Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 22:44:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2023/5ld2_4038_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2023/5ld2_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_2023/5ld2_4038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2023/5ld2_4038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2023/5ld2_4038_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ld2_4038/04_2023/5ld2_4038_neut_updated.pdb" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 13.22, per 1000 atoms: 0.55 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: 10.46 Conformation dependent library (CDL) restraints added in 3.5 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: 8.91 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: 9.21 Time building geometry restraints manager: 11.03 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: 13747 16.82 - 33.65: 537 33.65 - 50.47: 258 50.47 - 67.29: 98 67.29 - 84.11: 31 Dihedral angle restraints: 14671 sinusoidal: 6298 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 14668 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: 0.310 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: 0.010 Extract box with map and model: 3.790 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 68.440 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.020 ------------------------------------------------------------------------------- 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 : 13.024 84.114 9245 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 % 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 *********************** 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 : 2.977 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 outliers start: 6 outliers final: 1 residues processed: 376 average time/residue: 0.4223 time to fit residues: 237.4424 Evaluate side-chains 180 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 2.949 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2607 time to fit residues: 5.0718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 149 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 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: 2.1388 ------------------------------------------------------------------------------- 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 B1072 HIS B1133 HIS B1134 HIS C 8 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** 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: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 24602 Z= 0.233 Angle : 0.693 10.046 33606 Z= 0.354 Chirality : 0.041 0.216 3694 Planarity : 0.005 0.046 4238 Dihedral : 14.387 77.866 3675 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.45 % Rotamer Outliers : 1.03 % 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: -0.68 (0.13), residues: 1370 sheet: -0.39 (0.28), residues: 298 loop : -1.14 (0.17), residues: 1179 *********************** 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 255 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 230 time to evaluate : 2.880 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 outliers start: 25 outliers final: 9 residues processed: 249 average time/residue: 0.3894 time to fit residues: 151.0725 Evaluate side-chains 165 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 3.042 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2674 time to fit residues: 8.3779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 147 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 263 optimal weight: 6.9990 chunk 90 optimal weight: 50.0000 chunk 213 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 484 ASN B 562 GLN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1035 GLN 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 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: 0.8836 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 24602 Z= 0.408 Angle : 0.720 10.117 33606 Z= 0.362 Chirality : 0.042 0.193 3694 Planarity : 0.005 0.085 4238 Dihedral : 14.176 75.032 3675 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.74 % Favored : 95.15 % Rotamer Outliers : 1.36 % 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: -0.64 (0.15), residues: 2847 helix: 0.24 (0.14), residues: 1358 sheet: -0.30 (0.28), residues: 293 loop : -1.14 (0.17), residues: 1196 *********************** 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 189 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 181 average time/residue: 0.3366 time to fit residues: 101.4454 Evaluate side-chains 153 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 2.971 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.2453 time to fit residues: 11.0931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 137 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 282 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 252 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN B 307 HIS B 404 GLN B 714 HIS ** B1003 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1018 GLN ** 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 24602 Z= 0.195 Angle : 0.599 10.092 33606 Z= 0.303 Chirality : 0.039 0.153 3694 Planarity : 0.004 0.046 4238 Dihedral : 14.015 73.765 3675 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer Outliers : 1.03 % 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: -0.09 (0.15), residues: 2847 helix: 0.74 (0.14), residues: 1365 sheet: -0.03 (0.29), residues: 305 loop : -0.95 (0.17), residues: 1177 *********************** 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 195 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 6 residues processed: 190 average time/residue: 0.3452 time to fit residues: 107.7344 Evaluate side-chains 148 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 2.942 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2366 time to fit residues: 6.1700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 235 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 4 optimal weight: 0.0970 chunk 210 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 253 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 overall best weight: 2.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN B 624 ASN ** B 689 HIS ** 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 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 ASN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 24602 Z= 0.235 Angle : 0.608 9.311 33606 Z= 0.306 Chirality : 0.039 0.154 3694 Planarity : 0.004 0.044 4238 Dihedral : 13.851 76.102 3675 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.40 % Rotamer Outliers : 1.32 % 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: 0.06 (0.15), residues: 2847 helix: 0.86 (0.14), residues: 1376 sheet: 0.23 (0.30), residues: 281 loop : -0.93 (0.17), residues: 1190 *********************** 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 183 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 174 average time/residue: 0.3380 time to fit residues: 99.3505 Evaluate side-chains 151 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 2.941 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2337 time to fit residues: 8.1730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 94 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 165 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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** D 542 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 24602 Z= 0.274 Angle : 0.619 9.623 33606 Z= 0.309 Chirality : 0.039 0.187 3694 Planarity : 0.004 0.045 4238 Dihedral : 13.724 78.801 3675 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.15 % Rotamer Outliers : 0.95 % 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: 0.12 (0.16), residues: 2847 helix: 0.92 (0.14), residues: 1391 sheet: 0.18 (0.30), residues: 286 loop : -0.92 (0.18), residues: 1170 *********************** 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 165 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 161 average time/residue: 0.3451 time to fit residues: 93.5393 Evaluate side-chains 142 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 2.995 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3208 time to fit residues: 7.7363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 237 optimal weight: 8.9990 chunk 157 optimal weight: 0.7980 chunk 281 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** B1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.4029 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= 0.243 Angle : 0.603 9.045 33606 Z= 0.300 Chirality : 0.039 0.171 3694 Planarity : 0.004 0.045 4238 Dihedral : 13.611 80.192 3675 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Rotamer Outliers : 0.37 % 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: 0.28 (0.16), residues: 2847 helix: 1.08 (0.14), residues: 1379 sheet: 0.25 (0.32), residues: 262 loop : -0.84 (0.17), residues: 1206 *********************** 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 154 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.3434 time to fit residues: 87.3039 Evaluate side-chains 137 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 2.858 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2182 time to fit residues: 5.9183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 174 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 168 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 24602 Z= 0.178 Angle : 0.585 9.928 33606 Z= 0.291 Chirality : 0.038 0.219 3694 Planarity : 0.004 0.047 4238 Dihedral : 13.526 81.077 3675 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.68 % Rotamer Outliers : 0.25 % 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: 0.39 (0.16), residues: 2847 helix: 1.16 (0.14), residues: 1384 sheet: 0.40 (0.31), residues: 279 loop : -0.82 (0.18), residues: 1184 *********************** 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 156 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 154 average time/residue: 0.3683 time to fit residues: 94.5044 Evaluate side-chains 140 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 2.989 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2342 time to fit residues: 5.1773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 20.0000 chunk 269 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 262 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** 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: 0.8797 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 24602 Z= 0.212 Angle : 0.597 11.290 33606 Z= 0.295 Chirality : 0.038 0.159 3694 Planarity : 0.004 0.070 4238 Dihedral : 13.474 81.038 3675 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer Outliers : 0.21 % 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: 1.16 (0.14), residues: 1390 sheet: 0.39 (0.32), residues: 262 loop : -0.75 (0.18), residues: 1195 *********************** 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 146 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 144 average time/residue: 0.3511 time to fit residues: 84.0452 Evaluate side-chains 136 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 2.714 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2175 time to fit residues: 4.8867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 172 optimal weight: 0.9980 chunk 277 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 290 optimal weight: 20.0000 chunk 267 optimal weight: 0.6980 chunk 231 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 178 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 24602 Z= 0.226 Angle : 0.604 10.384 33606 Z= 0.300 Chirality : 0.039 0.199 3694 Planarity : 0.004 0.045 4238 Dihedral : 13.484 81.078 3675 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer Outliers : 0.16 % 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: 0.45 (0.16), residues: 2847 helix: 1.15 (0.14), residues: 1394 sheet: 0.51 (0.33), residues: 253 loop : -0.73 (0.18), residues: 1200 ********************** 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 145 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 143 average time/residue: 0.3845 time to fit residues: 91.7564 Evaluate side-chains 138 residues out of total 2425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 2.691 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2450 time to fit residues: 5.0365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 184 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN B 876 GLN B1103 GLN ** B1110 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.047911 restraints weight = 98389.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.049556 restraints weight = 51103.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.050665 restraints weight = 33016.626| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4465 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= 0.259 Angle : 0.628 12.809 33606 Z= 0.309 Chirality : 0.039 0.193 3694 Planarity : 0.004 0.045 4238 Dihedral : 13.476 81.215 3675 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer Outliers : 0.12 % 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: 0.46 (0.16), residues: 2847 helix: 1.17 (0.14), residues: 1390 sheet: 0.51 (0.33), residues: 253 loop : -0.72 (0.18), residues: 1204 =============================================================================== Job complete usr+sys time: 3481.46 seconds wall clock time: 65 minutes 21.14 seconds (3921.14 seconds total)