Starting phenix.real_space_refine on Thu Apr 11 12:59:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/04_2024/8jxu_36713_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/04_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_36713/04_2024/8jxu_36713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/04_2024/8jxu_36713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/04_2024/8jxu_36713_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxu_36713/04_2024/8jxu_36713_trim_updated.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 10.03, per 1000 atoms: 0.44 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: 19.27 Conformation dependent library (CDL) restraints added in 2.1 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... running ksdssp... Secondary structure from input PDB file: 59 helices and 5 sheets defined 62.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.12 Creating SS restraints... Processing helix chain 'A' and resid 3 through 5 No H-bonds generated for 'chain 'A' and resid 3 through 5' Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 25 through 28 No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 32 through 53 Proline residue: A 36 - end of helix 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) Processing helix chain 'A' and resid 63 through 89 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 98 through 123 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) removed outlier: 4.219A pdb=" N GLN A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP A 123 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 156 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 183 removed outlier: 3.686A pdb=" N SER A 165 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N CYS A 166 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA A 183 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 200 through 203 No H-bonds generated for 'chain 'A' and resid 200 through 203' Processing helix chain 'A' and resid 207 through 218 removed outlier: 4.250A pdb=" N SER A 211 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 214 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 235 through 261 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) Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 320 through 351 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 357 through 392 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 395 through 406 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 409 through 412 No H-bonds generated for 'chain 'A' and resid 409 through 412' Processing helix chain 'A' and resid 417 through 430 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) Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 438 through 457 removed outlier: 3.893A pdb=" N LEU A 441 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP A 442 " --> pdb=" O HIS A 439 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 443 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 445 " --> pdb=" O TRP A 442 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 446 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 507 removed outlier: 3.597A pdb=" N VAL A 467 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 473 " --> pdb=" O MET A 470 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 3.829A pdb=" N LEU A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR A 486 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 487 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 489 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 490 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 492 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP A 496 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 497 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN A 503 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLU A 504 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 518 through 567 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) Proline residue: A 554 - end of helix 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 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 586 through 617 removed outlier: 3.915A pdb=" N LEU A 589 " --> pdb=" O PHE A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix removed outlier: 3.504A pdb=" N MET A 595 " --> pdb=" O PRO A 592 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 596 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Proline residue: A 597 - end of helix removed outlier: 3.890A pdb=" N ILE A 600 " --> pdb=" O PRO A 597 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR A 610 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 613 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 614 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 617 " --> pdb=" O GLU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 removed outlier: 3.502A pdb=" N MET A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 727 through 736 removed outlier: 3.813A pdb=" N GLN A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 removed outlier: 4.131A pdb=" N MET A 745 " --> pdb=" O PRO A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 751 No H-bonds generated for 'chain 'A' and resid 749 through 751' Processing helix chain 'A' and resid 763 through 777 removed outlier: 3.609A pdb=" N TYR A 776 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 803 Processing helix chain 'A' and resid 822 through 827 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 822 through 827' Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 854 through 862 removed outlier: 3.659A pdb=" N PHE A 862 " --> pdb=" O ASN A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 976 through 1009 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) removed outlier: 4.760A pdb=" N ASP A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER A1007 " --> pdb=" O TRP A1003 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS A1008 " --> pdb=" O THR A1004 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1064 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 1069 through 1074 Processing helix chain 'A' and resid 1077 through 1085 removed outlier: 3.597A pdb=" N PHE A1084 " --> pdb=" O ILE A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1093 No H-bonds generated for 'chain 'A' and resid 1090 through 1093' Processing helix chain 'A' and resid 1095 through 1119 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 1123 through 1145 Proline residue: A1129 - end of helix removed outlier: 3.781A pdb=" N SER A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A1142 " --> pdb=" O MET A1139 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SER A1143 " --> pdb=" O PHE A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1154 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 1157 through 1168 Processing helix chain 'A' and resid 1171 through 1176 Processing helix chain 'A' and resid 1179 through 1228 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) Processing helix chain 'A' and resid 1236 through 1277 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) removed outlier: 4.747A pdb=" N VAL A1267 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA A1268 " --> pdb=" O THR A1264 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) 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) removed outlier: 3.811A pdb=" N LYS A1277 " --> pdb=" O THR A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1347 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) Processing helix chain 'A' and resid 1374 through 1376 No H-bonds generated for 'chain 'A' and resid 1374 through 1376' Processing helix chain 'A' and resid 1391 through 1395 Processing helix chain 'A' and resid 1403 through 1412 Processing helix chain 'A' and resid 1416 through 1421 Processing helix chain 'A' and resid 1432 through 1434 No H-bonds generated for 'chain 'A' and resid 1432 through 1434' Processing helix chain 'A' and resid 1439 through 1453 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) Processing helix chain 'A' and resid 1469 through 1481 Processing helix chain 'A' and resid 1518 through 1523 Processing helix chain 'A' and resid 1527 through 1535 Processing sheet with id= A, first strand: chain 'A' and resid 659 through 661 removed outlier: 3.656A pdb=" N MET A 637 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS A 694 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.685A pdb=" N ILE A 781 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL A 704 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU A 783 " --> pdb=" O VAL A 704 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1322 through 1324 Processing sheet with id= D, first strand: chain 'A' and resid 1511 through 1516 removed outlier: 6.370A pdb=" N VAL A1506 " --> pdb=" O ILE A1513 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS A1515 " --> pdb=" O VAL A1504 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A1504 " --> pdb=" O CYS A1515 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A1507 " --> pdb=" O VAL A1333 " (cutoff:3.500A) 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) Processing sheet with id= E, first strand: chain 'A' and resid 831 through 834 546 hydrogen bonds defined for protein. 1314 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: 9.16 Time building geometry restraints manager: 19.71 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: 695 2.13 - 2.75: 42605 2.75 - 3.37: 65449 3.37 - 3.98: 78977 3.98 - 4.60: 126166 Nonbonded interactions: 313892 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 313887 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.320 Extract box with map and model: 4.180 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 77.620 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.580 ------------------------------------------------------------------------------- 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= 0.231 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 : 1.983 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: 0.4269 time to fit residues: 177.3888 Evaluate side-chains 204 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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: 9.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A1193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11503 Z= 0.271 Angle : 0.647 8.691 15604 Z= 0.358 Chirality : 0.039 0.142 1824 Planarity : 0.005 0.063 1924 Dihedral : 6.641 77.351 1554 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.56 % Allowed : 20.18 % Favored : 77.26 % 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: -1.48 (0.21), residues: 1404 helix: -0.68 (0.17), residues: 871 sheet: -1.89 (0.57), residues: 66 loop : -1.12 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 358 HIS 0.003 0.001 HIS A1428 PHE 0.018 0.001 PHE A 977 TYR 0.020 0.001 TYR A 967 ARG 0.004 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 234 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 1.746 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: A 978 SER cc_start: 0.9192 (m) cc_final: 0.8935 (p) REVERT: A 988 MET cc_start: 0.8429 (tmm) cc_final: 0.8056 (tmm) REVERT: A 1187 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7706 (tm-30) outliers start: 32 outliers final: 23 residues processed: 219 average time/residue: 0.4735 time to fit residues: 160.3464 Evaluate side-chains 211 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 1.884 ------------------------------------------------------------------------------- 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 105 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 144 THR 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 431 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 994 ILE 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 1490 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 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: 5.9990 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8179 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11503 Z= 0.248 Angle : 0.593 7.625 15604 Z= 0.322 Chirality : 0.038 0.162 1824 Planarity : 0.004 0.057 1924 Dihedral : 6.162 87.896 1549 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.56 % Allowed : 20.50 % Favored : 76.94 % 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: -1.45 (0.21), residues: 1404 helix: -0.65 (0.17), residues: 872 sheet: -1.75 (0.57), residues: 66 loop : -1.14 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 309 HIS 0.004 0.001 HIS A1428 PHE 0.015 0.001 PHE A1037 TYR 0.013 0.001 TYR A 967 ARG 0.004 0.000 ARG A1083 *********************** 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 : 1.849 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: A 599 MET cc_start: 0.8537 (tmm) cc_final: 0.8196 (tmm) REVERT: A 978 SER cc_start: 0.9166 (m) cc_final: 0.8930 (p) outliers start: 32 outliers final: 25 residues processed: 214 average time/residue: 0.4340 time to fit residues: 143.7254 Evaluate side-chains 203 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 1.803 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 182 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 431 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 595 MET 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 1130 LEU Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1490 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 136 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1247 ASN A1371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11503 Z= 0.270 Angle : 0.597 6.903 15604 Z= 0.324 Chirality : 0.037 0.148 1824 Planarity : 0.004 0.057 1924 Dihedral : 5.980 88.440 1549 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.88 % Allowed : 21.62 % Favored : 75.50 % 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: -1.41 (0.21), residues: 1404 helix: -0.64 (0.17), residues: 877 sheet: -1.58 (0.59), residues: 66 loop : -1.12 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 309 HIS 0.004 0.001 HIS A1428 PHE 0.021 0.001 PHE A1037 TYR 0.010 0.001 TYR A 967 ARG 0.004 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 225 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 189 time to evaluate : 1.866 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: A 599 MET cc_start: 0.8549 (tmm) cc_final: 0.8221 (tmm) REVERT: A 978 SER cc_start: 0.9196 (m) cc_final: 0.8939 (p) REVERT: A 1069 MET cc_start: 0.7956 (tpp) cc_final: 0.7710 (tpp) REVERT: A 1458 LEU cc_start: 0.9290 (tt) cc_final: 0.9087 (mt) outliers start: 36 outliers final: 29 residues processed: 213 average time/residue: 0.4620 time to fit residues: 151.9853 Evaluate side-chains 201 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 66 LEU 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 133 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 236 LYS 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 431 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 595 MET 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 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 1382 GLN 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: 0.9990 chunk 77 optimal weight: 9.9990 chunk 1 optimal weight: 0.0770 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- 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: 0.8181 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11503 Z= 0.173 Angle : 0.564 6.480 15604 Z= 0.296 Chirality : 0.037 0.147 1824 Planarity : 0.003 0.052 1924 Dihedral : 5.777 84.511 1549 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.48 % Allowed : 22.42 % Favored : 75.10 % 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: -0.92 (0.22), residues: 1404 helix: -0.20 (0.17), residues: 876 sheet: -1.78 (0.55), residues: 76 loop : -0.95 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 646 HIS 0.003 0.001 HIS A 692 PHE 0.012 0.001 PHE A 5 TYR 0.012 0.001 TYR A 967 ARG 0.004 0.000 ARG A1083 *********************** 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 222 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 1.597 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: A 172 TYR cc_start: 0.9087 (t80) cc_final: 0.8840 (t80) REVERT: A 599 MET cc_start: 0.8447 (tmm) cc_final: 0.8124 (tmm) REVERT: A 978 SER cc_start: 0.9147 (m) cc_final: 0.8909 (p) REVERT: A 1069 MET cc_start: 0.7912 (tpp) cc_final: 0.7601 (tpp) REVERT: A 1217 LEU cc_start: 0.9212 (tt) cc_final: 0.8958 (tp) REVERT: A 1458 LEU cc_start: 0.9278 (tt) cc_final: 0.9063 (mt) REVERT: A 1489 ILE cc_start: 0.9540 (mp) cc_final: 0.9289 (tp) outliers start: 31 outliers final: 25 residues processed: 210 average time/residue: 0.4473 time to fit residues: 145.0168 Evaluate side-chains 202 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.815 ------------------------------------------------------------------------------- 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 66 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 138 LEU 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 431 LEU Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 819 THR 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 1107 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1382 GLN 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: 1.9990 chunk 122 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11503 Z= 0.231 Angle : 0.582 7.224 15604 Z= 0.310 Chirality : 0.037 0.142 1824 Planarity : 0.003 0.052 1924 Dihedral : 5.781 85.981 1549 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.88 % Allowed : 22.74 % Favored : 74.38 % 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: -0.88 (0.22), residues: 1404 helix: -0.18 (0.17), residues: 877 sheet: -1.74 (0.55), residues: 76 loop : -0.90 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.016 0.001 HIS A 439 PHE 0.050 0.001 PHE A1037 TYR 0.007 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 215 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.733 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 599 MET cc_start: 0.8475 (tmm) cc_final: 0.8166 (tmm) REVERT: A 978 SER cc_start: 0.9148 (m) cc_final: 0.8915 (p) REVERT: A 1069 MET cc_start: 0.7976 (tpp) cc_final: 0.7726 (tpp) REVERT: A 1217 LEU cc_start: 0.9218 (tt) cc_final: 0.8981 (tp) REVERT: A 1489 ILE cc_start: 0.9555 (mp) cc_final: 0.9315 (tp) outliers start: 36 outliers final: 33 residues processed: 199 average time/residue: 0.4441 time to fit residues: 135.3014 Evaluate side-chains 203 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU 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 66 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 134 LEU 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 330 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 819 THR 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 1212 GLU Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1505 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 135 optimal weight: 9.9990 chunk 85 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11503 Z= 0.158 Angle : 0.571 6.118 15604 Z= 0.294 Chirality : 0.038 0.143 1824 Planarity : 0.003 0.047 1924 Dihedral : 5.643 81.103 1549 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.32 % Allowed : 23.54 % Favored : 74.14 % 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: -0.49 (0.22), residues: 1404 helix: 0.14 (0.18), residues: 879 sheet: -1.62 (0.56), residues: 76 loop : -0.76 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 309 HIS 0.004 0.001 HIS A 439 PHE 0.060 0.001 PHE A1037 TYR 0.010 0.001 TYR A 172 ARG 0.003 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 213 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 1.690 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: A 599 MET cc_start: 0.8466 (tmm) cc_final: 0.8178 (tmm) REVERT: A 978 SER cc_start: 0.9152 (m) cc_final: 0.8904 (p) REVERT: A 1069 MET cc_start: 0.7921 (tpp) cc_final: 0.7644 (tpp) REVERT: A 1217 LEU cc_start: 0.9185 (tt) cc_final: 0.8955 (tp) REVERT: A 1489 ILE cc_start: 0.9531 (mp) cc_final: 0.9314 (tp) outliers start: 29 outliers final: 27 residues processed: 204 average time/residue: 0.4407 time to fit residues: 139.2988 Evaluate side-chains 198 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 66 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 LEU 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 451 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 819 THR 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 1351 LEU Chi-restraints excluded: chain A residue 1451 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 118 optimal weight: 0.4980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3863 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= 0.221 Angle : 0.572 6.013 15604 Z= 0.304 Chirality : 0.037 0.137 1824 Planarity : 0.003 0.049 1924 Dihedral : 5.678 83.712 1549 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.88 % Allowed : 22.66 % Favored : 74.46 % 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: -0.51 (0.22), residues: 1404 helix: 0.16 (0.17), residues: 866 sheet: -1.55 (0.57), residues: 76 loop : -0.86 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 309 HIS 0.004 0.001 HIS A 439 PHE 0.052 0.001 PHE A1037 TYR 0.007 0.001 TYR A 172 ARG 0.003 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 211 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 2.076 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 599 MET cc_start: 0.8497 (tmm) cc_final: 0.8226 (tmm) REVERT: A 978 SER cc_start: 0.9145 (m) cc_final: 0.8908 (p) REVERT: A 1069 MET cc_start: 0.7979 (tpp) cc_final: 0.7722 (tpp) REVERT: A 1217 LEU cc_start: 0.9199 (tt) cc_final: 0.8969 (tp) REVERT: A 1489 ILE cc_start: 0.9535 (mp) cc_final: 0.9330 (tp) outliers start: 36 outliers final: 32 residues processed: 196 average time/residue: 0.4200 time to fit residues: 129.5771 Evaluate side-chains 195 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 66 LEU 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 134 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 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 431 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 819 THR 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 1187 GLU Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1505 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3956 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= 0.160 Angle : 0.572 6.643 15604 Z= 0.293 Chirality : 0.037 0.144 1824 Planarity : 0.003 0.046 1924 Dihedral : 5.600 79.799 1549 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.56 % Allowed : 23.30 % Favored : 74.14 % 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: -0.24 (0.22), residues: 1404 helix: 0.36 (0.18), residues: 872 sheet: -1.52 (0.56), residues: 76 loop : -0.71 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.003 0.001 HIS A 823 PHE 0.047 0.001 PHE A1037 TYR 0.009 0.001 TYR A 967 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: 32 poor density : 177 time to evaluate : 2.128 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 599 MET cc_start: 0.8440 (tmm) cc_final: 0.8175 (tmm) REVERT: A 978 SER cc_start: 0.9136 (m) cc_final: 0.8900 (p) REVERT: A 1069 MET cc_start: 0.7942 (tpp) cc_final: 0.7681 (tpp) REVERT: A 1217 LEU cc_start: 0.9190 (tt) cc_final: 0.8970 (tp) REVERT: A 1383 ASP cc_start: 0.8782 (p0) cc_final: 0.8462 (p0) outliers start: 32 outliers final: 30 residues processed: 194 average time/residue: 0.4357 time to fit residues: 131.5389 Evaluate side-chains 202 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 66 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 180 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 451 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 988 MET 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 1187 GLU Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1351 LEU 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: 4.9990 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11503 Z= 0.162 Angle : 0.568 6.903 15604 Z= 0.292 Chirality : 0.037 0.143 1824 Planarity : 0.003 0.045 1924 Dihedral : 5.559 79.134 1549 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.40 % Allowed : 23.62 % Favored : 73.98 % 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: 0.43 (0.18), residues: 866 sheet: -1.48 (0.56), residues: 76 loop : -0.67 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 11 HIS 0.002 0.001 HIS A 439 PHE 0.045 0.001 PHE A1037 TYR 0.008 0.001 TYR A 967 ARG 0.003 0.000 ARG A1271 ********************** 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 202 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.840 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 978 SER cc_start: 0.9129 (m) cc_final: 0.8897 (p) REVERT: A 1069 MET cc_start: 0.7943 (tpp) cc_final: 0.7689 (tpp) REVERT: A 1217 LEU cc_start: 0.9191 (tt) cc_final: 0.8960 (tp) REVERT: A 1383 ASP cc_start: 0.8824 (p0) cc_final: 0.8491 (p0) outliers start: 30 outliers final: 29 residues processed: 188 average time/residue: 0.4231 time to fit residues: 124.7758 Evaluate side-chains 197 residues out of total 1249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 66 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 LEU 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 451 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 551 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 988 MET 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 1209 ILE Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1351 LEU 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: 6.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.052117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.041738 restraints weight = 188630.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.043636 restraints weight = 81850.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.044999 restraints weight = 47226.515| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4151 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= 0.224 Angle : 0.581 6.273 15604 Z= 0.307 Chirality : 0.037 0.138 1824 Planarity : 0.003 0.047 1924 Dihedral : 5.656 83.359 1549 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.08 % Allowed : 24.26 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1404 helix: 0.35 (0.18), residues: 865 sheet: -1.49 (0.56), residues: 76 loop : -0.70 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 309 HIS 0.004 0.001 HIS A1428 PHE 0.044 0.001 PHE A1037 TYR 0.007 0.001 TYR A 967 ARG 0.003 0.000 ARG A1271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4533.55 seconds wall clock time: 82 minutes 25.74 seconds (4945.74 seconds total)