Starting phenix.real_space_refine on Thu Apr 11 23:07:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2024/5ld2_4038_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2024/5ld2_4038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2024/5ld2_4038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2024/5ld2_4038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2024/5ld2_4038_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2024/5ld2_4038_neut_updated.pdb" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 P 53 5.49 5 Mg 1 5.21 5 S 101 5.16 5 C 14991 2.51 5 N 4229 2.21 5 O 4606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 19": "NH1" <-> "NH2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ASP 639": "OD1" <-> "OD2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "B ARG 683": "NH1" <-> "NH2" Residue "B ARG 728": "NH1" <-> "NH2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 840": "NH1" <-> "NH2" Residue "B ARG 895": "NH1" <-> "NH2" Residue "B TYR 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1015": "NH1" <-> "NH2" Residue "B PHE 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1106": "NH1" <-> "NH2" Residue "B ARG 1120": "NH1" <-> "NH2" Residue "B TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 348": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 433": "NH1" <-> "NH2" Residue "C TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 445": "NH1" <-> "NH2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 530": "NH1" <-> "NH2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 742": "NH1" <-> "NH2" Residue "C TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 799": "NH1" <-> "NH2" Residue "C ARG 839": "NH1" <-> "NH2" Residue "C ARG 858": "NH1" <-> "NH2" Residue "C ARG 877": "NH1" <-> "NH2" Residue "C ARG 896": "NH1" <-> "NH2" Residue "C ARG 900": "NH1" <-> "NH2" Residue "C ARG 902": "NH1" <-> "NH2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C ARG 1001": "NH1" <-> "NH2" Residue "C ARG 1007": "NH1" <-> "NH2" Residue "C GLU 1029": "OE1" <-> "OE2" Residue "C ARG 1118": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 509": "NH1" <-> "NH2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23981 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 9164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1151, 9164 Classifications: {'peptide': 1151} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 51, 'TRANS': 1099} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4672 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 25, 'TRANS': 579} Chain: "X" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1035 Classifications: {'DNA': 51} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 20 residue: pdb=" N UNK B 913 " occ=0.00 ... (2 atoms not shown) pdb=" O UNK B 913 " occ=0.00 residue: pdb=" N UNK B 914 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 914 " occ=0.00 residue: pdb=" N UNK B 915 " occ=0.00 ... (2 atoms not shown) pdb=" O UNK B 915 " occ=0.00 residue: pdb=" N UNK B 916 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 916 " occ=0.00 residue: pdb=" N UNK B 917 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 917 " occ=0.00 residue: pdb=" N UNK B 918 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 918 " occ=0.00 residue: pdb=" N UNK B 919 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 919 " occ=0.00 residue: pdb=" N UNK B 920 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 920 " occ=0.00 residue: pdb=" N UNK B 921 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 921 " occ=0.00 residue: pdb=" N UNK B 922 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 922 " occ=0.00 residue: pdb=" N UNK B 923 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 923 " occ=0.00 residue: pdb=" N UNK B 924 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 924 " occ=0.00 ... (remaining 8 not shown) Time building chain proxies: 13.45, per 1000 atoms: 0.56 Number of scatterers: 23981 At special positions: 0 Unit cell: (152.76, 148.74, 127.3, 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) S 101 16.00 P 53 15.00 Mg 1 11.99 O 4606 8.00 N 4229 7.00 C 14991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.34 Conformation dependent library (CDL) restraints added in 4.2 seconds 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5426 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 16 sheets defined 48.0% alpha, 7.9% beta 18 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 11.49 Creating SS restraints... Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.707A pdb=" N ILE B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 66 through 89 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 107 through 122 removed outlier: 5.068A pdb=" N ASP B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.901A pdb=" N GLN B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 157 through 170 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.636A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 removed outlier: 3.592A pdb=" N ARG B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 239 removed outlier: 3.989A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.507A pdb=" N ALA B 263 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 283 through 288 removed outlier: 3.729A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 4.543A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 346 removed outlier: 3.722A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 365 through 377 removed outlier: 3.558A pdb=" N GLU B 368 " --> pdb=" O GLU B 365 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 375 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 421 through 423 No H-bonds generated for 'chain 'B' and resid 421 through 423' Processing helix chain 'B' and resid 427 through 436 Processing helix chain 'B' and resid 451 through 461 removed outlier: 3.664A pdb=" N ASN B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 534 Processing helix chain 'B' and resid 561 through 573 removed outlier: 3.842A pdb=" N ALA B 570 " --> pdb=" O GLN B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.676A pdb=" N THR B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 616 removed outlier: 4.140A pdb=" N ALA B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 632 Processing helix chain 'B' and resid 635 through 655 removed outlier: 3.517A pdb=" N GLN B 650 " --> pdb=" O ASP B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 668 Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.938A pdb=" N LEU B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.200A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 716 removed outlier: 3.597A pdb=" N SER B 712 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 784 through 808 removed outlier: 3.915A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 835 Processing helix chain 'B' and resid 837 through 842 removed outlier: 3.704A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 860 removed outlier: 3.998A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 910 removed outlier: 3.720A pdb=" N GLN B 910 " --> pdb=" O SER B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 961 removed outlier: 3.690A pdb=" N PHE B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 980 Processing helix chain 'B' and resid 984 through 999 Proline residue: B 988 - end of helix removed outlier: 4.094A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B 995 " --> pdb=" O THR B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1011 No H-bonds generated for 'chain 'B' and resid 1009 through 1011' Processing helix chain 'B' and resid 1034 through 1043 removed outlier: 3.612A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1048 No H-bonds generated for 'chain 'B' and resid 1046 through 1048' Processing helix chain 'B' and resid 1095 through 1105 removed outlier: 3.503A pdb=" N ALA B1099 " --> pdb=" O GLN B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1125 Processing helix chain 'B' and resid 1131 through 1134 No H-bonds generated for 'chain 'B' and resid 1131 through 1134' Processing helix chain 'B' and resid 1164 through 1173 removed outlier: 3.712A pdb=" N GLU B1170 " --> pdb=" O ALA B1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 65 through 76 removed outlier: 3.583A pdb=" N VAL C 74 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.604A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 115 removed outlier: 3.686A pdb=" N LEU C 115 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 141 Processing helix chain 'C' and resid 143 through 151 removed outlier: 3.540A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 178 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 186 through 198 removed outlier: 3.611A pdb=" N TYR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.503A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 279 through 282 No H-bonds generated for 'chain 'C' and resid 279 through 282' Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 305 through 316 removed outlier: 3.927A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 382 through 399 removed outlier: 3.527A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 415 through 428 Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 467 through 475 removed outlier: 3.594A pdb=" N LEU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 474 " --> pdb=" O VAL C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 487 through 499 removed outlier: 3.549A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 514 removed outlier: 3.531A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 536 Processing helix chain 'C' and resid 556 through 577 removed outlier: 3.537A pdb=" N ALA C 565 " --> pdb=" O GLY C 562 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 568 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET C 569 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TRP C 574 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 587 No H-bonds generated for 'chain 'C' and resid 584 through 587' Processing helix chain 'C' and resid 590 through 598 Processing helix chain 'C' and resid 605 through 626 Processing helix chain 'C' and resid 634 through 645 removed outlier: 3.921A pdb=" N ASP C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 722 removed outlier: 3.721A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 791 through 794 Processing helix chain 'C' and resid 807 through 810 No H-bonds generated for 'chain 'C' and resid 807 through 810' Processing helix chain 'C' and resid 834 through 850 removed outlier: 4.423A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Proline residue: C 844 - end of helix removed outlier: 3.761A pdb=" N PHE C 848 " --> pdb=" O PRO C 844 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 889 removed outlier: 3.525A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 904 Processing helix chain 'C' and resid 910 through 934 removed outlier: 3.766A pdb=" N GLN C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 989 removed outlier: 3.548A pdb=" N TYR C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1032 removed outlier: 3.651A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1049 Processing helix chain 'C' and resid 1061 through 1075 removed outlier: 3.960A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR C1069 " --> pdb=" O GLN C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1091 No H-bonds generated for 'chain 'C' and resid 1088 through 1091' Processing helix chain 'C' and resid 1099 through 1119 removed outlier: 3.835A pdb=" N LEU C1114 " --> pdb=" O GLN C1110 " (cutoff:3.500A) Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 12 removed outlier: 3.746A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'D' and resid 33 through 47 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 81 through 87 Processing helix chain 'D' and resid 110 through 124 Processing helix chain 'D' and resid 134 through 144 Processing helix chain 'D' and resid 153 through 163 Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 206 through 222 removed outlier: 3.592A pdb=" N GLN D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 276 through 285 removed outlier: 4.120A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 319 removed outlier: 4.151A pdb=" N TYR D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 317 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 332 removed outlier: 3.674A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 366 through 374 Processing helix chain 'D' and resid 378 through 386 removed outlier: 3.636A pdb=" N LYS D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 423 removed outlier: 4.008A pdb=" N ALA D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 437 removed outlier: 3.612A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU D 437 " --> pdb=" O GLN D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 464 removed outlier: 4.047A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 541 No H-bonds generated for 'chain 'D' and resid 539 through 541' Processing helix chain 'D' and resid 563 through 572 Processing helix chain 'D' and resid 583 through 591 removed outlier: 3.788A pdb=" N ALA D 591 " --> pdb=" O SER D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 605 removed outlier: 3.958A pdb=" N SER D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 408 through 413 removed outlier: 5.835A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 443 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 60 through 62 Processing sheet with id= C, first strand: chain 'B' and resid 487 through 490 Processing sheet with id= D, first strand: chain 'B' and resid 865 through 869 removed outlier: 6.504A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N CYS B 813 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TRP B 502 " --> pdb=" O CYS B 813 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 815 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLN B 737 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL B 558 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 739 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 767 through 769 Processing sheet with id= F, first strand: chain 'B' and resid 1017 through 1019 removed outlier: 3.803A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 1021 through 1027 Processing sheet with id= H, first strand: chain 'C' and resid 321 through 325 removed outlier: 6.182A pdb=" N ILE C 236 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N TYR C 5 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU C 238 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER C 7 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE C 240 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N MET C 34 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N CYS C 214 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU C 36 " --> pdb=" O CYS C 214 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 365 through 367 Processing sheet with id= J, first strand: chain 'C' and resid 781 through 783 removed outlier: 8.714A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU C 727 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N HIS C 377 " --> pdb=" O LEU C 727 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE C 729 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N CYS C 379 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYR C 731 " --> pdb=" O CYS C 379 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASN C 660 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL C 412 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS C 662 " --> pdb=" O VAL C 412 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 831 through 833 removed outlier: 6.527A pdb=" N GLN C 951 " --> pdb=" O VAL C 832 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 963 through 967 removed outlier: 6.438A pdb=" N GLU C 995 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N ARG C 966 " --> pdb=" O GLU C 995 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG C 997 " --> pdb=" O ARG C 966 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 100 through 102 Processing sheet with id= N, first strand: chain 'D' and resid 352 through 355 removed outlier: 8.551A pdb=" N CYS D 353 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL D 168 " --> pdb=" O CYS D 353 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU D 355 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER D 170 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL D 292 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE D 169 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE D 294 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY D 171 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY D 296 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 535 through 537 removed outlier: 8.869A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N HIS D 548 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU D 441 " --> pdb=" O HIS D 548 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA D 550 " --> pdb=" O LEU D 441 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG D 576 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LEU D 551 " --> pdb=" O ARG D 576 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER D 578 " --> pdb=" O LEU D 551 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 530 through 532 removed outlier: 7.170A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2469 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 10.41 Time building geometry restraints manager: 11.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6317 1.33 - 1.45: 4644 1.45 - 1.57: 13368 1.57 - 1.69: 102 1.69 - 1.81: 171 Bond restraints: 24602 Sorted by residual: bond pdb=" C LYS C 259 " pdb=" N LEU C 260 " ideal model delta sigma weight residual 1.331 1.537 -0.207 1.48e-02 4.57e+03 1.95e+02 bond pdb=" C LEU C 260 " pdb=" N LEU C 261 " ideal model delta sigma weight residual 1.332 1.490 -0.158 1.52e-02 4.33e+03 1.09e+02 bond pdb=" C TYR D 359 " pdb=" N ARG D 360 " ideal model delta sigma weight residual 1.334 1.460 -0.126 1.27e-02 6.20e+03 9.82e+01 bond pdb=" O3A ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.700 1.547 0.153 2.00e-02 2.50e+03 5.89e+01 bond pdb=" O1B ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.501 1.378 0.123 2.00e-02 2.50e+03 3.80e+01 ... (remaining 24597 not shown) Histogram of bond angle deviations from ideal: 91.35 - 100.84: 77 100.84 - 110.34: 7218 110.34 - 119.83: 14915 119.83 - 129.33: 11176 129.33 - 138.82: 220 Bond angle restraints: 33606 Sorted by residual: angle pdb=" N ILE B 738 " pdb=" CA ILE B 738 " pdb=" C ILE B 738 " ideal model delta sigma weight residual 107.75 91.35 16.40 1.46e+00 4.69e-01 1.26e+02 angle pdb=" N ILE B 738 " pdb=" CA ILE B 738 " pdb=" CB ILE B 738 " ideal model delta sigma weight residual 111.64 122.21 -10.57 1.30e+00 5.92e-01 6.61e+01 angle pdb=" N GLN C 688 " pdb=" CA GLN C 688 " pdb=" C GLN C 688 " ideal model delta sigma weight residual 108.41 119.44 -11.03 1.63e+00 3.76e-01 4.58e+01 angle pdb=" N GLN B 737 " pdb=" CA GLN B 737 " pdb=" C GLN B 737 " ideal model delta sigma weight residual 107.62 94.56 13.06 1.97e+00 2.58e-01 4.39e+01 angle pdb=" N GLN C 854 " pdb=" CA GLN C 854 " pdb=" C GLN C 854 " ideal model delta sigma weight residual 113.23 120.87 -7.64 1.22e+00 6.72e-01 3.92e+01 ... (remaining 33601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 13766 16.82 - 33.65: 569 33.65 - 50.47: 259 50.47 - 67.29: 108 67.29 - 84.11: 33 Dihedral angle restraints: 14735 sinusoidal: 6362 harmonic: 8373 Sorted by residual: dihedral pdb=" CA SER B 720 " pdb=" C SER B 720 " pdb=" N ASN B 721 " pdb=" CA ASN B 721 " ideal model delta harmonic sigma weight residual -180.00 -144.28 -35.72 0 5.00e+00 4.00e-02 5.10e+01 dihedral pdb=" C GLN B 737 " pdb=" N GLN B 737 " pdb=" CA GLN B 737 " pdb=" CB GLN B 737 " ideal model delta harmonic sigma weight residual -122.60 -106.02 -16.58 0 2.50e+00 1.60e-01 4.40e+01 dihedral pdb=" CA PHE B 127 " pdb=" C PHE B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 14732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3492 0.101 - 0.202: 194 0.202 - 0.303: 6 0.303 - 0.404: 1 0.404 - 0.504: 1 Chirality restraints: 3694 Sorted by residual: chirality pdb=" CA GLN B 737 " pdb=" N GLN B 737 " pdb=" C GLN B 737 " pdb=" CB GLN B 737 " both_signs ideal model delta sigma weight residual False 2.51 3.01 -0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" CA GLN C 854 " pdb=" N GLN C 854 " pdb=" C GLN C 854 " pdb=" CB GLN C 854 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA GLN C 688 " pdb=" N GLN C 688 " pdb=" C GLN C 688 " pdb=" CB GLN C 688 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3691 not shown) Planarity restraints: 4238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 259 " 0.035 2.00e-02 2.50e+03 6.95e-02 4.83e+01 pdb=" C LYS C 259 " -0.120 2.00e-02 2.50e+03 pdb=" O LYS C 259 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU C 260 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 260 " -0.028 2.00e-02 2.50e+03 5.09e-02 2.60e+01 pdb=" C LEU C 260 " 0.088 2.00e-02 2.50e+03 pdb=" O LEU C 260 " -0.033 2.00e-02 2.50e+03 pdb=" N LEU C 261 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 530 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C HIS D 530 " -0.050 2.00e-02 2.50e+03 pdb=" O HIS D 530 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU D 531 " 0.017 2.00e-02 2.50e+03 ... (remaining 4235 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 226 2.56 - 3.14: 21596 3.14 - 3.73: 36683 3.73 - 4.31: 52238 4.31 - 4.90: 83468 Nonbonded interactions: 194211 Sorted by model distance: nonbonded pdb=" OG1 THR B 30 " pdb="MG MG B1502 " model vdw 1.975 2.170 nonbonded pdb=" O HIS C1018 " pdb=" OG SER C1021 " model vdw 2.036 2.440 nonbonded pdb=" O GLY C 577 " pdb=" NH2 ARG C 582 " model vdw 2.098 2.520 nonbonded pdb=" OE1 GLU C 398 " pdb=" OH TYR C 802 " model vdw 2.099 2.440 nonbonded pdb=" NH2 ARG D 425 " pdb=" O ASP D 503 " model vdw 2.104 2.520 ... (remaining 194206 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 2.840 Check model and map are aligned: 0.390 Set scattering table: 0.190 Process input model: 73.300 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 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 : 0.010 0.207 24602 Z= 0.619 Angle : 1.047 16.402 33606 Z= 0.601 Chirality : 0.052 0.504 3694 Planarity : 0.005 0.070 4238 Dihedral : 13.274 84.114 9309 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.73 % Favored : 94.03 % Rotamer: Outliers : 0.25 % Allowed : 1.24 % Favored : 98.52 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.12), residues: 2847 helix: -3.31 (0.09), residues: 1369 sheet: -0.97 (0.28), residues: 270 loop : -1.78 (0.15), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 598 HIS 0.018 0.003 HIS C 377 PHE 0.034 0.003 PHE C 376 TYR 0.035 0.003 TYR B1111 ARG 0.018 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 371 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLU cc_start: 0.9067 (tp30) cc_final: 0.8823 (tm-30) REVERT: B 133 CYS cc_start: 0.8763 (m) cc_final: 0.8263 (p) REVERT: B 518 MET cc_start: 0.8906 (mmm) cc_final: 0.8633 (mmm) REVERT: B 589 GLU cc_start: 0.9507 (tt0) cc_final: 0.9273 (tm-30) REVERT: B 596 MET cc_start: 0.8841 (mmm) cc_final: 0.8611 (mmm) REVERT: B 793 GLU cc_start: 0.9654 (mt-10) cc_final: 0.9300 (mt-10) REVERT: B 1061 MET cc_start: 0.8405 (mmt) cc_final: 0.7717 (mmm) REVERT: B 1150 HIS cc_start: 0.8153 (m-70) cc_final: 0.7765 (m90) REVERT: C 34 MET cc_start: 0.8830 (mmt) cc_final: 0.8484 (mmt) REVERT: C 643 GLN cc_start: 0.9516 (tt0) cc_final: 0.9059 (tm-30) REVERT: C 781 THR cc_start: 0.9509 (m) cc_final: 0.9203 (p) REVERT: C 1031 MET cc_start: 0.9247 (mmp) cc_final: 0.8934 (mmm) REVERT: D 284 ASP cc_start: 0.9624 (m-30) cc_final: 0.9124 (p0) REVERT: D 359 TYR cc_start: 0.7794 (m-80) cc_final: 0.6830 (p90) REVERT: D 409 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9396 (mm-30) outliers start: 6 outliers final: 1 residues processed: 376 average time/residue: 0.4319 time to fit residues: 245.8323 Evaluate side-chains 184 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 354 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 265 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 138 ASN B 150 GLN B 181 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 HIS B 458 ASN B 463 GLN B 610 ASN B 695 GLN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 734 HIS B 879 GLN B 889 ASN ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1057 GLN B1072 HIS B1133 HIS B1134 HIS B1150 HIS C 8 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS C 510 ASN C 522 HIS C 660 ASN C 768 ASN C 881 ASN C 920 GLN C 951 GLN C 979 GLN D 13 HIS D 22 GLN D 50 HIS D 115 ASN D 473 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24602 Z= 0.244 Angle : 0.697 10.093 33606 Z= 0.355 Chirality : 0.042 0.211 3694 Planarity : 0.005 0.046 4238 Dihedral : 14.604 77.918 3741 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 1.11 % Allowed : 7.59 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 2847 helix: -0.67 (0.13), residues: 1369 sheet: -0.43 (0.28), residues: 298 loop : -1.15 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 652 HIS 0.009 0.001 HIS B 689 PHE 0.029 0.002 PHE C 73 TYR 0.030 0.002 TYR B1111 ARG 0.007 0.001 ARG B 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLU cc_start: 0.9004 (tp30) cc_final: 0.8727 (tm-30) REVERT: B 133 CYS cc_start: 0.8610 (m) cc_final: 0.8067 (p) REVERT: B 453 MET cc_start: 0.8411 (mmp) cc_final: 0.7891 (tpp) REVERT: B 499 MET cc_start: 0.9374 (tmm) cc_final: 0.8743 (tmm) REVERT: B 518 MET cc_start: 0.8848 (mmm) cc_final: 0.8553 (tmm) REVERT: B 563 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8829 (pt0) REVERT: B 728 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8376 (ptt180) REVERT: B 793 GLU cc_start: 0.9602 (mt-10) cc_final: 0.9401 (mt-10) REVERT: C 1 MET cc_start: 0.7992 (tmm) cc_final: 0.7727 (tmm) REVERT: C 91 MET cc_start: 0.9050 (mtp) cc_final: 0.8833 (mtp) REVERT: C 516 LEU cc_start: 0.9082 (mt) cc_final: 0.8857 (mp) REVERT: C 697 MET cc_start: 0.9213 (mtm) cc_final: 0.8909 (mtm) REVERT: C 718 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8949 (mt-10) REVERT: C 781 THR cc_start: 0.9451 (m) cc_final: 0.8917 (p) REVERT: C 1079 MET cc_start: 0.9057 (ppp) cc_final: 0.8613 (ppp) REVERT: D 284 ASP cc_start: 0.9431 (m-30) cc_final: 0.9063 (p0) REVERT: D 584 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8635 (ptt-90) outliers start: 27 outliers final: 9 residues processed: 249 average time/residue: 0.3865 time to fit residues: 150.1163 Evaluate side-chains 172 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 584 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 220 optimal weight: 0.7980 chunk 180 optimal weight: 0.0000 chunk 73 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 263 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 213 optimal weight: 6.9990 overall best weight: 5.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN B 278 ASN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 484 ASN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1078 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24602 Z= 0.357 Angle : 0.687 10.148 33606 Z= 0.346 Chirality : 0.041 0.174 3694 Planarity : 0.004 0.045 4238 Dihedral : 14.256 75.289 3739 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.46 % Favored : 95.40 % Rotamer: Outliers : 1.61 % Allowed : 8.91 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.56 (0.15), residues: 2847 helix: 0.31 (0.14), residues: 1357 sheet: -0.34 (0.28), residues: 304 loop : -1.10 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 652 HIS 0.012 0.001 HIS C 377 PHE 0.023 0.002 PHE C 73 TYR 0.025 0.002 TYR B 648 ARG 0.008 0.001 ARG B 974 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 161 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 499 MET cc_start: 0.9432 (tmm) cc_final: 0.8814 (tmm) REVERT: B 518 MET cc_start: 0.8889 (mmm) cc_final: 0.8636 (mmm) REVERT: B 596 MET cc_start: 0.8470 (mmm) cc_final: 0.7935 (ttm) REVERT: B 728 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8538 (ptt180) REVERT: B 793 GLU cc_start: 0.9608 (mt-10) cc_final: 0.9394 (mt-10) REVERT: B 1061 MET cc_start: 0.8285 (mmt) cc_final: 0.7690 (mmp) REVERT: C 1 MET cc_start: 0.8157 (tmm) cc_final: 0.7880 (tmm) REVERT: C 91 MET cc_start: 0.9087 (mtp) cc_final: 0.8872 (mtp) REVERT: C 287 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: C 781 THR cc_start: 0.9520 (m) cc_final: 0.9113 (p) REVERT: C 1079 MET cc_start: 0.9113 (ppp) cc_final: 0.8685 (ppp) REVERT: D 261 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8691 (pp) REVERT: D 282 LEU cc_start: 0.9540 (tt) cc_final: 0.9327 (tp) REVERT: D 284 ASP cc_start: 0.9425 (m-30) cc_final: 0.9007 (p0) REVERT: D 584 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8428 (ptt-90) outliers start: 39 outliers final: 17 residues processed: 193 average time/residue: 0.3493 time to fit residues: 110.3816 Evaluate side-chains 160 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 584 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 262 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 266 optimal weight: 7.9990 chunk 282 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 chunk 76 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 562 GLN B 714 HIS ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 ASN C 881 ASN C 920 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24602 Z= 0.202 Angle : 0.590 9.939 33606 Z= 0.298 Chirality : 0.039 0.175 3694 Planarity : 0.004 0.045 4238 Dihedral : 13.990 73.369 3739 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 1.65 % Allowed : 9.40 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.07 (0.15), residues: 2847 helix: 0.77 (0.14), residues: 1374 sheet: 0.02 (0.30), residues: 292 loop : -0.98 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 652 HIS 0.013 0.001 HIS D 241 PHE 0.019 0.001 PHE C 68 TYR 0.025 0.001 TYR B1111 ARG 0.005 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8924 (tp) REVERT: B 133 CYS cc_start: 0.8523 (m) cc_final: 0.8009 (p) REVERT: B 499 MET cc_start: 0.9406 (tmm) cc_final: 0.8838 (tmm) REVERT: B 504 MET cc_start: 0.8708 (mmm) cc_final: 0.8496 (ttt) REVERT: B 518 MET cc_start: 0.8860 (mmm) cc_final: 0.8594 (mmm) REVERT: B 596 MET cc_start: 0.8391 (mmm) cc_final: 0.7855 (ttm) REVERT: B 728 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8359 (ptt180) REVERT: B 1061 MET cc_start: 0.8173 (mmt) cc_final: 0.7555 (mmp) REVERT: B 1098 MET cc_start: 0.9004 (ptp) cc_final: 0.8793 (ptp) REVERT: B 1102 MET cc_start: 0.8956 (tpp) cc_final: 0.8751 (tpp) REVERT: C 1 MET cc_start: 0.8383 (tmm) cc_final: 0.8050 (tmm) REVERT: C 287 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: C 606 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.9179 (mp0) REVERT: C 697 MET cc_start: 0.9299 (mtm) cc_final: 0.8658 (mtm) REVERT: C 781 THR cc_start: 0.9530 (m) cc_final: 0.9136 (p) REVERT: C 1031 MET cc_start: 0.8916 (mmt) cc_final: 0.8312 (mmm) REVERT: C 1079 MET cc_start: 0.9142 (ppp) cc_final: 0.8921 (pmm) REVERT: D 284 ASP cc_start: 0.9340 (m-30) cc_final: 0.8929 (p0) outliers start: 40 outliers final: 17 residues processed: 201 average time/residue: 0.3422 time to fit residues: 112.8736 Evaluate side-chains 163 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 253 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN C 8 ASN C 162 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 ASN C 881 ASN C 920 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24602 Z= 0.348 Angle : 0.649 9.204 33606 Z= 0.325 Chirality : 0.040 0.156 3694 Planarity : 0.004 0.045 4238 Dihedral : 13.877 76.144 3739 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.12 % Rotamer: Outliers : 2.19 % Allowed : 10.35 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.04 (0.15), residues: 2847 helix: 0.82 (0.14), residues: 1380 sheet: 0.08 (0.30), residues: 271 loop : -1.01 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 652 HIS 0.011 0.001 HIS C 377 PHE 0.019 0.002 PHE C 912 TYR 0.020 0.002 TYR B1111 ARG 0.005 0.000 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 140 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8661 (m) cc_final: 0.8088 (p) REVERT: B 307 HIS cc_start: 0.8319 (OUTLIER) cc_final: 0.7260 (p90) REVERT: B 499 MET cc_start: 0.9401 (tmm) cc_final: 0.8781 (tmm) REVERT: B 518 MET cc_start: 0.8824 (mmm) cc_final: 0.8591 (mmm) REVERT: B 596 MET cc_start: 0.8489 (mmm) cc_final: 0.7946 (ttm) REVERT: B 604 MET cc_start: 0.9329 (tpp) cc_final: 0.8828 (ttt) REVERT: B 728 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8498 (ptt180) REVERT: B 793 GLU cc_start: 0.9620 (mt-10) cc_final: 0.9411 (mt-10) REVERT: B 1061 MET cc_start: 0.8144 (mmt) cc_final: 0.7622 (mmp) REVERT: B 1094 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8935 (p) REVERT: B 1098 MET cc_start: 0.8986 (ptp) cc_final: 0.8677 (ptp) REVERT: C 1 MET cc_start: 0.8455 (tmm) cc_final: 0.8044 (tmm) REVERT: C 72 MET cc_start: 0.8991 (mtp) cc_final: 0.8320 (mmp) REVERT: C 96 MET cc_start: 0.9174 (ttp) cc_final: 0.8936 (ttm) REVERT: C 287 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: C 387 GLU cc_start: 0.9579 (OUTLIER) cc_final: 0.9378 (tp30) REVERT: C 606 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.9071 (mp0) REVERT: C 697 MET cc_start: 0.9193 (mtm) cc_final: 0.8885 (mtm) REVERT: C 781 THR cc_start: 0.9522 (m) cc_final: 0.9136 (p) REVERT: C 1031 MET cc_start: 0.9102 (mmt) cc_final: 0.8565 (mmm) REVERT: D 284 ASP cc_start: 0.9405 (m-30) cc_final: 0.9110 (p0) outliers start: 53 outliers final: 25 residues processed: 182 average time/residue: 0.3496 time to fit residues: 105.8241 Evaluate side-chains 166 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 8.9990 chunk 254 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 282 optimal weight: 10.0000 chunk 234 optimal weight: 0.0870 chunk 130 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 ASN C 881 ASN C 920 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24602 Z= 0.233 Angle : 0.593 9.129 33606 Z= 0.297 Chirality : 0.039 0.168 3694 Planarity : 0.004 0.045 4238 Dihedral : 13.775 79.295 3739 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.53 % Favored : 95.36 % Rotamer: Outliers : 1.94 % Allowed : 10.68 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.15 (0.16), residues: 2847 helix: 0.96 (0.14), residues: 1392 sheet: 0.22 (0.32), residues: 265 loop : -0.92 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 652 HIS 0.008 0.001 HIS C 377 PHE 0.014 0.001 PHE C 912 TYR 0.020 0.001 TYR C 190 ARG 0.004 0.000 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8601 (m) cc_final: 0.8093 (p) REVERT: B 146 MET cc_start: 0.9190 (mmm) cc_final: 0.8909 (mmm) REVERT: B 264 LYS cc_start: 0.9293 (pttm) cc_final: 0.9068 (pttm) REVERT: B 307 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7219 (p90) REVERT: B 354 MET cc_start: 0.9121 (mtm) cc_final: 0.8865 (ptp) REVERT: B 499 MET cc_start: 0.9418 (tmm) cc_final: 0.8794 (tmm) REVERT: B 518 MET cc_start: 0.8833 (mmm) cc_final: 0.8467 (mmm) REVERT: B 596 MET cc_start: 0.8427 (mmm) cc_final: 0.7867 (ttm) REVERT: B 604 MET cc_start: 0.9301 (tpp) cc_final: 0.8815 (ttt) REVERT: B 728 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8457 (ptt180) REVERT: B 832 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8400 (t70) REVERT: B 1021 MET cc_start: 0.8515 (mmm) cc_final: 0.8051 (tpt) REVERT: B 1061 MET cc_start: 0.8164 (mmt) cc_final: 0.7546 (mmp) REVERT: B 1094 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8939 (p) REVERT: B 1098 MET cc_start: 0.8984 (ptp) cc_final: 0.8682 (ptp) REVERT: C 1 MET cc_start: 0.8502 (tmm) cc_final: 0.8144 (tmm) REVERT: C 72 MET cc_start: 0.8997 (mtp) cc_final: 0.8313 (mmp) REVERT: C 287 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: C 606 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.9099 (mp0) REVERT: C 697 MET cc_start: 0.9255 (mtm) cc_final: 0.8909 (mtm) REVERT: C 718 GLU cc_start: 0.9062 (tt0) cc_final: 0.8851 (mt-10) REVERT: C 781 THR cc_start: 0.9524 (m) cc_final: 0.9132 (p) REVERT: C 1031 MET cc_start: 0.9040 (mmt) cc_final: 0.8473 (mmm) REVERT: D 284 ASP cc_start: 0.9374 (m-30) cc_final: 0.8904 (t0) outliers start: 47 outliers final: 28 residues processed: 178 average time/residue: 0.3492 time to fit residues: 103.0163 Evaluate side-chains 173 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 594 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 206 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 281 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 531 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 24602 Z= 0.310 Angle : 0.622 8.774 33606 Z= 0.310 Chirality : 0.039 0.158 3694 Planarity : 0.004 0.046 4238 Dihedral : 13.690 79.844 3739 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.84 % Rotamer: Outliers : 1.69 % Allowed : 11.13 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.24 (0.16), residues: 2847 helix: 1.11 (0.14), residues: 1375 sheet: 0.14 (0.32), residues: 262 loop : -0.92 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 652 HIS 0.010 0.001 HIS C 377 PHE 0.019 0.002 PHE C 912 TYR 0.021 0.002 TYR B1111 ARG 0.005 0.000 ARG D 425 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8714 (m) cc_final: 0.8170 (p) REVERT: B 136 MET cc_start: 0.8811 (tpp) cc_final: 0.8489 (tpp) REVERT: B 307 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7199 (p90) REVERT: B 499 MET cc_start: 0.9419 (tmm) cc_final: 0.8817 (tmm) REVERT: B 518 MET cc_start: 0.8851 (mmm) cc_final: 0.8612 (mmm) REVERT: B 596 MET cc_start: 0.8458 (mmm) cc_final: 0.7907 (ttm) REVERT: B 604 MET cc_start: 0.9272 (tpp) cc_final: 0.8817 (ttt) REVERT: B 728 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8529 (ptt180) REVERT: B 793 GLU cc_start: 0.9615 (mt-10) cc_final: 0.9399 (mt-10) REVERT: B 832 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8426 (t70) REVERT: B 1021 MET cc_start: 0.8715 (mmm) cc_final: 0.8404 (tpt) REVERT: B 1061 MET cc_start: 0.8147 (mmt) cc_final: 0.7540 (mmp) REVERT: B 1094 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8740 (p) REVERT: B 1098 MET cc_start: 0.9012 (ptp) cc_final: 0.8695 (ptp) REVERT: C 1 MET cc_start: 0.8615 (tmm) cc_final: 0.8222 (tmm) REVERT: C 72 MET cc_start: 0.8933 (mtp) cc_final: 0.8296 (mmp) REVERT: C 287 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: C 697 MET cc_start: 0.9235 (mtm) cc_final: 0.8870 (mtm) REVERT: C 781 THR cc_start: 0.9503 (m) cc_final: 0.9136 (p) REVERT: C 1031 MET cc_start: 0.9114 (mmt) cc_final: 0.8591 (mmm) REVERT: D 261 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8608 (pp) REVERT: D 284 ASP cc_start: 0.9425 (m-30) cc_final: 0.8958 (t0) outliers start: 41 outliers final: 29 residues processed: 172 average time/residue: 0.3496 time to fit residues: 99.7670 Evaluate side-chains 172 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 489 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN C 228 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 HIS C 768 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24602 Z= 0.279 Angle : 0.602 10.181 33606 Z= 0.301 Chirality : 0.039 0.156 3694 Planarity : 0.004 0.046 4238 Dihedral : 13.627 81.062 3739 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 1.73 % Allowed : 11.42 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.30 (0.16), residues: 2847 helix: 1.15 (0.14), residues: 1381 sheet: 0.23 (0.32), residues: 258 loop : -0.89 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 652 HIS 0.009 0.001 HIS C 377 PHE 0.015 0.001 PHE C 912 TYR 0.021 0.002 TYR C 190 ARG 0.004 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8786 (m) cc_final: 0.8241 (p) REVERT: B 136 MET cc_start: 0.8754 (tpp) cc_final: 0.8455 (tpp) REVERT: B 307 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7119 (p90) REVERT: B 354 MET cc_start: 0.9130 (ptp) cc_final: 0.8894 (ptp) REVERT: B 499 MET cc_start: 0.9408 (tmm) cc_final: 0.8808 (tmm) REVERT: B 518 MET cc_start: 0.8819 (mmm) cc_final: 0.8594 (mmm) REVERT: B 596 MET cc_start: 0.8457 (mmm) cc_final: 0.7900 (ttm) REVERT: B 604 MET cc_start: 0.9278 (tpp) cc_final: 0.8818 (ttt) REVERT: B 728 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8495 (ptt180) REVERT: B 793 GLU cc_start: 0.9602 (mt-10) cc_final: 0.9386 (mt-10) REVERT: B 832 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8448 (t70) REVERT: B 1094 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8757 (p) REVERT: B 1098 MET cc_start: 0.9042 (ptp) cc_final: 0.8734 (ptp) REVERT: B 1102 MET cc_start: 0.9131 (tpp) cc_final: 0.8827 (tpp) REVERT: C 1 MET cc_start: 0.8660 (tmm) cc_final: 0.8256 (tmm) REVERT: C 72 MET cc_start: 0.8941 (mtp) cc_final: 0.8285 (mmp) REVERT: C 287 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: C 697 MET cc_start: 0.9246 (mtm) cc_final: 0.8881 (mtm) REVERT: C 781 THR cc_start: 0.9504 (m) cc_final: 0.9146 (p) REVERT: C 1031 MET cc_start: 0.9042 (mmt) cc_final: 0.8507 (mmm) REVERT: D 261 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8577 (pp) REVERT: D 284 ASP cc_start: 0.9394 (m-30) cc_final: 0.8935 (t0) outliers start: 42 outliers final: 29 residues processed: 176 average time/residue: 0.3297 time to fit residues: 98.0908 Evaluate side-chains 173 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 489 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 10.0000 chunk 269 optimal weight: 0.0370 chunk 245 optimal weight: 4.9990 chunk 262 optimal weight: 20.0000 chunk 157 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 248 optimal weight: 0.5980 chunk 261 optimal weight: 8.9990 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN B 876 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 HIS C 768 ASN ** C 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24602 Z= 0.175 Angle : 0.580 13.094 33606 Z= 0.288 Chirality : 0.038 0.163 3694 Planarity : 0.004 0.046 4238 Dihedral : 13.537 81.240 3739 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.57 % Rotamer: Outliers : 1.36 % Allowed : 11.88 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.41 (0.16), residues: 2847 helix: 1.23 (0.14), residues: 1387 sheet: 0.28 (0.31), residues: 279 loop : -0.87 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 652 HIS 0.007 0.001 HIS C 377 PHE 0.012 0.001 PHE C 193 TYR 0.022 0.001 TYR C 190 ARG 0.004 0.000 ARG D 584 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8703 (m) cc_final: 0.8207 (p) REVERT: B 136 MET cc_start: 0.8701 (tpp) cc_final: 0.8409 (tpp) REVERT: B 307 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.6993 (p90) REVERT: B 354 MET cc_start: 0.9057 (ptp) cc_final: 0.8825 (ptp) REVERT: B 499 MET cc_start: 0.9392 (tmm) cc_final: 0.8825 (tmm) REVERT: B 518 MET cc_start: 0.8800 (mmm) cc_final: 0.8559 (mmm) REVERT: B 596 MET cc_start: 0.8365 (mmm) cc_final: 0.7897 (ttm) REVERT: B 604 MET cc_start: 0.9263 (tpp) cc_final: 0.8787 (ttt) REVERT: B 658 MET cc_start: 0.9345 (mmm) cc_final: 0.9047 (tpp) REVERT: B 728 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8409 (ptt180) REVERT: B 832 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8438 (t70) REVERT: B 1061 MET cc_start: 0.7972 (mmt) cc_final: 0.7440 (mmt) REVERT: B 1086 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7409 (pt) REVERT: B 1102 MET cc_start: 0.9095 (tpp) cc_final: 0.8830 (tpp) REVERT: B 1114 TYR cc_start: 0.9498 (m-80) cc_final: 0.9239 (m-10) REVERT: C 1 MET cc_start: 0.8646 (tmm) cc_final: 0.8239 (tmm) REVERT: C 72 MET cc_start: 0.8913 (mtp) cc_final: 0.8235 (mmp) REVERT: C 287 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: C 697 MET cc_start: 0.9234 (mtm) cc_final: 0.8854 (mtm) REVERT: C 781 THR cc_start: 0.9501 (m) cc_final: 0.9131 (p) REVERT: C 1031 MET cc_start: 0.8897 (mmt) cc_final: 0.8348 (mmm) REVERT: D 284 ASP cc_start: 0.9360 (m-30) cc_final: 0.8937 (t0) REVERT: D 314 CYS cc_start: 0.9186 (m) cc_final: 0.8823 (t) outliers start: 33 outliers final: 23 residues processed: 180 average time/residue: 0.3349 time to fit residues: 100.0784 Evaluate side-chains 168 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 379 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 6.9990 chunk 277 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 290 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 24 optimal weight: 40.0000 chunk 178 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN ** B 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 ASN C 793 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24602 Z= 0.253 Angle : 0.607 12.573 33606 Z= 0.301 Chirality : 0.039 0.183 3694 Planarity : 0.004 0.045 4238 Dihedral : 13.505 80.884 3739 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 1.28 % Allowed : 12.29 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.42 (0.16), residues: 2847 helix: 1.22 (0.14), residues: 1394 sheet: 0.25 (0.31), residues: 276 loop : -0.82 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 652 HIS 0.009 0.001 HIS C 377 PHE 0.014 0.001 PHE C 912 TYR 0.020 0.001 TYR B1111 ARG 0.009 0.000 ARG C 491 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8689 (m) cc_final: 0.8171 (p) REVERT: B 307 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.6947 (p90) REVERT: B 354 MET cc_start: 0.9084 (ptp) cc_final: 0.8864 (ptp) REVERT: B 499 MET cc_start: 0.9412 (tmm) cc_final: 0.8767 (tmm) REVERT: B 501 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8773 (mtm) REVERT: B 596 MET cc_start: 0.8416 (mmm) cc_final: 0.8149 (ttm) REVERT: B 604 MET cc_start: 0.9221 (tpp) cc_final: 0.8831 (ttt) REVERT: B 660 MET cc_start: 0.8844 (ppp) cc_final: 0.8637 (ppp) REVERT: B 728 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8532 (ptt180) REVERT: B 793 GLU cc_start: 0.9590 (mt-10) cc_final: 0.9385 (mt-10) REVERT: B 832 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8470 (t70) REVERT: B 1021 MET cc_start: 0.8891 (tpp) cc_final: 0.8651 (tpt) REVERT: B 1061 MET cc_start: 0.8027 (mmt) cc_final: 0.7510 (mmt) REVERT: B 1086 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7441 (pt) REVERT: B 1098 MET cc_start: 0.9170 (ptp) cc_final: 0.8725 (ptp) REVERT: B 1102 MET cc_start: 0.9125 (tpp) cc_final: 0.8866 (tpp) REVERT: B 1114 TYR cc_start: 0.9522 (m-80) cc_final: 0.9271 (m-10) REVERT: C 1 MET cc_start: 0.8667 (tmm) cc_final: 0.8277 (tmm) REVERT: C 72 MET cc_start: 0.8926 (mtp) cc_final: 0.8265 (mmp) REVERT: C 287 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: C 697 MET cc_start: 0.9221 (mtm) cc_final: 0.8832 (mtm) REVERT: C 781 THR cc_start: 0.9495 (m) cc_final: 0.9127 (p) REVERT: C 1031 MET cc_start: 0.8971 (mmt) cc_final: 0.8456 (mmm) REVERT: D 284 ASP cc_start: 0.9386 (m-30) cc_final: 0.8985 (t0) outliers start: 31 outliers final: 22 residues processed: 167 average time/residue: 0.3510 time to fit residues: 97.3579 Evaluate side-chains 168 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 379 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.046966 restraints weight = 99295.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.048541 restraints weight = 52646.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.049619 restraints weight = 34572.840| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24602 Z= 0.319 Angle : 0.639 12.611 33606 Z= 0.317 Chirality : 0.039 0.192 3694 Planarity : 0.004 0.046 4238 Dihedral : 13.529 80.913 3739 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.80 % Rotamer: Outliers : 1.36 % Allowed : 12.49 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.37 (0.16), residues: 2847 helix: 1.16 (0.14), residues: 1386 sheet: 0.26 (0.32), residues: 263 loop : -0.80 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 652 HIS 0.010 0.001 HIS C 377 PHE 0.018 0.001 PHE C 912 TYR 0.027 0.002 TYR B1076 ARG 0.008 0.000 ARG C 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3722.84 seconds wall clock time: 69 minutes 59.58 seconds (4199.58 seconds total)