Starting phenix.real_space_refine on Tue Jul 23 17:25:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/07_2024/8jxu_36713_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/07_2024/8jxu_36713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/07_2024/8jxu_36713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/07_2024/8jxu_36713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/07_2024/8jxu_36713_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/07_2024/8jxu_36713_neut_trim.cif" } resolution = 3.55 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= 0.006 sd= 0.046 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: 7 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7296 2.51 5 N 1865 2.21 5 O 2040 1.98 5 H 11485 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 620": "OD1" <-> "OD2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "A PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1092": "OD1" <-> "OD2" Residue "A ASP 1152": "OD1" <-> "OD2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1270": "OE1" <-> "OE2" Residue "A TYR 1275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A GLU 1375": "OE1" <-> "OE2" Residue "A PHE 1387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1470": "OE1" <-> "OE2" Residue "A PHE 1530": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 22749 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 22690 Classifications: {'peptide': 1410} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 42, 'TRANS': 1367} Chain breaks: 2 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.43, per 1000 atoms: 0.46 Number of scatterers: 22749 At special positions: 0 Unit cell: (88.81, 117.7, 155.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 57 16.00 P 5 15.00 Mg 1 11.99 O 2040 8.00 N 1865 7.00 C 7296 6.00 H 11485 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 26 " distance=2.03 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: 17.11 Conformation dependent library (CDL) restraints added in 2.6 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 5 sheets defined 70.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.774A pdb=" N CYS A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 18 removed outlier: 3.776A pdb=" N LEU A 16 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.513A pdb=" N GLN A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 54 removed outlier: 3.790A pdb=" N LEU A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.688A pdb=" N TYR A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 54 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 90 removed outlier: 3.850A pdb=" N LEU A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 121 removed outlier: 3.726A pdb=" N TYR A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.663A pdb=" N TYR A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 124 No H-bonds generated for 'chain 'A' and resid 122 through 124' Processing helix chain 'A' and resid 129 through 157 removed outlier: 3.531A pdb=" N TRP A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLN A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 184 removed outlier: 4.740A pdb=" N LEU A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 170 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.612A pdb=" N SER A 196 " --> pdb=" O ASN A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.641A pdb=" N ILE A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 234 through 262 removed outlier: 3.667A pdb=" N THR A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 319 through 352 removed outlier: 3.704A pdb=" N SER A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Proline residue: A 340 - end of helix Processing helix chain 'A' and resid 356 through 393 removed outlier: 3.513A pdb=" N CYS A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 384 " --> pdb=" O CYS A 380 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 removed outlier: 4.457A pdb=" N TYR A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.591A pdb=" N VAL A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N THR A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 456 removed outlier: 4.162A pdb=" N VAL A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 508 removed outlier: 3.838A pdb=" N GLY A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 474 " --> pdb=" O MET A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 4.026A pdb=" N ILE A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 Processing helix chain 'A' and resid 517 through 551 removed outlier: 3.959A pdb=" N GLN A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 3.524A pdb=" N SER A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.934A pdb=" N ALA A 576 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 588 Processing helix chain 'A' and resid 589 through 618 Proline residue: A 597 - end of helix removed outlier: 3.516A pdb=" N SER A 601 " --> pdb=" O PRO A 597 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A 612 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 685 removed outlier: 3.502A pdb=" N MET A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.813A pdb=" N GLN A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 removed outlier: 4.131A pdb=" N MET A 745 " --> pdb=" O PRO A 741 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 746 " --> pdb=" O ASP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 752 removed outlier: 3.507A pdb=" N LEU A 751 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 778 removed outlier: 3.517A pdb=" N ASN A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 Processing helix chain 'A' and resid 821 through 828 removed outlier: 4.336A pdb=" N PHE A 824 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 825 " --> pdb=" O MET A 822 " (cutoff:3.500A) Proline residue: A 826 - end of helix No H-bonds generated for 'chain 'A' and resid 821 through 828' Processing helix chain 'A' and resid 844 through 851 removed outlier: 3.956A pdb=" N LYS A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 863 removed outlier: 3.659A pdb=" N PHE A 862 " --> pdb=" O ASN A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 974 removed outlier: 3.986A pdb=" N TYR A 967 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1005 removed outlier: 3.512A pdb=" N PHE A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 992 " --> pdb=" O MET A 988 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A1005 " --> pdb=" O SER A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1010 removed outlier: 3.601A pdb=" N ILE A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1065 removed outlier: 4.016A pdb=" N VAL A1024 " --> pdb=" O ARG A1020 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A1062 " --> pdb=" O LYS A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1075 removed outlier: 3.696A pdb=" N PHE A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1086 removed outlier: 3.920A pdb=" N ILE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A1084 " --> pdb=" O ILE A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1120 removed outlier: 5.278A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Proline residue: A1096 - end of helix removed outlier: 3.550A pdb=" N ARG A1100 " --> pdb=" O PRO A1096 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A1103 " --> pdb=" O LEU A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1125 Processing helix chain 'A' and resid 1126 through 1146 removed outlier: 4.590A pdb=" N SER A1143 " --> pdb=" O MET A1139 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THR A1144 " --> pdb=" O PHE A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1155 removed outlier: 3.894A pdb=" N LEU A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1169 removed outlier: 3.786A pdb=" N TYR A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1178 through 1229 removed outlier: 3.595A pdb=" N LYS A1184 " --> pdb=" O GLN A1180 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS A1185 " --> pdb=" O ARG A1181 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A1191 " --> pdb=" O GLU A1187 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP A1200 " --> pdb=" O CYS A1196 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A1207 " --> pdb=" O SER A1203 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A1229 " --> pdb=" O MET A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1266 removed outlier: 4.057A pdb=" N GLY A1239 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET A1258 " --> pdb=" O TRP A1254 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1276 removed outlier: 3.662A pdb=" N TYR A1275 " --> pdb=" O ARG A1271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A1276 " --> pdb=" O ILE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1348 removed outlier: 3.894A pdb=" N THR A1344 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A1347 " --> pdb=" O LEU A1343 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1375 removed outlier: 4.663A pdb=" N ARG A1374 " --> pdb=" O HIS A1371 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU A1375 " --> pdb=" O ASP A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1402 through 1413 removed outlier: 3.563A pdb=" N ILE A1406 " --> pdb=" O SER A1402 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1413 " --> pdb=" O ALA A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1422 Processing helix chain 'A' and resid 1431 through 1435 Processing helix chain 'A' and resid 1438 through 1454 removed outlier: 4.008A pdb=" N ALA A1450 " --> pdb=" O CYS A1446 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A1453 " --> pdb=" O ARG A1449 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A1454 " --> pdb=" O ALA A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1480 Processing helix chain 'A' and resid 1494 through 1498 removed outlier: 4.308A pdb=" N THR A1497 " --> pdb=" O ARG A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1524 Processing helix chain 'A' and resid 1526 through 1536 Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.720A pdb=" N HIS A 694 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET A 637 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL A 657 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER A 643 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG A 655 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.720A pdb=" N HIS A 694 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 689 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.268A pdb=" N ALA A 702 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP A 785 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 704 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N TYR A 782 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 818 " --> pdb=" O TYR A 782 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU A 784 " --> pdb=" O VAL A 818 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 666 " --> pdb=" O GLU A 830 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL A 832 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA A 668 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU A 834 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE A 670 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1317 through 1324 removed outlier: 7.014A pdb=" N ARG A1318 " --> pdb=" O GLN A1306 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN A1306 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A1320 " --> pdb=" O ASN A1304 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N PHE A1302 " --> pdb=" O ILE A1359 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE A1359 " --> pdb=" O PHE A1302 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ASN A1304 " --> pdb=" O GLN A1357 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLN A1357 " --> pdb=" O ASN A1304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1377 through 1380 removed outlier: 6.570A pdb=" N THR A1378 " --> pdb=" O VAL A1459 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP A1461 " --> pdb=" O THR A1378 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A1380 " --> pdb=" O ASP A1461 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A1458 " --> pdb=" O ILE A1489 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A1491 " --> pdb=" O LEU A1458 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU A1460 " --> pdb=" O ILE A1491 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A1330 " --> pdb=" O THR A1490 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A1507 " --> pdb=" O VAL A1333 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A1504 " --> pdb=" O CYS A1515 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS A1515 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A1506 " --> pdb=" O ILE A1513 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1839 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: 8.62 Time building geometry restraints manager: 18.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11467 1.03 - 1.23: 31 1.23 - 1.42: 4720 1.42 - 1.62: 6676 1.62 - 1.81: 94 Bond restraints: 22988 Sorted by residual: bond pdb=" CA GLN A 383 " pdb=" C GLN A 383 " ideal model delta sigma weight residual 1.522 1.473 0.050 1.38e-02 5.25e+03 1.29e+01 bond pdb=" CA ASN A1345 " pdb=" C ASN A1345 " ideal model delta sigma weight residual 1.522 1.501 0.021 1.38e-02 5.25e+03 2.40e+00 bond pdb=" C4 ADP A1601 " pdb=" C5 ADP A1601 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C PHE A 382 " pdb=" N GLN A 383 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.38e-02 5.25e+03 1.58e+00 bond pdb=" CA ILE A 197 " pdb=" C ILE A 197 " ideal model delta sigma weight residual 1.527 1.518 0.009 8.50e-03 1.38e+04 1.02e+00 ... (remaining 22983 not shown) Histogram of bond angle deviations from ideal: 65.35 - 80.47: 2 80.47 - 95.58: 0 95.58 - 110.70: 24816 110.70 - 125.81: 16565 125.81 - 140.93: 255 Bond angle restraints: 41638 Sorted by residual: angle pdb=" C ILE A 754 " pdb=" N GLY A 755 " pdb=" CA GLY A 755 " ideal model delta sigma weight residual 119.92 140.93 -21.01 9.60e-01 1.09e+00 4.79e+02 angle pdb=" C ILE A 754 " pdb=" N GLY A 755 " pdb=" H GLY A 755 " ideal model delta sigma weight residual 125.19 75.58 49.61 3.00e+00 1.11e-01 2.73e+02 angle pdb=" CA GLY A 755 " pdb=" N GLY A 755 " pdb=" H GLY A 755 " ideal model delta sigma weight residual 114.89 65.35 49.54 3.00e+00 1.11e-01 2.73e+02 angle pdb=" CA MET A 988 " pdb=" CB MET A 988 " pdb=" CG MET A 988 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" N VAL A 390 " pdb=" CA VAL A 390 " pdb=" C VAL A 390 " ideal model delta sigma weight residual 113.07 109.22 3.85 1.37e+00 5.33e-01 7.91e+00 ... (remaining 41633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.65: 9720 19.65 - 39.30: 781 39.30 - 58.95: 218 58.95 - 78.60: 21 78.60 - 98.25: 7 Dihedral angle restraints: 10747 sinusoidal: 5845 harmonic: 4902 Sorted by residual: dihedral pdb=" O1B ADP A1601 " pdb=" O3A ADP A1601 " pdb=" PB ADP A1601 " pdb=" PA ADP A1601 " ideal model delta sinusoidal sigma weight residual -60.00 -158.25 98.25 1 2.00e+01 2.50e-03 2.74e+01 dihedral pdb=" C4' ADP A1601 " pdb=" C5' ADP A1601 " pdb=" O5' ADP A1601 " pdb=" PA ADP A1601 " ideal model delta sinusoidal sigma weight residual -180.00 -117.90 -62.10 1 2.00e+01 2.50e-03 1.28e+01 dihedral pdb=" CA GLU A 647 " pdb=" C GLU A 647 " pdb=" N HIS A 648 " pdb=" CA HIS A 648 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 10744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1614 0.058 - 0.115: 195 0.115 - 0.173: 12 0.173 - 0.230: 0 0.230 - 0.288: 3 Chirality restraints: 1824 Sorted by residual: chirality pdb=" C2' ATP A1602 " pdb=" C1' ATP A1602 " pdb=" C3' ATP A1602 " pdb=" O2' ATP A1602 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C3' ATP A1602 " pdb=" C2' ATP A1602 " pdb=" C4' ATP A1602 " pdb=" O3' ATP A1602 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C4' ATP A1602 " pdb=" C3' ATP A1602 " pdb=" C5' ATP A1602 " pdb=" O4' ATP A1602 " both_signs ideal model delta sigma weight residual False -2.49 -2.74 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 1821 not shown) Planarity restraints: 3289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 596 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A 597 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 597 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 597 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 474 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 475 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1383 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ASP A1383 " 0.025 2.00e-02 2.50e+03 pdb=" O ASP A1383 " -0.009 2.00e-02 2.50e+03 pdb=" N PRO A1384 " -0.009 2.00e-02 2.50e+03 ... (remaining 3286 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 648 2.13 - 2.75: 42517 2.75 - 3.37: 65426 3.37 - 3.98: 78941 3.98 - 4.60: 125978 Nonbonded interactions: 313510 Sorted by model distance: nonbonded pdb=" OE1 GLU A1352 " pdb=" H GLU A1352 " model vdw 1.513 1.850 nonbonded pdb=" OE1 GLU A 3 " pdb=" H GLU A 3 " model vdw 1.555 1.850 nonbonded pdb=" OE1 GLU A 504 " pdb=" H SER A1388 " model vdw 1.611 1.850 nonbonded pdb="HD21 ASN A 422 " pdb=" OD1 ASP A 496 " model vdw 1.612 1.850 nonbonded pdb=" OE1 GLU A1470 " pdb=" H GLU A1470 " model vdw 1.624 1.850 ... (remaining 313505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.350 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 72.150 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11503 Z= 0.235 Angle : 0.583 21.010 15604 Z= 0.348 Chirality : 0.038 0.288 1824 Planarity : 0.003 0.065 1924 Dihedral : 16.101 98.250 4202 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.24 % Allowed : 15.77 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1404 helix: -0.22 (0.18), residues: 850 sheet: -1.91 (0.59), residues: 67 loop : -1.14 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 999 HIS 0.002 0.001 HIS A1162 PHE 0.016 0.001 PHE A1530 TYR 0.014 0.001 TYR A 356 ARG 0.004 0.000 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 268 time to evaluate : 1.653 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ILE cc_start: 0.9418 (mt) cc_final: 0.9202 (mt) REVERT: A 378 LEU cc_start: 0.9256 (tp) cc_final: 0.9047 (tt) REVERT: A 978 SER cc_start: 0.9162 (m) cc_final: 0.8936 (p) REVERT: A 1069 MET cc_start: 0.7993 (mmm) cc_final: 0.7657 (mmm) outliers start: 3 outliers final: 3 residues processed: 269 average time/residue: 0.3993 time to fit residues: 165.6395 Evaluate side-chains 204 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 574 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 0.0050 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A1193 ASN A1247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11503 Z= 0.269 Angle : 0.678 9.477 15604 Z= 0.371 Chirality : 0.040 0.191 1824 Planarity : 0.004 0.061 1924 Dihedral : 6.558 79.010 1554 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.96 % Allowed : 19.14 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), residues: 1404 helix: -0.24 (0.17), residues: 886 sheet: -2.07 (0.58), residues: 66 loop : -1.16 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.006 0.001 HIS A1042 PHE 0.020 0.002 PHE A1037 TYR 0.018 0.001 TYR A 967 ARG 0.006 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.8268 (tmm) cc_final: 0.8032 (tmm) REVERT: A 988 MET cc_start: 0.8493 (tmm) cc_final: 0.8015 (tmm) REVERT: A 1094 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8406 (t) REVERT: A 1187 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7692 (tm-30) outliers start: 37 outliers final: 24 residues processed: 234 average time/residue: 0.4205 time to fit residues: 152.0042 Evaluate side-chains 212 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1490 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.0980 chunk 39 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1304 ASN ** A1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11503 Z= 0.201 Angle : 0.594 7.509 15604 Z= 0.318 Chirality : 0.038 0.172 1824 Planarity : 0.004 0.055 1924 Dihedral : 6.051 84.326 1549 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.56 % Allowed : 20.82 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.22), residues: 1404 helix: 0.09 (0.17), residues: 888 sheet: -2.03 (0.54), residues: 76 loop : -1.02 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 709 HIS 0.003 0.001 HIS A1371 PHE 0.027 0.001 PHE A1037 TYR 0.012 0.001 TYR A 967 ARG 0.003 0.000 ARG A1271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1187 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7598 (tm-30) outliers start: 32 outliers final: 23 residues processed: 214 average time/residue: 0.4221 time to fit residues: 139.5069 Evaluate side-chains 207 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 507 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 GLN A1394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11503 Z= 0.205 Angle : 0.586 6.726 15604 Z= 0.313 Chirality : 0.038 0.156 1824 Planarity : 0.003 0.051 1924 Dihedral : 5.862 86.701 1549 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.04 % Allowed : 22.18 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1404 helix: 0.29 (0.17), residues: 886 sheet: -1.74 (0.57), residues: 76 loop : -0.99 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 709 HIS 0.004 0.001 HIS A1371 PHE 0.022 0.001 PHE A1037 TYR 0.010 0.001 TYR A 967 ARG 0.003 0.000 ARG A1271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 213 average time/residue: 0.4210 time to fit residues: 139.4944 Evaluate side-chains 202 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1099 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11503 Z= 0.226 Angle : 0.592 6.562 15604 Z= 0.315 Chirality : 0.038 0.144 1824 Planarity : 0.003 0.053 1924 Dihedral : 5.797 86.724 1549 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.96 % Allowed : 22.10 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1404 helix: 0.43 (0.17), residues: 885 sheet: -1.69 (0.57), residues: 76 loop : -1.01 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 309 HIS 0.003 0.001 HIS A1371 PHE 0.014 0.001 PHE A1037 TYR 0.008 0.001 TYR A 967 ARG 0.003 0.000 ARG A1271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 LEU cc_start: 0.9328 (mt) cc_final: 0.9113 (tp) REVERT: A 1392 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8448 (tpt-90) outliers start: 37 outliers final: 29 residues processed: 204 average time/residue: 0.4243 time to fit residues: 132.1797 Evaluate side-chains 203 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1505 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 5.9990 chunk 122 optimal weight: 0.1980 chunk 26 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11503 Z= 0.260 Angle : 0.598 6.799 15604 Z= 0.321 Chirality : 0.038 0.145 1824 Planarity : 0.003 0.055 1924 Dihedral : 5.794 88.798 1549 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.48 % Allowed : 24.26 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1404 helix: 0.47 (0.17), residues: 891 sheet: -1.73 (0.57), residues: 76 loop : -1.02 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.004 0.001 HIS A1371 PHE 0.014 0.001 PHE A1037 TYR 0.009 0.001 TYR A 967 ARG 0.004 0.000 ARG A1271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1217 LEU cc_start: 0.9244 (tt) cc_final: 0.8995 (tp) REVERT: A 1383 ASP cc_start: 0.8869 (p0) cc_final: 0.8455 (p0) REVERT: A 1392 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8451 (tpt-90) outliers start: 31 outliers final: 26 residues processed: 196 average time/residue: 0.4301 time to fit residues: 129.9264 Evaluate side-chains 196 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11503 Z= 0.329 Angle : 0.627 6.642 15604 Z= 0.340 Chirality : 0.038 0.142 1824 Planarity : 0.004 0.059 1924 Dihedral : 5.835 88.429 1549 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.80 % Allowed : 24.34 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1404 helix: 0.36 (0.17), residues: 893 sheet: -1.76 (0.57), residues: 76 loop : -1.05 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.004 0.001 HIS A1428 PHE 0.015 0.001 PHE A1037 TYR 0.009 0.001 TYR A 217 ARG 0.004 0.000 ARG A1271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1217 LEU cc_start: 0.9250 (tt) cc_final: 0.9008 (tp) REVERT: A 1392 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8496 (tpt-90) outliers start: 35 outliers final: 30 residues processed: 194 average time/residue: 0.3954 time to fit residues: 120.2650 Evaluate side-chains 194 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1505 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11503 Z= 0.179 Angle : 0.593 8.460 15604 Z= 0.303 Chirality : 0.038 0.185 1824 Planarity : 0.003 0.055 1924 Dihedral : 5.762 86.553 1549 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.24 % Allowed : 24.90 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1404 helix: 0.82 (0.17), residues: 890 sheet: -1.63 (0.57), residues: 76 loop : -0.89 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 309 HIS 0.003 0.001 HIS A1371 PHE 0.020 0.001 PHE A1418 TYR 0.009 0.001 TYR A 967 ARG 0.004 0.000 ARG A1271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1217 LEU cc_start: 0.9198 (tt) cc_final: 0.8961 (tp) REVERT: A 1383 ASP cc_start: 0.8935 (p0) cc_final: 0.8523 (p0) REVERT: A 1392 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8455 (tpt-90) outliers start: 28 outliers final: 25 residues processed: 197 average time/residue: 0.4167 time to fit residues: 126.6771 Evaluate side-chains 199 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11503 Z= 0.177 Angle : 0.595 7.994 15604 Z= 0.304 Chirality : 0.038 0.144 1824 Planarity : 0.003 0.053 1924 Dihedral : 5.662 83.123 1549 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.32 % Allowed : 25.06 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1404 helix: 1.07 (0.17), residues: 888 sheet: -1.51 (0.58), residues: 76 loop : -0.82 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.004 0.001 HIS A 823 PHE 0.015 0.001 PHE A1037 TYR 0.008 0.001 TYR A 217 ARG 0.003 0.000 ARG A1271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1217 LEU cc_start: 0.9190 (tt) cc_final: 0.8960 (tp) REVERT: A 1383 ASP cc_start: 0.8940 (p0) cc_final: 0.8545 (p0) REVERT: A 1392 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8437 (tpt-90) REVERT: A 1489 ILE cc_start: 0.9522 (mp) cc_final: 0.9280 (tp) outliers start: 29 outliers final: 27 residues processed: 199 average time/residue: 0.4312 time to fit residues: 131.3424 Evaluate side-chains 204 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1187 GLU Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11503 Z= 0.298 Angle : 0.634 8.188 15604 Z= 0.336 Chirality : 0.038 0.215 1824 Planarity : 0.004 0.056 1924 Dihedral : 5.773 87.156 1549 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.56 % Allowed : 24.82 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1404 helix: 0.82 (0.17), residues: 894 sheet: -1.49 (0.58), residues: 76 loop : -0.93 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 309 HIS 0.004 0.001 HIS A1371 PHE 0.018 0.001 PHE A 135 TYR 0.010 0.001 TYR A 217 ARG 0.004 0.000 ARG A1150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1217 LEU cc_start: 0.9219 (tt) cc_final: 0.8995 (tp) REVERT: A 1392 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8498 (tpt-90) outliers start: 32 outliers final: 29 residues processed: 189 average time/residue: 0.4160 time to fit residues: 121.7431 Evaluate side-chains 192 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1187 GLU Chi-restraints excluded: chain A residue 1212 GLU Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1392 ARG Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 112 optimal weight: 0.0870 chunk 46 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 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 = 0.3238 r_free = 0.3238 target = 0.052862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.042378 restraints weight = 183110.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.044329 restraints weight = 78908.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.045743 restraints weight = 45280.784| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11503 Z= 0.168 Angle : 0.609 8.350 15604 Z= 0.304 Chirality : 0.039 0.175 1824 Planarity : 0.003 0.047 1924 Dihedral : 5.633 79.702 1549 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.92 % Allowed : 25.78 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.23), residues: 1404 helix: 1.26 (0.17), residues: 891 sheet: -1.39 (0.59), residues: 76 loop : -0.78 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 517 HIS 0.002 0.001 HIS A 694 PHE 0.010 0.001 PHE A1037 TYR 0.010 0.001 TYR A 967 ARG 0.004 0.000 ARG A1150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4412.37 seconds wall clock time: 78 minutes 1.78 seconds (4681.78 seconds total)