cc_final: 0.6385 (t0) REVERT: F 398 ARG cc_start: 0.7213 (mtp-110) cc_final: 0.6860 (mtm110) REVERT: F 401 ASN cc_start: 0.8768 (m-40) cc_final: 0.8507 (m-40) outliers start: 67 outliers final: 34 residues processed: 297 average time/residue: 1.2828 time to fit residues: 430.7001 Evaluate side-chains 280 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 237 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 880 ASN Chi-restraints excluded: chain B residue 888 CYS Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1025 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 185 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.9990 chunk 211 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 195 optimal weight: 20.0000 chunk 108 optimal weight: 0.1980 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN B 533 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN D 95 ASN F 115 HIS F 261 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 20517 Z= 0.183 Angle : 0.786 81.794 28068 Z= 0.322 Chirality : 0.049 1.537 3044 Planarity : 0.005 0.059 3537 Dihedral : 9.901 149.758 2874 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.59 % Allowed : 15.75 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2455 helix: 0.92 (0.15), residues: 1273 sheet: -0.95 (0.40), residues: 173 loop : -0.82 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 523 HIS 0.007 0.001 HIS A 133 PHE 0.015 0.001 PHE F 198 TYR 0.015 0.001 TYR F 104 ARG 0.006 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 252 time to evaluate : 1.659 Fit side-chains revert: symmetry clash REVERT: B 83 TYR cc_start: 0.8163 (m-80) cc_final: 0.7216 (m-80) REVERT: B 151 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7470 (ttt) REVERT: B 158 THR cc_start: 0.7807 (m) cc_final: 0.7453 (p) REVERT: B 171 GLU cc_start: 0.6676 (tt0) cc_final: 0.5563 (tp30) REVERT: B 212 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: B 235 ARG cc_start: 0.7670 (mtt180) cc_final: 0.7352 (mtt180) REVERT: B 325 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6984 (t0) REVERT: B 342 GLU cc_start: 0.7021 (tt0) cc_final: 0.6293 (mm-30) REVERT: B 349 ARG cc_start: 0.6571 (mpt90) cc_final: 0.6257 (mmm-85) REVERT: B 352 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7096 (pm20) REVERT: B 406 VAL cc_start: 0.6682 (t) cc_final: 0.6230 (m) REVERT: B 460 ARG cc_start: 0.7225 (ttm110) cc_final: 0.6868 (mmm160) REVERT: B 510 GLN cc_start: 0.7043 (mt0) cc_final: 0.6068 (tp-100) REVERT: B 530 THR cc_start: 0.7579 (t) cc_final: 0.7288 (m) REVERT: B 616 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7173 (tptt) REVERT: B 743 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7606 (mp0) REVERT: B 752 LYS cc_start: 0.7157 (mttm) cc_final: 0.6409 (tttp) REVERT: B 762 GLU cc_start: 0.7358 (tp30) cc_final: 0.6882 (tt0) REVERT: B 836 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6434 (tp30) REVERT: B 870 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7673 (t0) REVERT: B 1024 LEU cc_start: 0.7113 (tp) cc_final: 0.6798 (tp) REVERT: C 124 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6409 (mt-10) REVERT: C 193 ASP cc_start: 0.7450 (m-30) cc_final: 0.7179 (m-30) REVERT: C 228 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6977 (mt-10) REVERT: C 381 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.8001 (mt) REVERT: C 393 GLU cc_start: 0.7507 (tt0) cc_final: 0.7022 (tt0) REVERT: D 9 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7203 (ttp) REVERT: D 52 ASP cc_start: 0.7630 (t70) cc_final: 0.7401 (t70) REVERT: D 139 GLN cc_start: 0.8812 (pt0) cc_final: 0.8571 (pt0) REVERT: E 83 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8090 (ttp) REVERT: E 162 MET cc_start: 0.7518 (tpt) cc_final: 0.5979 (tmt) REVERT: F 93 MET cc_start: 0.6300 (mmp) cc_final: 0.5830 (mmp) REVERT: F 106 ASP cc_start: 0.7449 (t70) cc_final: 0.7218 (t0) REVERT: F 119 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7031 (mt-10) REVERT: F 242 MET cc_start: 0.6978 (ttp) cc_final: 0.6571 (ptm) REVERT: F 342 TRP cc_start: 0.7471 (t-100) cc_final: 0.6823 (t-100) REVERT: F 365 ASP cc_start: 0.6801 (t0) cc_final: 0.6456 (t0) REVERT: F 401 ASN cc_start: 0.8800 (m-40) cc_final: 0.8549 (m-40) outliers start: 53 outliers final: 21 residues processed: 284 average time/residue: 1.3060 time to fit residues: 418.2853 Evaluate side-chains 274 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 888 CYS Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1010 ARG Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain I residue 28 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 234 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 0.0980 chunk 144 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN F 115 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 20517 Z= 0.186 Angle : 0.786 81.735 28068 Z= 0.321 Chirality : 0.049 1.549 3044 Planarity : 0.004 0.059 3537 Dihedral : 9.647 147.710 2874 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.69 % Allowed : 15.70 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2455 helix: 1.09 (0.15), residues: 1264 sheet: -0.89 (0.40), residues: 173 loop : -0.75 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 286 HIS 0.005 0.001 HIS A 133 PHE 0.014 0.001 PHE F 198 TYR 0.016 0.001 TYR F 104 ARG 0.007 0.000 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 252 time to evaluate : 1.901 Fit side-chains revert: symmetry clash REVERT: B 83 TYR cc_start: 0.8214 (m-80) cc_final: 0.7267 (m-80) REVERT: B 151 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7464 (ttt) REVERT: B 158 THR cc_start: 0.7789 (m) cc_final: 0.7415 (p) REVERT: B 171 GLU cc_start: 0.6631 (tt0) cc_final: 0.5511 (tp30) REVERT: B 235 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7348 (mtt180) REVERT: B 342 GLU cc_start: 0.7056 (tt0) cc_final: 0.6387 (mm-30) REVERT: B 352 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: B 406 VAL cc_start: 0.6679 (t) cc_final: 0.6270 (m) REVERT: B 422 MET cc_start: 0.7916 (mpp) cc_final: 0.7638 (mtt) REVERT: B 460 ARG cc_start: 0.7139 (ttm110) cc_final: 0.6826 (mmm160) REVERT: B 530 THR cc_start: 0.7564 (t) cc_final: 0.7276 (m) REVERT: B 616 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7158 (tptt) REVERT: B 644 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7897 (tt) REVERT: B 743 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7547 (mp0) REVERT: B 752 LYS cc_start: 0.7154 (mttm) cc_final: 0.6396 (tttp) REVERT: B 762 GLU cc_start: 0.7347 (tp30) cc_final: 0.6853 (tt0) REVERT: B 836 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6492 (tp30) REVERT: B 870 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7647 (t0) REVERT: B 1024 LEU cc_start: 0.7128 (tp) cc_final: 0.6817 (tp) REVERT: C 124 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6435 (mt-10) REVERT: C 193 ASP cc_start: 0.7419 (m-30) cc_final: 0.7211 (m-30) REVERT: C 228 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6966 (mt-10) REVERT: C 296 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: C 381 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8029 (mt) REVERT: C 393 GLU cc_start: 0.7570 (tt0) cc_final: 0.7236 (tt0) REVERT: D 9 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7170 (ttp) REVERT: D 43 GLU cc_start: 0.7424 (tt0) cc_final: 0.7186 (tt0) REVERT: D 52 ASP cc_start: 0.7624 (t70) cc_final: 0.7403 (t70) REVERT: D 139 GLN cc_start: 0.8804 (pt0) cc_final: 0.8552 (pt0) REVERT: D 172 MET cc_start: 0.7673 (mtp) cc_final: 0.7373 (mtp) REVERT: E 83 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8120 (ttp) REVERT: E 162 MET cc_start: 0.7486 (tpt) cc_final: 0.6152 (tmt) REVERT: E 167 SER cc_start: 0.8502 (p) cc_final: 0.8282 (p) REVERT: F 93 MET cc_start: 0.6289 (mmp) cc_final: 0.5852 (mmp) REVERT: F 106 ASP cc_start: 0.7455 (t70) cc_final: 0.7210 (t0) REVERT: F 119 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7016 (mt-10) REVERT: F 242 MET cc_start: 0.6958 (ttp) cc_final: 0.6554 (ptm) REVERT: F 258 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.5218 (tptp) REVERT: F 342 TRP cc_start: 0.7430 (t-100) cc_final: 0.6779 (t-100) REVERT: F 365 ASP cc_start: 0.6812 (t0) cc_final: 0.6445 (t0) REVERT: F 401 ASN cc_start: 0.8795 (m-40) cc_final: 0.8496 (m110) outliers start: 55 outliers final: 22 residues processed: 287 average time/residue: 1.3475 time to fit residues: 437.0113 Evaluate side-chains 271 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1010 ARG Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain D residue 9 MET Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain I residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 163 GLN B 325 ASN B 533 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN F 115 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 20517 Z= 0.183 Angle : 0.784 81.884 28068 Z= 0.319 Chirality : 0.049 1.538 3044 Planarity : 0.004 0.058 3537 Dihedral : 9.507 147.571 2874 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.25 % Allowed : 16.63 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2455 helix: 1.14 (0.15), residues: 1268 sheet: -0.94 (0.40), residues: 173 loop : -0.69 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 286 HIS 0.005 0.001 HIS C 246 PHE 0.015 0.001 PHE C 448 TYR 0.016 0.001 TYR F 104 ARG 0.009 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 249 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.6422 (mtm-85) cc_final: 0.5839 (mtm180) REVERT: B 83 TYR cc_start: 0.8178 (m-80) cc_final: 0.7260 (m-80) REVERT: B 151 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7503 (ttt) REVERT: B 158 THR cc_start: 0.7815 (m) cc_final: 0.7418 (p) REVERT: B 171 GLU cc_start: 0.6629 (tt0) cc_final: 0.5500 (tp30) REVERT: B 212 GLN cc_start: 0.7428 (mp10) cc_final: 0.7219 (mp10) REVERT: B 235 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7264 (mtt180) REVERT: B 342 GLU cc_start: 0.7117 (tt0) cc_final: 0.6371 (mm-30) REVERT: B 352 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: B 406 VAL cc_start: 0.6628 (t) cc_final: 0.6235 (m) REVERT: B 460 ARG cc_start: 0.7144 (ttm110) cc_final: 0.6845 (mmm160) REVERT: B 530 THR cc_start: 0.7482 (t) cc_final: 0.7207 (m) REVERT: B 616 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7150 (tptt) REVERT: B 644 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7919 (tt) REVERT: B 743 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7530 (mp0) REVERT: B 752 LYS cc_start: 0.7159 (mttm) cc_final: 0.6403 (tttp) REVERT: B 762 GLU cc_start: 0.7371 (tp30) cc_final: 0.6864 (tt0) REVERT: B 836 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6526 (tp30) REVERT: B 870 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7653 (t0) REVERT: B 1024 LEU cc_start: 0.7057 (tp) cc_final: 0.6766 (tp) REVERT: C 124 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: C 228 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6959 (mt-10) REVERT: C 381 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.8033 (mt) REVERT: C 451 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7550 (ptm160) REVERT: D 43 GLU cc_start: 0.7324 (tt0) cc_final: 0.7068 (tt0) REVERT: D 52 ASP cc_start: 0.7619 (t70) cc_final: 0.7385 (t70) REVERT: D 139 GLN cc_start: 0.8799 (pt0) cc_final: 0.8539 (pt0) REVERT: D 172 MET cc_start: 0.7665 (mtp) cc_final: 0.7363 (mtp) REVERT: E 83 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8158 (ttp) REVERT: E 162 MET cc_start: 0.7418 (tpt) cc_final: 0.5946 (tmt) REVERT: E 167 SER cc_start: 0.8523 (p) cc_final: 0.8296 (p) REVERT: F 93 MET cc_start: 0.6303 (mmp) cc_final: 0.5876 (mmp) REVERT: F 106 ASP cc_start: 0.7473 (t70) cc_final: 0.7232 (t0) REVERT: F 119 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7013 (mt-10) REVERT: F 242 MET cc_start: 0.6930 (ttp) cc_final: 0.6539 (ptm) REVERT: F 258 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.5248 (tptp) REVERT: F 342 TRP cc_start: 0.7363 (t-100) cc_final: 0.6718 (t-100) REVERT: F 365 ASP cc_start: 0.6847 (t0) cc_final: 0.6491 (t0) REVERT: F 401 ASN cc_start: 0.8785 (m-40) cc_final: 0.8494 (m110) outliers start: 46 outliers final: 23 residues processed: 281 average time/residue: 1.3552 time to fit residues: 429.9650 Evaluate side-chains 276 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 244 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1010 ARG Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain I residue 28 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 171 optimal weight: 0.0470 chunk 66 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 325 ASN B 533 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN F 115 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 20517 Z= 0.176 Angle : 0.782 82.099 28068 Z= 0.317 Chirality : 0.049 1.527 3044 Planarity : 0.004 0.058 3537 Dihedral : 9.291 147.192 2874 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.96 % Allowed : 17.21 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2455 helix: 1.19 (0.15), residues: 1269 sheet: -0.90 (0.40), residues: 173 loop : -0.65 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 286 HIS 0.005 0.001 HIS C 246 PHE 0.017 0.001 PHE C 448 TYR 0.016 0.001 TYR C 339 ARG 0.009 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 249 time to evaluate : 2.065 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.8504 (ttt) cc_final: 0.7971 (ttt) REVERT: B 83 TYR cc_start: 0.8185 (m-80) cc_final: 0.7280 (m-80) REVERT: B 151 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7500 (ttt) REVERT: B 158 THR cc_start: 0.7792 (m) cc_final: 0.7400 (p) REVERT: B 171 GLU cc_start: 0.6615 (tt0) cc_final: 0.5494 (tp30) REVERT: B 342 GLU cc_start: 0.7137 (tt0) cc_final: 0.6380 (mm-30) REVERT: B 352 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: B 406 VAL cc_start: 0.6642 (t) cc_final: 0.6246 (m) REVERT: B 460 ARG cc_start: 0.7150 (ttm110) cc_final: 0.6855 (mmm160) REVERT: B 530 THR cc_start: 0.7473 (t) cc_final: 0.7195 (m) REVERT: B 616 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7154 (tptt) REVERT: B 644 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7885 (tt) REVERT: B 752 LYS cc_start: 0.7159 (mttm) cc_final: 0.6397 (tttp) REVERT: B 762 GLU cc_start: 0.7422 (tp30) cc_final: 0.6894 (tt0) REVERT: B 836 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6446 (tp30) REVERT: B 870 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7558 (t70) REVERT: B 1024 LEU cc_start: 0.7039 (tp) cc_final: 0.6747 (tp) REVERT: C 124 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6436 (mt-10) REVERT: C 370 LYS cc_start: 0.6016 (mptt) cc_final: 0.5504 (mmtm) REVERT: C 381 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.8031 (mt) REVERT: C 393 GLU cc_start: 0.7545 (tt0) cc_final: 0.7284 (tt0) REVERT: C 451 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7532 (ptm160) REVERT: D 43 GLU cc_start: 0.7322 (tt0) cc_final: 0.7038 (tt0) REVERT: D 52 ASP cc_start: 0.7634 (t70) cc_final: 0.7394 (t70) REVERT: D 139 GLN cc_start: 0.8784 (pt0) cc_final: 0.8583 (pt0) REVERT: D 172 MET cc_start: 0.7663 (mtp) cc_final: 0.7420 (mtp) REVERT: E 83 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8167 (ttp) REVERT: E 162 MET cc_start: 0.7446 (tpt) cc_final: 0.5879 (tmt) REVERT: E 167 SER cc_start: 0.8522 (p) cc_final: 0.8302 (p) REVERT: F 93 MET cc_start: 0.6278 (mmp) cc_final: 0.5678 (mmp) REVERT: F 106 ASP cc_start: 0.7463 (t70) cc_final: 0.7214 (t0) REVERT: F 119 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7012 (mt-10) REVERT: F 242 MET cc_start: 0.6867 (ttp) cc_final: 0.6495 (ptm) REVERT: F 258 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.5381 (tptp) REVERT: F 342 TRP cc_start: 0.7325 (t-100) cc_final: 0.6685 (t-100) REVERT: F 365 ASP cc_start: 0.6852 (t0) cc_final: 0.6514 (t0) REVERT: F 401 ASN cc_start: 0.8792 (m-40) cc_final: 0.8512 (m110) REVERT: G 80 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7123 (tm) outliers start: 40 outliers final: 22 residues processed: 278 average time/residue: 1.3942 time to fit residues: 437.7660 Evaluate side-chains 275 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1010 ARG Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain I residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 242 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 118 optimal weight: 0.0670 chunk 153 optimal weight: 4.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 325 ASN B 533 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 446 ASN D 95 ASN F 115 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 20517 Z= 0.309 Angle : 0.856 80.932 28068 Z= 0.356 Chirality : 0.053 1.600 3044 Planarity : 0.005 0.060 3537 Dihedral : 9.768 147.872 2874 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.15 % Allowed : 17.41 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2455 helix: 0.93 (0.15), residues: 1272 sheet: -0.81 (0.40), residues: 173 loop : -0.73 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 31 HIS 0.009 0.002 HIS E 27 PHE 0.020 0.002 PHE I 33 TYR 0.017 0.002 TYR B 871 ARG 0.009 0.001 ARG B 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 1.993 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.6646 (tp30) cc_final: 0.6422 (tp30) REVERT: A 105 ARG cc_start: 0.6670 (mtm-85) cc_final: 0.6408 (mtm-85) REVERT: A 161 MET cc_start: 0.8599 (ttt) cc_final: 0.8060 (ttt) REVERT: B 151 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7269 (ttt) REVERT: B 158 THR cc_start: 0.7734 (m) cc_final: 0.7358 (p) REVERT: B 162 ARG cc_start: 0.7474 (ttp80) cc_final: 0.6930 (mtp85) REVERT: B 171 GLU cc_start: 0.6535 (tt0) cc_final: 0.5465 (tp30) REVERT: B 235 ARG cc_start: 0.7581 (mtt180) cc_final: 0.7187 (mtt180) REVERT: B 325 ASN cc_start: 0.6727 (t0) cc_final: 0.6425 (t0) REVERT: B 342 GLU cc_start: 0.7033 (tt0) cc_final: 0.6241 (mm-30) REVERT: B 349 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6401 (mpt90) REVERT: B 352 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: B 460 ARG cc_start: 0.7115 (ttm110) cc_final: 0.6769 (mmm160) REVERT: B 510 GLN cc_start: 0.6988 (mt0) cc_final: 0.6085 (tp-100) REVERT: B 530 THR cc_start: 0.7560 (t) cc_final: 0.7281 (m) REVERT: B 616 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7207 (tptt) REVERT: B 644 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7898 (tt) REVERT: B 743 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7645 (mp0) REVERT: B 752 LYS cc_start: 0.7177 (mttm) cc_final: 0.6343 (tptp) REVERT: B 762 GLU cc_start: 0.7421 (tp30) cc_final: 0.6933 (tt0) REVERT: B 836 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6598 (tp30) REVERT: B 1010 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7565 (mmt-90) REVERT: C 193 ASP cc_start: 0.7286 (m-30) cc_final: 0.6955 (m-30) REVERT: C 381 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.8024 (mt) REVERT: C 393 GLU cc_start: 0.7601 (tt0) cc_final: 0.7255 (tt0) REVERT: D 52 ASP cc_start: 0.7692 (t70) cc_final: 0.7466 (t70) REVERT: D 139 GLN cc_start: 0.8821 (pt0) cc_final: 0.8605 (pt0) REVERT: E 83 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8238 (ttp) REVERT: E 162 MET cc_start: 0.7523 (tpt) cc_final: 0.7297 (tmm) REVERT: F 93 MET cc_start: 0.6544 (mmp) cc_final: 0.6007 (mmp) REVERT: F 106 ASP cc_start: 0.7468 (t70) cc_final: 0.7226 (t0) REVERT: F 119 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7080 (mt-10) REVERT: F 342 TRP cc_start: 0.7461 (t-100) cc_final: 0.6753 (t-100) REVERT: F 365 ASP cc_start: 0.7006 (t0) cc_final: 0.6588 (t0) outliers start: 44 outliers final: 24 residues processed: 279 average time/residue: 1.3682 time to fit residues: 429.0456 Evaluate side-chains 273 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain B residue 76 CYS Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 907 THR Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 1010 ARG Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 381 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain I residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 80 optimal weight: 0.3980 chunk 198 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 35 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 533 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 446 ASN D 95 ASN F 115 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.161126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133849 restraints weight = 20386.068| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.28 r_work: 0.3448 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 20517 Z= 0.182 Angle : 0.795 81.952 28068 Z= 0.325 Chirality : 0.049 1.534 3044 Planarity : 0.004 0.058 3537 Dihedral : 9.359 148.967 2874 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.61 % Allowed : 18.04 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2455 helix: 1.09 (0.15), residues: 1270 sheet: -0.80 (0.41), residues: 173 loop : -0.68 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 523 HIS 0.006 0.001 HIS A 133 PHE 0.013 0.001 PHE F 198 TYR 0.017 0.001 TYR C 339 ARG 0.009 0.000 ARG B 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7260.18 seconds wall clock time: 127 minutes 19.24 seconds (7639.24 seconds total)