Starting phenix.real_space_refine on Mon Feb 19 00:38:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkc_27487/02_2024/8dkc_27487.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkc_27487/02_2024/8dkc_27487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkc_27487/02_2024/8dkc_27487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkc_27487/02_2024/8dkc_27487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkc_27487/02_2024/8dkc_27487.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkc_27487/02_2024/8dkc_27487.pdb" } resolution = 3.5 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= 0.035 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 14730 2.51 5 N 4027 2.21 5 O 4437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 211": "OE1" <-> "OE2" Residue "C ASP 218": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 385": "OD1" <-> "OD2" Residue "C TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C GLU 576": "OE1" <-> "OE2" Residue "C GLU 589": "OE1" <-> "OE2" Residue "C GLU 603": "OE1" <-> "OE2" Residue "C PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 638": "OD1" <-> "OD2" Residue "C GLU 660": "OE1" <-> "OE2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C GLU 683": "OE1" <-> "OE2" Residue "C TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 792": "OE1" <-> "OE2" Residue "C TYR 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 809": "OE1" <-> "OE2" Residue "C GLU 826": "OE1" <-> "OE2" Residue "C GLU 845": "OE1" <-> "OE2" Residue "C ASP 861": "OD1" <-> "OD2" Residue "C ASP 921": "OD1" <-> "OD2" Residue "C GLU 1011": "OE1" <-> "OE2" Residue "C ASP 1023": "OD1" <-> "OD2" Residue "C GLU 1066": "OE1" <-> "OE2" Residue "C PHE 1070": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1073": "OD1" <-> "OD2" Residue "C PHE 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1250": "OE1" <-> "OE2" Residue "C PHE 1266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D ASP 219": "OD1" <-> "OD2" Residue "D PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D GLU 314": "OE1" <-> "OE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D GLU 388": "OE1" <-> "OE2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 415": "OD1" <-> "OD2" Residue "D PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 492": "OE1" <-> "OE2" Residue "D TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 589": "OE1" <-> "OE2" Residue "D TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 629": "OD1" <-> "OD2" Residue "D GLU 655": "OE1" <-> "OE2" Residue "D GLU 668": "OE1" <-> "OE2" Residue "D GLU 751": "OE1" <-> "OE2" Residue "D PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 914": "OE1" <-> "OE2" Residue "D TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1254": "OE1" <-> "OE2" Residue "D ASP 1270": "OD1" <-> "OD2" Residue "D ASP 1279": "OD1" <-> "OD2" Residue "D ASP 1309": "OD1" <-> "OD2" Residue "D ASP 1318": "OD1" <-> "OD2" Residue "E TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23282 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1813 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "B" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1813 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "C" Number of atoms: 9356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9356 Classifications: {'peptide': 1184} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1124} Chain breaks: 1 Chain: "D" Number of atoms: 9457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1201, 9457 Classifications: {'peptide': 1201} Link IDs: {'CIS': 2, 'PTRANS': 48, 'TRANS': 1150} Chain breaks: 1 Chain: "E" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 843 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Time building chain proxies: 11.91, per 1000 atoms: 0.51 Number of scatterers: 23282 At special positions: 0 Unit cell: (129.05, 171.77, 171.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 4437 8.00 N 4027 7.00 C 14730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 815 " - pdb=" SG CYS D 896 " distance=2.00 Simple disulfide: pdb=" SG CYS D 815 " - pdb=" SG CYS D 899 " distance=2.07 Simple disulfide: pdb=" SG CYS D 896 " - pdb=" SG CYS D 899 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.15 Conformation dependent library (CDL) restraints added in 4.2 seconds 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5510 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 37 sheets defined 38.0% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 33 through 48 Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.628A pdb=" N ILE A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.874A pdb=" N GLU A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 230 removed outlier: 3.865A pdb=" N ALA A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 46 removed outlier: 3.643A pdb=" N THR B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 84 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.928A pdb=" N ALA B 160 " --> pdb=" O GLU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 231 removed outlier: 4.304A pdb=" N LEU B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 36 Processing helix chain 'C' and resid 49 through 58 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 319 through 330 Processing helix chain 'C' and resid 338 through 352 removed outlier: 3.700A pdb=" N SER C 352 " --> pdb=" O ASN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 382 through 398 Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 416 through 442 removed outlier: 3.555A pdb=" N GLN C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 removed outlier: 3.788A pdb=" N LEU C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 454 " --> pdb=" O PRO C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 454' Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.800A pdb=" N SER C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 470 " --> pdb=" O PHE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 506 through 510 Processing helix chain 'C' and resid 572 through 576 removed outlier: 4.141A pdb=" N GLU C 576 " --> pdb=" O ALA C 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 572 through 576' Processing helix chain 'C' and resid 639 through 651 Processing helix chain 'C' and resid 670 through 676 removed outlier: 3.526A pdb=" N SER C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 706 Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 825 through 831 removed outlier: 4.140A pdb=" N ASP C 831 " --> pdb=" O ASP C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 872 Processing helix chain 'C' and resid 913 through 942 Processing helix chain 'C' and resid 954 through 964 removed outlier: 4.157A pdb=" N SER C 964 " --> pdb=" O ILE C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 removed outlier: 4.273A pdb=" N SER C 982 " --> pdb=" O VAL C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1019 Processing helix chain 'C' and resid 1083 through 1086 Processing helix chain 'C' and resid 1092 through 1105 Processing helix chain 'C' and resid 1120 through 1131 Processing helix chain 'C' and resid 1167 through 1171 removed outlier: 3.533A pdb=" N ASP C1170 " --> pdb=" O MET C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1200 through 1210 removed outlier: 3.665A pdb=" N VAL C1204 " --> pdb=" O GLY C1200 " (cutoff:3.500A) Processing helix chain 'C' and resid 1214 through 1222 Processing helix chain 'C' and resid 1226 through 1240 Processing helix chain 'C' and resid 1249 through 1260 removed outlier: 3.622A pdb=" N LYS C1260 " --> pdb=" O LEU C1256 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 59 Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.702A pdb=" N ARG D 77 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 96 removed outlier: 3.524A pdb=" N VAL D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 96 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.762A pdb=" N PHE D 113 " --> pdb=" O HIS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 222 through 241 removed outlier: 3.756A pdb=" N SER D 241 " --> pdb=" O SER D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 251 removed outlier: 3.878A pdb=" N VAL D 251 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.530A pdb=" N LEU D 262 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 297 removed outlier: 3.514A pdb=" N ASP D 280 " --> pdb=" O SER D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 321 Processing helix chain 'D' and resid 339 through 345 Processing helix chain 'D' and resid 382 through 390 removed outlier: 3.822A pdb=" N TYR D 390 " --> pdb=" O ALA D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 406 through 416 removed outlier: 3.685A pdb=" N ARG D 416 " --> pdb=" O LYS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 429 Processing helix chain 'D' and resid 443 through 445 No H-bonds generated for 'chain 'D' and resid 443 through 445' Processing helix chain 'D' and resid 466 through 471 removed outlier: 3.610A pdb=" N PHE D 470 " --> pdb=" O SER D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 497 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 516 through 527 Processing helix chain 'D' and resid 542 through 552 Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 604 through 619 Processing helix chain 'D' and resid 619 through 642 removed outlier: 3.693A pdb=" N GLY D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 650 Processing helix chain 'D' and resid 653 through 676 removed outlier: 4.004A pdb=" N ASP D 657 " --> pdb=" O PRO D 653 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 658 " --> pdb=" O ASP D 654 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 661 " --> pdb=" O ASP D 657 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR D 664 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR D 665 " --> pdb=" O GLN D 661 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 666 " --> pdb=" O GLU D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 710 removed outlier: 3.770A pdb=" N VAL D 702 " --> pdb=" O ARG D 698 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP D 710 " --> pdb=" O GLN D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 723 Processing helix chain 'D' and resid 728 through 737 Processing helix chain 'D' and resid 769 through 803 removed outlier: 4.039A pdb=" N TYR D 796 " --> pdb=" O ALA D 792 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 797 " --> pdb=" O ASP D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 841 removed outlier: 3.526A pdb=" N ARG D 839 " --> pdb=" O SER D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 876 Processing helix chain 'D' and resid 896 through 901 removed outlier: 3.715A pdb=" N TYR D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY D 901 " --> pdb=" O ALA D 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 901' Processing helix chain 'D' and resid 916 through 926 Processing helix chain 'D' and resid 927 through 930 Processing helix chain 'D' and resid 1127 through 1136 Processing helix chain 'D' and resid 1205 through 1214 removed outlier: 4.109A pdb=" N ILE D1209 " --> pdb=" O THR D1205 " (cutoff:3.500A) Processing helix chain 'D' and resid 1214 through 1233 Processing helix chain 'D' and resid 1238 through 1250 removed outlier: 4.652A pdb=" N PHE D1242 " --> pdb=" O ASN D1238 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D1245 " --> pdb=" O HIS D1241 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D1247 " --> pdb=" O GLU D1243 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D1248 " --> pdb=" O VAL D1244 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET D1249 " --> pdb=" O ILE D1245 " (cutoff:3.500A) Processing helix chain 'D' and resid 1268 through 1276 removed outlier: 4.455A pdb=" N GLU D1273 " --> pdb=" O ASP D1270 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL D1274 " --> pdb=" O LYS D1271 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU D1276 " --> pdb=" O GLU D1273 " (cutoff:3.500A) Processing helix chain 'D' and resid 1338 through 1345 Processing helix chain 'D' and resid 1348 through 1354 Processing helix chain 'D' and resid 1357 through 1369 removed outlier: 3.623A pdb=" N VAL D1361 " --> pdb=" O GLU D1357 " (cutoff:3.500A) Processing helix chain 'D' and resid 1376 through 1384 Processing helix chain 'D' and resid 1389 through 1393 removed outlier: 3.985A pdb=" N LEU D1393 " --> pdb=" O GLY D1390 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 26 through 57 Processing helix chain 'E' and resid 70 through 81 Processing helix chain 'E' and resid 84 through 96 removed outlier: 3.526A pdb=" N ILE E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 4.675A pdb=" N THR A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL A 189 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 104 removed outlier: 6.758A pdb=" N GLU A 143 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 57 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER A 145 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.539A pdb=" N VAL A 153 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A 172 " --> pdb=" O VAL A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.248A pdb=" N ILE B 21 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 204 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS B 23 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 202 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLU B 25 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET B 200 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS B 27 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N LEU B 198 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 189 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE B 187 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU B 196 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU B 185 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 198 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA B 183 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N MET B 200 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS B 181 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 202 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B 179 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR B 204 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 177 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.816A pdb=" N LYS B 58 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 145 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B 56 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.712A pdb=" N GLU B 108 " --> pdb=" O HIS B 133 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS B 133 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 110 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.693A pdb=" N VAL B 153 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 172 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 5.869A pdb=" N ILE C 10 " --> pdb=" O ALA C1112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.590A pdb=" N TYR C 74 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS C 98 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE C 76 " --> pdb=" O PRO C 96 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 95 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY C 123 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU C 97 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE C 121 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA C 99 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP C 119 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU C 101 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE C 117 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 103 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR C 115 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N CYS C 105 " --> pdb=" O PHE C 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 134 through 136 Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 146 removed outlier: 6.270A pdb=" N SER C 145 " --> pdb=" O SER C 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AB8, first strand: chain 'C' and resid 152 through 160 removed outlier: 4.170A pdb=" N HIS C 160 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N THR C 164 " --> pdb=" O HIS C 160 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR C 167 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AC1, first strand: chain 'C' and resid 559 through 560 removed outlier: 3.687A pdb=" N ASP C 618 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 580 " --> pdb=" O ARG C 601 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 601 " --> pdb=" O VAL C 580 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 719 removed outlier: 6.275A pdb=" N ARG C 699 " --> pdb=" O VAL C 688 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL C 688 " --> pdb=" O ARG C 699 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AC4, first strand: chain 'C' and resid 756 through 757 Processing sheet with id=AC5, first strand: chain 'C' and resid 1138 through 1139 removed outlier: 7.660A pdb=" N ILE C 783 " --> pdb=" O SER C1060 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE C1062 " --> pdb=" O ILE C 783 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C 785 " --> pdb=" O ILE C1062 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N ILE C1079 " --> pdb=" O ASN C 766 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN C 768 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU C1081 " --> pdb=" O GLN C 768 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA C 770 " --> pdb=" O LEU C1081 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR C1155 " --> pdb=" O TYR C 771 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 813 through 814 removed outlier: 3.593A pdb=" N GLY C 813 " --> pdb=" O THR C 810 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU C 809 " --> pdb=" O ILE C1029 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE C1029 " --> pdb=" O GLU C 809 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY C 893 " --> pdb=" O ILE C 844 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 849 through 851 removed outlier: 6.826A pdb=" N LEU C 885 " --> pdb=" O LEU C 850 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 854 through 855 Processing sheet with id=AC9, first strand: chain 'C' and resid 1173 through 1175 removed outlier: 3.672A pdb=" N SER D 363 " --> pdb=" O ARG C1175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 16 through 17 Processing sheet with id=AD2, first strand: chain 'D' and resid 30 through 33 removed outlier: 8.018A pdb=" N HIS D 100 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLU D 33 " --> pdb=" O HIS D 100 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N HIS D 102 " --> pdb=" O GLU D 33 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY D 99 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD4, first strand: chain 'D' and resid 266 through 268 removed outlier: 3.543A pdb=" N VAL D 266 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 561 through 569 Processing sheet with id=AD6, first strand: chain 'D' and resid 821 through 823 Processing sheet with id=AD7, first strand: chain 'D' and resid 826 through 828 removed outlier: 3.768A pdb=" N LEU D 826 " --> pdb=" O ALA D 834 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 834 " --> pdb=" O LEU D 826 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN D 828 " --> pdb=" O VAL D 832 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL D 832 " --> pdb=" O GLN D 828 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 1151 through 1152 Processing sheet with id=AD9, first strand: chain 'D' and resid 1162 through 1163 removed outlier: 4.277A pdb=" N ILE D1179 " --> pdb=" O ARG D1163 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1253 through 1258 removed outlier: 6.570A pdb=" N THR D1331 " --> pdb=" O VAL D1256 " (cutoff:3.500A) 902 hydrogen bonds defined for protein. 2514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.48 Time building geometry restraints manager: 9.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5801 1.33 - 1.46: 5143 1.46 - 1.58: 12582 1.58 - 1.71: 0 1.71 - 1.83: 149 Bond restraints: 23675 Sorted by residual: bond pdb=" N ILE D 883 " pdb=" CA ILE D 883 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.17e+01 bond pdb=" N VAL D 574 " pdb=" CA VAL D 574 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.20e-02 6.94e+03 1.10e+01 bond pdb=" N VAL D 370 " pdb=" CA VAL D 370 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.15e+00 bond pdb=" N GLU D 572 " pdb=" CA GLU D 572 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.21e-02 6.83e+03 8.95e+00 bond pdb=" N ARG D 884 " pdb=" CA ARG D 884 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.34e-02 5.57e+03 8.20e+00 ... (remaining 23670 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.74: 420 104.74 - 112.06: 11363 112.06 - 119.38: 8371 119.38 - 126.70: 11608 126.70 - 134.02: 223 Bond angle restraints: 31985 Sorted by residual: angle pdb=" N VAL D1287 " pdb=" CA VAL D1287 " pdb=" C VAL D1287 " ideal model delta sigma weight residual 111.88 104.22 7.66 1.06e+00 8.90e-01 5.22e+01 angle pdb=" CA TYR D 635 " pdb=" CB TYR D 635 " pdb=" CG TYR D 635 " ideal model delta sigma weight residual 113.90 125.66 -11.76 1.80e+00 3.09e-01 4.27e+01 angle pdb=" N LEU C1259 " pdb=" CA LEU C1259 " pdb=" C LEU C1259 " ideal model delta sigma weight residual 111.28 104.31 6.97 1.09e+00 8.42e-01 4.09e+01 angle pdb=" N ILE A 91 " pdb=" CA ILE A 91 " pdb=" C ILE A 91 " ideal model delta sigma weight residual 113.71 107.79 5.92 9.50e-01 1.11e+00 3.88e+01 angle pdb=" CB LYS A 181 " pdb=" CG LYS A 181 " pdb=" CD LYS A 181 " ideal model delta sigma weight residual 111.30 97.43 13.87 2.30e+00 1.89e-01 3.64e+01 ... (remaining 31980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 13118 17.62 - 35.23: 1177 35.23 - 52.85: 180 52.85 - 70.47: 44 70.47 - 88.08: 30 Dihedral angle restraints: 14549 sinusoidal: 6000 harmonic: 8549 Sorted by residual: dihedral pdb=" CA GLU D 572 " pdb=" C GLU D 572 " pdb=" N LEU D 573 " pdb=" CA LEU D 573 " ideal model delta harmonic sigma weight residual 180.00 102.67 77.33 0 5.00e+00 4.00e-02 2.39e+02 dihedral pdb=" CB CYS D 815 " pdb=" SG CYS D 815 " pdb=" SG CYS D 896 " pdb=" CB CYS D 896 " ideal model delta sinusoidal sigma weight residual -86.00 -5.38 -80.62 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CA GLU D1310 " pdb=" C GLU D1310 " pdb=" N ASN D1311 " pdb=" CA ASN D1311 " ideal model delta harmonic sigma weight residual -180.00 -137.60 -42.40 0 5.00e+00 4.00e-02 7.19e+01 ... (remaining 14546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2991 0.073 - 0.146: 595 0.146 - 0.219: 44 0.219 - 0.292: 6 0.292 - 0.364: 2 Chirality restraints: 3638 Sorted by residual: chirality pdb=" CB ILE B 173 " pdb=" CA ILE B 173 " pdb=" CG1 ILE B 173 " pdb=" CG2 ILE B 173 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA LEU C1259 " pdb=" N LEU C1259 " pdb=" C LEU C1259 " pdb=" CB LEU C1259 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA TYR E 93 " pdb=" N TYR E 93 " pdb=" C TYR E 93 " pdb=" CB TYR E 93 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 3635 not shown) Planarity restraints: 4161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 635 " 0.046 2.00e-02 2.50e+03 3.11e-02 1.93e+01 pdb=" CG TYR D 635 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR D 635 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 635 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 635 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 635 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 635 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 635 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D1279 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ASP D1279 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP D1279 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG D1280 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 187 " -0.025 2.00e-02 2.50e+03 2.84e-02 1.41e+01 pdb=" CG PHE A 187 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 187 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 187 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 187 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 187 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 187 " -0.004 2.00e-02 2.50e+03 ... (remaining 4158 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 312 2.49 - 3.09: 18936 3.09 - 3.70: 36551 3.70 - 4.30: 50528 4.30 - 4.90: 78967 Nonbonded interactions: 185294 Sorted by model distance: nonbonded pdb=" NZ LYS C1260 " pdb=" CD2 LEU D 340 " model vdw 1.892 3.540 nonbonded pdb=" OG SER A 107 " pdb=" O LYS A 136 " model vdw 2.025 2.440 nonbonded pdb=" OG1 THR C1155 " pdb=" OD1 ASN D 646 " model vdw 2.034 2.440 nonbonded pdb=" OG SER C 825 " pdb=" OD1 ASP C 827 " model vdw 2.086 2.440 nonbonded pdb=" NE2 GLN B 85 " pdb=" OE2 GLU D 544 " model vdw 2.088 2.520 ... (remaining 185289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 8.250 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 62.190 Find NCS groups from input model: 0.980 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 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 : 0.007 0.075 23675 Z= 0.436 Angle : 1.008 13.874 31985 Z= 0.563 Chirality : 0.056 0.364 3638 Planarity : 0.006 0.080 4161 Dihedral : 14.110 88.085 9030 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 31.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.23 % Favored : 87.57 % Rotamer: Outliers : 0.04 % Allowed : 1.06 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.82 % Twisted General : 0.35 % 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: -2.77 (0.14), residues: 2936 helix: -0.97 (0.16), residues: 970 sheet: -1.15 (0.28), residues: 302 loop : -2.62 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 422 HIS 0.008 0.002 HIS D 806 PHE 0.063 0.003 PHE A 187 TYR 0.074 0.003 TYR D 635 ARG 0.020 0.001 ARG D 912 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 2.623 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: A 19 ASP cc_start: 0.9119 (t70) cc_final: 0.8845 (t70) REVERT: A 200 MET cc_start: 0.7540 (ttp) cc_final: 0.7284 (ttm) REVERT: B 96 ASP cc_start: 0.9339 (p0) cc_final: 0.9027 (p0) REVERT: B 140 LEU cc_start: 0.9497 (mt) cc_final: 0.9184 (mt) REVERT: C 645 MET cc_start: 0.8100 (mtm) cc_final: 0.7298 (tmm) REVERT: C 789 MET cc_start: 0.8423 (mmm) cc_final: 0.8126 (mmm) REVERT: C 1090 MET cc_start: 0.7646 (mpp) cc_final: 0.7159 (mmt) REVERT: C 1148 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8120 (tm-30) REVERT: C 1161 PHE cc_start: 0.7980 (t80) cc_final: 0.7319 (t80) REVERT: C 1194 PHE cc_start: 0.7231 (m-10) cc_final: 0.6789 (m-80) REVERT: C 1255 LEU cc_start: 0.8977 (tt) cc_final: 0.8684 (mt) REVERT: D 185 ASP cc_start: 0.9405 (m-30) cc_final: 0.9178 (t0) REVERT: D 477 ASP cc_start: 0.6995 (m-30) cc_final: 0.6683 (m-30) REVERT: D 479 MET cc_start: 0.8712 (mmm) cc_final: 0.8395 (mmm) REVERT: D 519 MET cc_start: 0.7825 (mpp) cc_final: 0.7407 (mpp) REVERT: D 602 LEU cc_start: 0.8386 (tt) cc_final: 0.8141 (tt) REVERT: D 721 MET cc_start: 0.8171 (tmm) cc_final: 0.7509 (tmm) REVERT: E 46 LYS cc_start: 0.9253 (pptt) cc_final: 0.8979 (pptt) REVERT: E 78 TYR cc_start: 0.9112 (t80) cc_final: 0.8901 (t80) REVERT: E 84 LYS cc_start: 0.8859 (mttt) cc_final: 0.8202 (mttp) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.3795 time to fit residues: 152.6873 Evaluate side-chains 189 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 171 optimal weight: 0.0050 chunk 266 optimal weight: 0.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 231 ASN C 57 ASN ** C 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 989 HIS C1257 HIS ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN D 672 GLN D 828 GLN ** D1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23675 Z= 0.237 Angle : 0.781 9.833 31985 Z= 0.408 Chirality : 0.049 0.245 3638 Planarity : 0.005 0.075 4161 Dihedral : 7.082 86.177 3213 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.35 % Favored : 89.58 % Rotamer: Outliers : 1.21 % Allowed : 9.70 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.21 (0.15), residues: 2936 helix: -0.26 (0.16), residues: 981 sheet: -1.13 (0.27), residues: 329 loop : -2.40 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C1205 HIS 0.005 0.001 HIS D 102 PHE 0.035 0.002 PHE A 187 TYR 0.046 0.002 TYR D 635 ARG 0.008 0.001 ARG D 912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.6822 (tmm) cc_final: 0.6559 (tmm) REVERT: A 19 ASP cc_start: 0.9070 (t70) cc_final: 0.8793 (t70) REVERT: A 106 ASN cc_start: 0.8897 (t0) cc_final: 0.8542 (t0) REVERT: B 96 ASP cc_start: 0.9325 (p0) cc_final: 0.8967 (p0) REVERT: B 191 GLN cc_start: 0.8550 (mm110) cc_final: 0.8298 (mm-40) REVERT: C 38 LEU cc_start: 0.8302 (tp) cc_final: 0.8067 (tp) REVERT: C 364 TYR cc_start: 0.9177 (m-80) cc_final: 0.8850 (m-80) REVERT: C 645 MET cc_start: 0.8033 (mtm) cc_final: 0.7829 (mtm) REVERT: C 651 ARG cc_start: 0.8286 (mtt-85) cc_final: 0.8058 (mtt90) REVERT: C 674 LYS cc_start: 0.9039 (tppt) cc_final: 0.8499 (pttt) REVERT: C 789 MET cc_start: 0.8406 (mmm) cc_final: 0.7982 (mmm) REVERT: C 1041 ARG cc_start: 0.7452 (ttp-170) cc_final: 0.6535 (ttm170) REVERT: C 1148 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8091 (tm-30) REVERT: C 1167 MET cc_start: 0.8311 (mpp) cc_final: 0.7578 (mpp) REVERT: D 98 MET cc_start: 0.6042 (mmp) cc_final: 0.5762 (mmp) REVERT: D 185 ASP cc_start: 0.9402 (m-30) cc_final: 0.9139 (t0) REVERT: D 479 MET cc_start: 0.8761 (mmm) cc_final: 0.8402 (mmm) REVERT: D 519 MET cc_start: 0.7594 (mpp) cc_final: 0.7314 (mpp) REVERT: D 721 MET cc_start: 0.8256 (tmm) cc_final: 0.7624 (tmm) REVERT: E 46 LYS cc_start: 0.9199 (pptt) cc_final: 0.8837 (pptt) REVERT: E 78 TYR cc_start: 0.9052 (t80) cc_final: 0.8837 (t80) REVERT: E 79 TYR cc_start: 0.7912 (m-80) cc_final: 0.7037 (m-80) REVERT: E 84 LYS cc_start: 0.8797 (mttt) cc_final: 0.8141 (mttp) outliers start: 31 outliers final: 21 residues processed: 249 average time/residue: 0.3616 time to fit residues: 140.7081 Evaluate side-chains 217 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain C residue 1100 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 1357 GLU Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain E residue 16 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 222 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 267 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 265 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 214 optimal weight: 20.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 HIS ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 HIS ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23675 Z= 0.316 Angle : 0.773 9.614 31985 Z= 0.404 Chirality : 0.049 0.257 3638 Planarity : 0.005 0.074 4161 Dihedral : 6.912 83.455 3213 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.48 % Favored : 88.49 % Rotamer: Outliers : 2.62 % Allowed : 13.26 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.14 (0.15), residues: 2936 helix: -0.15 (0.16), residues: 984 sheet: -1.06 (0.28), residues: 307 loop : -2.41 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1282 HIS 0.008 0.001 HIS C 932 PHE 0.038 0.002 PHE C1210 TYR 0.045 0.002 TYR D 635 ARG 0.007 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 206 time to evaluate : 2.858 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: A 15 MET cc_start: 0.6999 (tmm) cc_final: 0.6672 (tmm) REVERT: A 19 ASP cc_start: 0.9099 (t70) cc_final: 0.8857 (t70) REVERT: A 33 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5400 (m-80) REVERT: A 106 ASN cc_start: 0.8920 (t0) cc_final: 0.8479 (t0) REVERT: B 96 ASP cc_start: 0.9342 (p0) cc_final: 0.8938 (p0) REVERT: B 187 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6109 (p90) REVERT: B 191 GLN cc_start: 0.8592 (mm110) cc_final: 0.8318 (mm-40) REVERT: C 364 TYR cc_start: 0.9230 (m-80) cc_final: 0.8926 (m-80) REVERT: C 651 ARG cc_start: 0.8363 (mtt-85) cc_final: 0.8081 (mtt90) REVERT: C 674 LYS cc_start: 0.9073 (tppt) cc_final: 0.8552 (pttt) REVERT: C 789 MET cc_start: 0.8403 (mmm) cc_final: 0.8035 (mmm) REVERT: C 932 HIS cc_start: 0.9246 (t-90) cc_final: 0.8887 (t70) REVERT: C 1148 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 98 MET cc_start: 0.6430 (mmp) cc_final: 0.6170 (mmp) REVERT: D 185 ASP cc_start: 0.9393 (m-30) cc_final: 0.9146 (t70) REVERT: D 479 MET cc_start: 0.8773 (mmm) cc_final: 0.8369 (mmm) REVERT: D 519 MET cc_start: 0.7768 (mpp) cc_final: 0.7266 (mpp) REVERT: D 602 LEU cc_start: 0.8281 (tt) cc_final: 0.8049 (tt) REVERT: D 721 MET cc_start: 0.8210 (tmm) cc_final: 0.7758 (tmm) REVERT: D 1402 MET cc_start: 0.0616 (tpt) cc_final: 0.0257 (tpt) REVERT: E 46 LYS cc_start: 0.9192 (pptt) cc_final: 0.8870 (pptt) REVERT: E 78 TYR cc_start: 0.9090 (t80) cc_final: 0.8834 (t80) REVERT: E 79 TYR cc_start: 0.8004 (m-80) cc_final: 0.7383 (m-80) REVERT: E 84 LYS cc_start: 0.8807 (mttt) cc_final: 0.8149 (mttp) outliers start: 67 outliers final: 36 residues processed: 259 average time/residue: 0.3551 time to fit residues: 145.1770 Evaluate side-chains 226 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 188 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1007 GLU Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1100 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 444 ARG Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 268 optimal weight: 4.9990 chunk 284 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 23675 Z= 0.373 Angle : 0.809 13.058 31985 Z= 0.420 Chirality : 0.050 0.308 3638 Planarity : 0.005 0.073 4161 Dihedral : 6.944 78.916 3213 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.16 % Favored : 87.81 % Rotamer: Outliers : 3.68 % Allowed : 15.68 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.21 (0.15), residues: 2936 helix: -0.20 (0.16), residues: 987 sheet: -1.14 (0.29), residues: 287 loop : -2.43 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D1282 HIS 0.016 0.001 HIS C 932 PHE 0.043 0.002 PHE E 56 TYR 0.044 0.002 TYR D 635 ARG 0.010 0.001 ARG D 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 200 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.7144 (tmm) cc_final: 0.6869 (tmm) REVERT: A 19 ASP cc_start: 0.9134 (t70) cc_final: 0.8895 (t70) REVERT: A 33 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: A 106 ASN cc_start: 0.8999 (t0) cc_final: 0.8514 (t0) REVERT: B 96 ASP cc_start: 0.9316 (p0) cc_final: 0.8963 (p0) REVERT: B 187 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6274 (p90) REVERT: B 191 GLN cc_start: 0.8655 (mm110) cc_final: 0.8337 (mm110) REVERT: C 330 GLN cc_start: 0.4190 (OUTLIER) cc_final: 0.3468 (mp-120) REVERT: C 364 TYR cc_start: 0.9275 (m-80) cc_final: 0.8945 (m-80) REVERT: C 645 MET cc_start: 0.7860 (mtm) cc_final: 0.7623 (mtt) REVERT: C 789 MET cc_start: 0.8392 (mmm) cc_final: 0.8003 (mmm) REVERT: C 932 HIS cc_start: 0.9349 (t-90) cc_final: 0.9012 (t70) REVERT: C 1041 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6399 (ttm170) REVERT: C 1092 LEU cc_start: 0.5184 (OUTLIER) cc_final: 0.4428 (pt) REVERT: D 98 MET cc_start: 0.6724 (mmp) cc_final: 0.6454 (mmp) REVERT: D 467 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7539 (p) REVERT: D 479 MET cc_start: 0.8779 (mmm) cc_final: 0.8382 (mmm) REVERT: D 519 MET cc_start: 0.7725 (mpp) cc_final: 0.7365 (mpp) REVERT: D 721 MET cc_start: 0.8246 (tmm) cc_final: 0.7657 (tmm) REVERT: D 735 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5884 (mp) REVERT: D 1402 MET cc_start: 0.0526 (tpt) cc_final: 0.0148 (tpt) REVERT: E 46 LYS cc_start: 0.9218 (pptt) cc_final: 0.8924 (pptt) REVERT: E 78 TYR cc_start: 0.9119 (t80) cc_final: 0.8813 (t80) REVERT: E 79 TYR cc_start: 0.8084 (m-80) cc_final: 0.7399 (m-80) REVERT: E 84 LYS cc_start: 0.8821 (mttt) cc_final: 0.8154 (mttp) outliers start: 94 outliers final: 58 residues processed: 271 average time/residue: 0.3446 time to fit residues: 148.2873 Evaluate side-chains 255 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 190 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1067 ASP Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1136 ASP Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 444 ARG Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 623 THR Chi-restraints excluded: chain D residue 628 ASP Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1268 VAL Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 0.9980 chunk 161 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 242 optimal weight: 40.0000 chunk 196 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 40.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23675 Z= 0.227 Angle : 0.737 14.702 31985 Z= 0.376 Chirality : 0.047 0.287 3638 Planarity : 0.005 0.072 4161 Dihedral : 6.491 74.963 3213 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.80 % Favored : 89.17 % Rotamer: Outliers : 3.60 % Allowed : 17.21 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.98 (0.15), residues: 2936 helix: 0.04 (0.16), residues: 994 sheet: -0.97 (0.28), residues: 311 loop : -2.36 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 111 HIS 0.016 0.001 HIS C 932 PHE 0.042 0.002 PHE E 56 TYR 0.028 0.002 TYR D 635 ARG 0.004 0.000 ARG D 912 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 204 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.7299 (tmm) cc_final: 0.6988 (tmm) REVERT: A 19 ASP cc_start: 0.9141 (t70) cc_final: 0.8902 (t70) REVERT: A 33 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.5015 (m-80) REVERT: A 106 ASN cc_start: 0.8943 (t0) cc_final: 0.8457 (t0) REVERT: B 96 ASP cc_start: 0.9309 (p0) cc_final: 0.8870 (p0) REVERT: B 187 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6163 (p90) REVERT: C 330 GLN cc_start: 0.4093 (OUTLIER) cc_final: 0.3521 (mp-120) REVERT: C 364 TYR cc_start: 0.9292 (m-10) cc_final: 0.8960 (m-80) REVERT: C 651 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7918 (mtt90) REVERT: C 674 LYS cc_start: 0.9106 (tppt) cc_final: 0.8646 (pttt) REVERT: C 789 MET cc_start: 0.8456 (mmm) cc_final: 0.8102 (mmm) REVERT: C 1041 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6564 (ttm170) REVERT: C 1092 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4671 (pt) REVERT: D 98 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6469 (mmp) REVERT: D 191 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5709 (pt) REVERT: D 479 MET cc_start: 0.8747 (mmm) cc_final: 0.8329 (mmm) REVERT: D 519 MET cc_start: 0.7652 (mpp) cc_final: 0.7332 (mpp) REVERT: D 721 MET cc_start: 0.8286 (tmm) cc_final: 0.7606 (tmm) REVERT: D 735 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5776 (mp) REVERT: D 1357 GLU cc_start: 0.8745 (tp30) cc_final: 0.8491 (tm-30) REVERT: D 1379 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7921 (pp20) REVERT: D 1402 MET cc_start: 0.0414 (tpt) cc_final: 0.0085 (tpt) REVERT: E 46 LYS cc_start: 0.9189 (pptt) cc_final: 0.8901 (pptt) REVERT: E 78 TYR cc_start: 0.9091 (t80) cc_final: 0.8779 (t80) REVERT: E 79 TYR cc_start: 0.8068 (m-80) cc_final: 0.7354 (m-80) REVERT: E 84 LYS cc_start: 0.8749 (mttt) cc_final: 0.8084 (mttp) REVERT: E 102 MET cc_start: 0.6936 (mmp) cc_final: 0.6154 (tmm) outliers start: 92 outliers final: 54 residues processed: 273 average time/residue: 0.3491 time to fit residues: 151.3244 Evaluate side-chains 250 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 187 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1067 ASP Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1100 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1136 ASP Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 497 MET Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1268 VAL Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 166 optimal weight: 0.0570 chunk 70 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 637 HIS ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1266 GLN E 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23675 Z= 0.293 Angle : 0.763 13.551 31985 Z= 0.391 Chirality : 0.048 0.309 3638 Planarity : 0.005 0.092 4161 Dihedral : 6.468 70.327 3213 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.75 % Favored : 88.22 % Rotamer: Outliers : 3.91 % Allowed : 17.64 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.03 (0.15), residues: 2936 helix: -0.05 (0.16), residues: 1002 sheet: -0.96 (0.28), residues: 312 loop : -2.38 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 111 HIS 0.007 0.001 HIS D 806 PHE 0.045 0.002 PHE E 56 TYR 0.036 0.002 TYR C1001 ARG 0.006 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 188 time to evaluate : 3.043 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: A 15 MET cc_start: 0.7308 (tmm) cc_final: 0.7068 (tmm) REVERT: A 19 ASP cc_start: 0.9164 (t70) cc_final: 0.8939 (t70) REVERT: A 33 TYR cc_start: 0.6287 (OUTLIER) cc_final: 0.4905 (m-80) REVERT: A 106 ASN cc_start: 0.8961 (t0) cc_final: 0.8470 (t0) REVERT: B 96 ASP cc_start: 0.9322 (p0) cc_final: 0.8954 (p0) REVERT: B 187 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6197 (p90) REVERT: B 191 GLN cc_start: 0.8474 (mm110) cc_final: 0.8143 (mm110) REVERT: C 330 GLN cc_start: 0.4132 (OUTLIER) cc_final: 0.3585 (mp10) REVERT: C 364 TYR cc_start: 0.9319 (m-10) cc_final: 0.8996 (m-80) REVERT: C 651 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.8060 (mtt90) REVERT: C 674 LYS cc_start: 0.9151 (tppt) cc_final: 0.8652 (pttt) REVERT: C 789 MET cc_start: 0.8363 (mmm) cc_final: 0.7981 (mmm) REVERT: C 1041 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7015 (ttm170) REVERT: C 1092 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4243 (pt) REVERT: D 98 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6599 (mmp) REVERT: D 191 ILE cc_start: 0.6174 (OUTLIER) cc_final: 0.5761 (pt) REVERT: D 215 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7596 (ppt90) REVERT: D 479 MET cc_start: 0.8771 (mmm) cc_final: 0.8339 (mmm) REVERT: D 519 MET cc_start: 0.7710 (mpp) cc_final: 0.7337 (mpp) REVERT: D 637 MET cc_start: 0.8067 (tpp) cc_final: 0.7763 (tpp) REVERT: D 721 MET cc_start: 0.8296 (tmm) cc_final: 0.7610 (tmm) REVERT: D 735 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5860 (mp) REVERT: D 1379 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8073 (pp20) REVERT: D 1402 MET cc_start: -0.0452 (tpt) cc_final: -0.0734 (tpt) REVERT: E 46 LYS cc_start: 0.9218 (pptt) cc_final: 0.8880 (pptt) REVERT: E 78 TYR cc_start: 0.9121 (t80) cc_final: 0.8789 (t80) REVERT: E 79 TYR cc_start: 0.8028 (m-80) cc_final: 0.7318 (m-80) REVERT: E 84 LYS cc_start: 0.8858 (mttt) cc_final: 0.8201 (mttp) REVERT: E 102 MET cc_start: 0.7113 (mmp) cc_final: 0.6288 (tmm) outliers start: 100 outliers final: 67 residues processed: 265 average time/residue: 0.3673 time to fit residues: 153.7175 Evaluate side-chains 259 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 182 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1067 ASP Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1136 ASP Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 763 ASN Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 918 VAL Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1268 VAL Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 283 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 23675 Z= 0.446 Angle : 0.871 15.092 31985 Z= 0.450 Chirality : 0.051 0.296 3638 Planarity : 0.006 0.076 4161 Dihedral : 6.859 61.635 3213 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 29.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.49 % Favored : 86.48 % Rotamer: Outliers : 4.30 % Allowed : 18.54 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.40 (0.15), residues: 2936 helix: -0.42 (0.15), residues: 1000 sheet: -1.17 (0.29), residues: 287 loop : -2.54 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 111 HIS 0.010 0.002 HIS D 806 PHE 0.046 0.003 PHE E 56 TYR 0.051 0.002 TYR D 635 ARG 0.010 0.001 ARG D 781 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 187 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASN cc_start: 0.6119 (t0) cc_final: 0.5866 (t0) REVERT: A 15 MET cc_start: 0.7308 (tmm) cc_final: 0.7096 (tmm) REVERT: A 19 ASP cc_start: 0.9219 (t70) cc_final: 0.8992 (t70) REVERT: A 33 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.4526 (m-80) REVERT: A 106 ASN cc_start: 0.9128 (t0) cc_final: 0.8713 (t0) REVERT: B 66 PHE cc_start: 0.5675 (OUTLIER) cc_final: 0.5359 (m-80) REVERT: B 96 ASP cc_start: 0.9322 (p0) cc_final: 0.8905 (p0) REVERT: B 187 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6506 (p90) REVERT: B 219 GLN cc_start: 0.6813 (tm-30) cc_final: 0.6582 (tm-30) REVERT: C 330 GLN cc_start: 0.4189 (OUTLIER) cc_final: 0.3545 (mp-120) REVERT: C 364 TYR cc_start: 0.9362 (m-10) cc_final: 0.9078 (m-80) REVERT: C 651 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.8042 (mtt90) REVERT: C 706 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.8718 (mp0) REVERT: C 1041 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6354 (ttm170) REVERT: D 98 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6980 (mmp) REVERT: D 215 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7798 (ppt90) REVERT: D 479 MET cc_start: 0.8836 (mmm) cc_final: 0.8461 (mmt) REVERT: D 519 MET cc_start: 0.7736 (mpp) cc_final: 0.7310 (mpp) REVERT: D 721 MET cc_start: 0.8368 (tmm) cc_final: 0.7755 (tmm) REVERT: D 735 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5949 (mp) REVERT: D 1357 GLU cc_start: 0.8892 (tp30) cc_final: 0.8546 (tm-30) REVERT: D 1379 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8085 (pp20) REVERT: D 1402 MET cc_start: -0.0376 (tpt) cc_final: -0.0651 (tpt) REVERT: E 46 LYS cc_start: 0.9202 (pptt) cc_final: 0.8889 (pptt) REVERT: E 78 TYR cc_start: 0.9194 (t80) cc_final: 0.8857 (t80) REVERT: E 79 TYR cc_start: 0.8134 (m-80) cc_final: 0.7437 (m-80) REVERT: E 84 LYS cc_start: 0.8979 (mttt) cc_final: 0.8296 (mttp) REVERT: E 102 MET cc_start: 0.7417 (mmp) cc_final: 0.6659 (tmm) outliers start: 110 outliers final: 75 residues processed: 274 average time/residue: 0.3761 time to fit residues: 161.2781 Evaluate side-chains 261 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 176 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1067 ASP Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1136 ASP Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 481 VAL Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 763 ASN Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 918 VAL Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 50.0000 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 180 optimal weight: 30.0000 chunk 193 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1266 GLN D1363 ASN E 39 ASN E 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23675 Z= 0.269 Angle : 0.775 14.124 31985 Z= 0.394 Chirality : 0.048 0.277 3638 Planarity : 0.005 0.071 4161 Dihedral : 6.475 55.143 3213 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 23.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.55 % Favored : 88.42 % Rotamer: Outliers : 3.75 % Allowed : 19.52 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.21 (0.15), residues: 2936 helix: -0.23 (0.16), residues: 1004 sheet: -1.07 (0.29), residues: 297 loop : -2.45 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 111 HIS 0.007 0.001 HIS D 806 PHE 0.045 0.002 PHE E 56 TYR 0.038 0.002 TYR C1001 ARG 0.007 0.001 ARG D 781 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 192 time to evaluate : 2.653 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: A 11 ASN cc_start: 0.6264 (t0) cc_final: 0.5977 (t0) REVERT: A 19 ASP cc_start: 0.9243 (t70) cc_final: 0.9021 (t70) REVERT: A 33 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.4792 (m-80) REVERT: A 106 ASN cc_start: 0.9054 (t0) cc_final: 0.8688 (t0) REVERT: A 178 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7855 (ttm-80) REVERT: B 66 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.5344 (m-80) REVERT: B 96 ASP cc_start: 0.9296 (p0) cc_final: 0.8871 (p0) REVERT: B 187 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6421 (p90) REVERT: B 191 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8195 (mm-40) REVERT: C 330 GLN cc_start: 0.4141 (OUTLIER) cc_final: 0.3516 (mp-120) REVERT: C 364 TYR cc_start: 0.9372 (m-10) cc_final: 0.9074 (m-80) REVERT: C 789 MET cc_start: 0.8427 (mmm) cc_final: 0.7985 (mmm) REVERT: C 1041 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6880 (ttm170) REVERT: C 1172 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7413 (ttt) REVERT: D 191 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5612 (pt) REVERT: D 215 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7704 (ppt90) REVERT: D 479 MET cc_start: 0.8690 (mmm) cc_final: 0.8323 (mmm) REVERT: D 519 MET cc_start: 0.7665 (mpp) cc_final: 0.7315 (mpp) REVERT: D 721 MET cc_start: 0.8379 (tmm) cc_final: 0.7642 (tmm) REVERT: D 735 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5908 (mp) REVERT: D 1357 GLU cc_start: 0.8820 (tp30) cc_final: 0.8484 (tm-30) REVERT: D 1379 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8157 (pp20) REVERT: D 1402 MET cc_start: -0.0310 (tpt) cc_final: -0.0534 (tpt) REVERT: E 46 LYS cc_start: 0.9200 (pptt) cc_final: 0.8916 (pptt) REVERT: E 78 TYR cc_start: 0.9162 (t80) cc_final: 0.8824 (t80) REVERT: E 79 TYR cc_start: 0.8048 (m-80) cc_final: 0.7347 (m-80) REVERT: E 84 LYS cc_start: 0.8970 (mttt) cc_final: 0.8294 (mttp) REVERT: E 102 MET cc_start: 0.7403 (mmp) cc_final: 0.6635 (tmm) outliers start: 96 outliers final: 69 residues processed: 268 average time/residue: 0.3480 time to fit residues: 147.6847 Evaluate side-chains 261 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 182 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1067 ASP Chi-restraints excluded: chain C residue 1100 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1136 ASP Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 763 ASN Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 918 VAL Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1268 VAL Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 8.9990 chunk 271 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 207 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 238 optimal weight: 4.9990 chunk 249 optimal weight: 0.5980 chunk 263 optimal weight: 8.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 GLN C 932 HIS C1004 HIS ** C1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23675 Z= 0.231 Angle : 0.765 16.619 31985 Z= 0.386 Chirality : 0.048 0.368 3638 Planarity : 0.005 0.072 4161 Dihedral : 6.232 52.899 3213 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.21 % Favored : 88.73 % Rotamer: Outliers : 3.48 % Allowed : 20.14 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.08 (0.15), residues: 2936 helix: -0.10 (0.16), residues: 1005 sheet: -0.89 (0.29), residues: 306 loop : -2.42 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 111 HIS 0.005 0.001 HIS D 806 PHE 0.049 0.002 PHE E 56 TYR 0.036 0.002 TYR C1001 ARG 0.011 0.000 ARG C 651 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 204 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASN cc_start: 0.6303 (t0) cc_final: 0.6051 (t0) REVERT: A 19 ASP cc_start: 0.9241 (t70) cc_final: 0.9016 (t70) REVERT: A 33 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.4856 (m-80) REVERT: A 106 ASN cc_start: 0.9019 (t0) cc_final: 0.8693 (t0) REVERT: B 66 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.5356 (m-80) REVERT: B 96 ASP cc_start: 0.9278 (p0) cc_final: 0.8815 (p0) REVERT: B 122 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.3950 (m-80) REVERT: B 142 MET cc_start: 0.7395 (pmm) cc_final: 0.6920 (pmm) REVERT: B 187 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6324 (p90) REVERT: B 191 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8240 (mm-40) REVERT: B 219 GLN cc_start: 0.6778 (tm-30) cc_final: 0.6572 (tm-30) REVERT: C 330 GLN cc_start: 0.4157 (OUTLIER) cc_final: 0.3569 (mp10) REVERT: C 364 TYR cc_start: 0.9367 (m-10) cc_final: 0.9058 (m-80) REVERT: C 651 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7603 (mtt180) REVERT: C 789 MET cc_start: 0.8493 (mmm) cc_final: 0.8039 (mmm) REVERT: C 1041 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6506 (ttm170) REVERT: C 1172 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7253 (ttt) REVERT: D 98 MET cc_start: 0.6839 (mmp) cc_final: 0.6619 (mmm) REVERT: D 191 ILE cc_start: 0.5931 (OUTLIER) cc_final: 0.5518 (pt) REVERT: D 215 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7663 (ppt90) REVERT: D 479 MET cc_start: 0.8704 (mmm) cc_final: 0.8321 (mmm) REVERT: D 519 MET cc_start: 0.7643 (mpp) cc_final: 0.7313 (mpp) REVERT: D 637 MET cc_start: 0.8133 (tpp) cc_final: 0.7888 (tpp) REVERT: D 721 MET cc_start: 0.8349 (tmm) cc_final: 0.7640 (tmm) REVERT: D 735 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5822 (mp) REVERT: D 1233 GLN cc_start: 0.8750 (mp-120) cc_final: 0.8501 (mm-40) REVERT: D 1357 GLU cc_start: 0.8769 (tp30) cc_final: 0.8403 (tm-30) REVERT: D 1379 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8155 (pp20) REVERT: D 1402 MET cc_start: -0.0422 (tpt) cc_final: -0.0634 (tpt) REVERT: E 46 LYS cc_start: 0.9224 (pptt) cc_final: 0.8931 (pptt) REVERT: E 78 TYR cc_start: 0.9146 (t80) cc_final: 0.8801 (t80) REVERT: E 79 TYR cc_start: 0.8030 (m-80) cc_final: 0.7327 (m-80) REVERT: E 84 LYS cc_start: 0.8956 (mttt) cc_final: 0.8317 (mttp) REVERT: E 102 MET cc_start: 0.7390 (mmp) cc_final: 0.6567 (tmm) outliers start: 89 outliers final: 72 residues processed: 270 average time/residue: 0.3500 time to fit residues: 150.1400 Evaluate side-chains 271 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 188 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 422 TYR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 604 SER Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 816 GLU Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 995 LYS Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1067 ASP Chi-restraints excluded: chain C residue 1100 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1136 ASP Chi-restraints excluded: chain C residue 1161 PHE Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 563 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 763 ASN Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 918 VAL Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1245 ILE Chi-restraints excluded: chain D residue 1268 VAL Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 3.9990 chunk 279 optimal weight: 0.0570 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 292 optimal weight: 0.8980 chunk 269 optimal weight: 8.9990 chunk 233 optimal weight: 9.9990 chunk 24 optimal weight: 0.0970 chunk 180 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23675 Z= 0.193 Angle : 0.753 17.142 31985 Z= 0.375 Chirality : 0.048 0.394 3638 Planarity : 0.005 0.072 4161 Dihedral : 5.954 53.214 3213 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.63 % Favored : 89.34 % Rotamer: Outliers : 3.13 % Allowed : 20.69 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.87 (0.15), residues: 2936 helix: 0.07 (0.16), residues: 1005 sheet: -0.73 (0.30), residues: 306 loop : -2.30 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 111 HIS 0.007 0.001 HIS C 932 PHE 0.048 0.002 PHE E 56 TYR 0.033 0.001 TYR C1001 ARG 0.008 0.000 ARG C 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5872 Ramachandran restraints generated. 2936 Oldfield, 0 Emsley, 2936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 209 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.9205 (t70) cc_final: 0.8985 (t70) REVERT: A 33 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.5093 (m-80) REVERT: A 106 ASN cc_start: 0.8944 (t0) cc_final: 0.8479 (t0) REVERT: B 66 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.5709 (m-80) REVERT: B 96 ASP cc_start: 0.9248 (p0) cc_final: 0.8771 (p0) REVERT: B 122 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.3989 (m-80) REVERT: B 142 MET cc_start: 0.7278 (pmm) cc_final: 0.6817 (pmm) REVERT: B 187 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.6237 (p90) REVERT: B 191 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8156 (mm-40) REVERT: C 330 GLN cc_start: 0.4030 (OUTLIER) cc_final: 0.3479 (mp10) REVERT: C 364 TYR cc_start: 0.9349 (m-10) cc_final: 0.9026 (m-80) REVERT: C 554 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: C 706 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8983 (mm-30) REVERT: C 789 MET cc_start: 0.8573 (mmm) cc_final: 0.8131 (mmm) REVERT: C 1041 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6465 (ttm170) REVERT: C 1172 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7189 (tpt) REVERT: D 191 ILE cc_start: 0.5863 (OUTLIER) cc_final: 0.5440 (pt) REVERT: D 215 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7605 (ppt90) REVERT: D 479 MET cc_start: 0.8652 (mmm) cc_final: 0.8269 (mmm) REVERT: D 519 MET cc_start: 0.7624 (mpp) cc_final: 0.7287 (mpp) REVERT: D 637 MET cc_start: 0.8063 (tpp) cc_final: 0.7800 (tpp) REVERT: D 721 MET cc_start: 0.8355 (tmm) cc_final: 0.7720 (tmm) REVERT: D 1341 ARG cc_start: 0.8430 (ptt180) cc_final: 0.8198 (ptt-90) REVERT: D 1379 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8145 (pp20) REVERT: E 46 LYS cc_start: 0.9196 (pptt) cc_final: 0.8869 (pptt) REVERT: E 78 TYR cc_start: 0.9102 (t80) cc_final: 0.8755 (t80) REVERT: E 79 TYR cc_start: 0.7982 (m-80) cc_final: 0.7267 (m-80) REVERT: E 84 LYS cc_start: 0.8912 (mttt) cc_final: 0.8304 (mttp) REVERT: E 102 MET cc_start: 0.7388 (mmp) cc_final: 0.6724 (tmm) outliers start: 80 outliers final: 52 residues processed: 269 average time/residue: 0.3437 time to fit residues: 147.5350 Evaluate side-chains 263 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 199 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 PHE Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 610 THR Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain C residue 927 ARG Chi-restraints excluded: chain C residue 1041 ARG Chi-restraints excluded: chain C residue 1067 ASP Chi-restraints excluded: chain C residue 1100 LEU Chi-restraints excluded: chain C residue 1109 VAL Chi-restraints excluded: chain C residue 1136 ASP Chi-restraints excluded: chain C residue 1172 MET Chi-restraints excluded: chain C residue 1201 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 467 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 635 TYR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 738 MET Chi-restraints excluded: chain D residue 784 LEU Chi-restraints excluded: chain D residue 815 CYS Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 818 LEU Chi-restraints excluded: chain D residue 857 ILE Chi-restraints excluded: chain D residue 887 LEU Chi-restraints excluded: chain D residue 923 SER Chi-restraints excluded: chain D residue 1135 PHE Chi-restraints excluded: chain D residue 1268 VAL Chi-restraints excluded: chain D residue 1363 ASN Chi-restraints excluded: chain D residue 1379 GLU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 34 optimal weight: 0.0980 chunk 64 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 29 optimal weight: 30.0000 chunk 43 optimal weight: 0.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.128040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.094916 restraints weight = 95345.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.097831 restraints weight = 47207.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099676 restraints weight = 31029.083| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23675 Z= 0.260 Angle : 0.777 15.951 31985 Z= 0.392 Chirality : 0.049 0.279 3638 Planarity : 0.005 0.072 4161 Dihedral : 6.056 53.129 3213 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.48 % Favored : 88.49 % Rotamer: Outliers : 2.78 % Allowed : 21.39 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.95 (0.15), residues: 2936 helix: -0.01 (0.16), residues: 1009 sheet: -0.83 (0.30), residues: 311 loop : -2.33 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 111 HIS 0.006 0.001 HIS C 932 PHE 0.049 0.002 PHE E 56 TYR 0.033 0.002 TYR C1001 ARG 0.007 0.000 ARG C 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5143.52 seconds wall clock time: 94 minutes 41.97 seconds (5681.97 seconds total)