Starting phenix.real_space_refine on Sat Jul 26 06:11:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v69_21060/07_2025/6v69_21060.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v69_21060/07_2025/6v69_21060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v69_21060/07_2025/6v69_21060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v69_21060/07_2025/6v69_21060.map" model { file = "/net/cci-nas-00/data/ceres_data/6v69_21060/07_2025/6v69_21060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v69_21060/07_2025/6v69_21060.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 5447 2.51 5 N 1390 2.21 5 O 1475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8353 Number of models: 1 Model: "" Number of chains: 2 Chain: "J" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3977 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 474} Chain breaks: 13 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 4376 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 543, 4361 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 18, 'TRANS': 524} Chain breaks: 6 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 543, 4361 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 18, 'TRANS': 524} Chain breaks: 6 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 4443 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" CD GLU I 367 " occ=0.50 ... (13 atoms not shown) pdb=" CG BGLU I 367 " occ=0.50 residue: pdb=" N AGLU I 472 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU I 472 " occ=0.50 Time building chain proxies: 7.39, per 1000 atoms: 0.88 Number of scatterers: 8353 At special positions: 0 Unit cell: (136.17, 92.115, 148.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1475 8.00 N 1390 7.00 C 5447 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 74.5% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'J' and resid 267 through 280 removed outlier: 3.955A pdb=" N ILE J 271 " --> pdb=" O GLU J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 336 removed outlier: 3.675A pdb=" N VAL J 323 " --> pdb=" O ALA J 319 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU J 327 " --> pdb=" O VAL J 323 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 334 " --> pdb=" O PHE J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 360 through 388 removed outlier: 3.621A pdb=" N ALA J 367 " --> pdb=" O ALA J 363 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE J 372 " --> pdb=" O LEU J 368 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 373 " --> pdb=" O TYR J 369 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER J 374 " --> pdb=" O LYS J 370 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU J 378 " --> pdb=" O SER J 374 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE J 382 " --> pdb=" O GLU J 378 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS J 385 " --> pdb=" O GLU J 381 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 394 through 402 removed outlier: 4.000A pdb=" N ASP J 400 " --> pdb=" O ALA J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 402 through 416 removed outlier: 4.031A pdb=" N GLN J 408 " --> pdb=" O PRO J 404 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS J 410 " --> pdb=" O LEU J 406 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL J 411 " --> pdb=" O SER J 407 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU J 412 " --> pdb=" O GLN J 408 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS J 414 " --> pdb=" O LYS J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 420 removed outlier: 3.764A pdb=" N VAL J 420 " --> pdb=" O SER J 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 417 through 420' Processing helix chain 'J' and resid 428 through 446 removed outlier: 3.536A pdb=" N ALA J 433 " --> pdb=" O ASN J 429 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU J 436 " --> pdb=" O ARG J 432 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR J 441 " --> pdb=" O LEU J 437 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU J 445 " --> pdb=" O TYR J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 482 removed outlier: 4.001A pdb=" N GLU J 467 " --> pdb=" O SER J 463 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR J 468 " --> pdb=" O LEU J 464 " (cutoff:3.500A) Proline residue: J 471 - end of helix Processing helix chain 'J' and resid 552 through 571 removed outlier: 4.611A pdb=" N LYS J 557 " --> pdb=" O LYS J 553 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN J 558 " --> pdb=" O PRO J 554 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA J 562 " --> pdb=" O GLN J 558 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER J 565 " --> pdb=" O MET J 561 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU J 569 " --> pdb=" O SER J 565 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS J 570 " --> pdb=" O MET J 566 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN J 571 " --> pdb=" O GLN J 567 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 648 Proline residue: J 644 - end of helix removed outlier: 3.829A pdb=" N ALA J 647 " --> pdb=" O ASP J 643 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE J 648 " --> pdb=" O PRO J 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 687 through 690 Processing helix chain 'J' and resid 691 through 710 removed outlier: 3.672A pdb=" N ILE J 695 " --> pdb=" O LEU J 691 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN J 698 " --> pdb=" O HIS J 694 " (cutoff:3.500A) Processing helix chain 'J' and resid 716 through 724 Processing helix chain 'J' and resid 734 through 744 removed outlier: 3.672A pdb=" N PHE J 738 " --> pdb=" O THR J 734 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE J 742 " --> pdb=" O PHE J 738 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP J 744 " --> pdb=" O THR J 740 " (cutoff:3.500A) Processing helix chain 'J' and resid 756 through 764 removed outlier: 3.610A pdb=" N VAL J 760 " --> pdb=" O SER J 756 " (cutoff:3.500A) Processing helix chain 'J' and resid 806 through 811 removed outlier: 3.994A pdb=" N ILE J 811 " --> pdb=" O TRP J 807 " (cutoff:3.500A) Processing helix chain 'J' and resid 814 through 838 removed outlier: 3.580A pdb=" N GLN J 818 " --> pdb=" O SER J 814 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS J 819 " --> pdb=" O LEU J 815 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE J 820 " --> pdb=" O GLU J 816 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN J 830 " --> pdb=" O LEU J 826 " (cutoff:3.500A) Processing helix chain 'J' and resid 881 through 902 removed outlier: 3.928A pdb=" N LEU J 885 " --> pdb=" O HIS J 881 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU J 886 " --> pdb=" O ARG J 882 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS J 889 " --> pdb=" O LEU J 885 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE J 893 " --> pdb=" O LYS J 889 " (cutoff:3.500A) Processing helix chain 'J' and resid 907 through 918 removed outlier: 3.649A pdb=" N HIS J 915 " --> pdb=" O LEU J 911 " (cutoff:3.500A) Processing helix chain 'J' and resid 922 through 941 removed outlier: 3.715A pdb=" N LEU J 926 " --> pdb=" O ASP J 922 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE J 927 " --> pdb=" O LEU J 923 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR J 933 " --> pdb=" O ILE J 929 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR J 936 " --> pdb=" O ARG J 932 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP J 939 " --> pdb=" O SER J 935 " (cutoff:3.500A) Processing helix chain 'J' and resid 950 through 967 removed outlier: 3.623A pdb=" N ILE J 954 " --> pdb=" O VAL J 950 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN J 959 " --> pdb=" O MET J 955 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU J 960 " --> pdb=" O LYS J 956 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA J 961 " --> pdb=" O VAL J 957 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA J 965 " --> pdb=" O ALA J 961 " (cutoff:3.500A) Processing helix chain 'J' and resid 980 through 999 removed outlier: 3.927A pdb=" N GLU J 984 " --> pdb=" O ILE J 980 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER J 985 " --> pdb=" O GLU J 981 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP J 986 " --> pdb=" O LYS J 982 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN J 989 " --> pdb=" O SER J 985 " (cutoff:3.500A) Processing helix chain 'J' and resid 1000 through 1001 No H-bonds generated for 'chain 'J' and resid 1000 through 1001' Processing helix chain 'J' and resid 1007 through 1013 removed outlier: 3.751A pdb=" N LEU J1010 " --> pdb=" O PHE J1007 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 9 Processing helix chain 'I' and resid 38 through 62 removed outlier: 4.229A pdb=" N LEU I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP I 51 " --> pdb=" O ARG I 47 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR I 52 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 114 removed outlier: 3.518A pdb=" N PHE I 89 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER I 95 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL I 96 " --> pdb=" O GLY I 92 " (cutoff:3.500A) Proline residue: I 99 - end of helix removed outlier: 4.049A pdb=" N LEU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU I 108 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 126 removed outlier: 4.086A pdb=" N VAL I 122 " --> pdb=" O SER I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 147 Proline residue: I 134 - end of helix removed outlier: 4.301A pdb=" N VAL I 138 " --> pdb=" O PRO I 134 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL I 139 " --> pdb=" O SER I 135 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL I 140 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE I 143 " --> pdb=" O VAL I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 151 No H-bonds generated for 'chain 'I' and resid 149 through 151' Processing helix chain 'I' and resid 152 through 160 removed outlier: 4.027A pdb=" N TYR I 158 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS I 160 " --> pdb=" O THR I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 194 removed outlier: 4.221A pdb=" N LYS I 174 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY I 181 " --> pdb=" O ALA I 177 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL I 182 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET I 183 " --> pdb=" O CYS I 179 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU I 192 " --> pdb=" O SER I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 285 removed outlier: 3.523A pdb=" N GLU I 281 " --> pdb=" O LEU I 277 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL I 283 " --> pdb=" O VAL I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 317 removed outlier: 3.658A pdb=" N THR I 306 " --> pdb=" O ASN I 302 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE I 307 " --> pdb=" O GLN I 303 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA I 308 " --> pdb=" O GLU I 304 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN I 316 " --> pdb=" O HIS I 312 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN I 317 " --> pdb=" O ARG I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 346 removed outlier: 4.350A pdb=" N GLN I 327 " --> pdb=" O VAL I 323 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL I 328 " --> pdb=" O ASP I 324 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL I 329 " --> pdb=" O PHE I 325 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG I 331 " --> pdb=" O GLN I 327 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU I 343 " --> pdb=" O HIS I 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 361 removed outlier: 3.509A pdb=" N GLN I 353 " --> pdb=" O ASP I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 376 removed outlier: 3.828A pdb=" N PHE I 369 " --> pdb=" O ARG I 365 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA I 371 " --> pdb=" O AGLU I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 382 removed outlier: 3.610A pdb=" N LYS I 381 " --> pdb=" O GLN I 377 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR I 382 " --> pdb=" O HIS I 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 377 through 382' Processing helix chain 'I' and resid 387 through 403 removed outlier: 3.520A pdb=" N VAL I 392 " --> pdb=" O THR I 388 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN I 393 " --> pdb=" O GLU I 389 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL I 394 " --> pdb=" O HIS I 390 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA I 395 " --> pdb=" O ASP I 391 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS I 401 " --> pdb=" O GLN I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 450 Processing helix chain 'I' and resid 460 through 464 removed outlier: 3.953A pdb=" N ILE I 464 " --> pdb=" O PRO I 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 499 removed outlier: 3.795A pdb=" N ASN I 475 " --> pdb=" O LEU I 471 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS I 494 " --> pdb=" O GLU I 490 " (cutoff:3.500A) Processing helix chain 'I' and resid 500 through 502 No H-bonds generated for 'chain 'I' and resid 500 through 502' Processing helix chain 'I' and resid 512 through 530 removed outlier: 4.353A pdb=" N MET I 520 " --> pdb=" O LEU I 516 " (cutoff:3.500A) Processing helix chain 'I' and resid 535 through 548 removed outlier: 4.184A pdb=" N SER I 541 " --> pdb=" O GLU I 537 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN I 548 " --> pdb=" O LEU I 544 " (cutoff:3.500A) Processing helix chain 'I' and resid 553 through 571 removed outlier: 3.685A pdb=" N ASP I 561 " --> pdb=" O ARG I 557 " (cutoff:3.500A) Processing helix chain 'I' and resid 575 through 598 removed outlier: 3.545A pdb=" N ASN I 583 " --> pdb=" O PHE I 579 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU I 584 " --> pdb=" O HIS I 580 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS I 590 " --> pdb=" O LEU I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 606 through 630 removed outlier: 4.238A pdb=" N ILE I 613 " --> pdb=" O ALA I 609 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU I 614 " --> pdb=" O GLN I 610 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL I 615 " --> pdb=" O LEU I 611 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS I 616 " --> pdb=" O SER I 612 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY I 617 " --> pdb=" O ILE I 613 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG I 620 " --> pdb=" O LYS I 616 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 648 removed outlier: 4.109A pdb=" N GLN I 643 " --> pdb=" O SER I 639 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU I 646 " --> pdb=" O ALA I 642 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG I 647 " --> pdb=" O GLN I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 651 through 656 removed outlier: 3.551A pdb=" N THR I 655 " --> pdb=" O ASN I 651 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 17 through 18 removed outlier: 3.579A pdb=" N GLN I 26 " --> pdb=" O THR I 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 414 through 418 removed outlier: 3.654A pdb=" N HIS I 415 " --> pdb=" O SER I 455 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1297 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: 2.03 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2637 1.34 - 1.46: 1829 1.46 - 1.57: 3998 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 8529 Sorted by residual: bond pdb=" CA ASP J 713 " pdb=" C ASP J 713 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.05e-01 bond pdb=" N TYR J 714 " pdb=" CA TYR J 714 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.94e-01 bond pdb=" CA PHE J1007 " pdb=" C PHE J1007 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 5.64e-01 bond pdb=" C LYS I 457 " pdb=" N VAL I 458 " ideal model delta sigma weight residual 1.334 1.324 0.009 1.29e-02 6.01e+03 5.38e-01 bond pdb=" C VAL J 805 " pdb=" O VAL J 805 " ideal model delta sigma weight residual 1.232 1.239 -0.006 8.90e-03 1.26e+04 5.07e-01 ... (remaining 8524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 11413 1.78 - 3.56: 99 3.56 - 5.34: 24 5.34 - 7.12: 6 7.12 - 8.90: 2 Bond angle restraints: 11544 Sorted by residual: angle pdb=" N VAL J 420 " pdb=" CA VAL J 420 " pdb=" C VAL J 420 " ideal model delta sigma weight residual 113.53 109.20 4.33 9.80e-01 1.04e+00 1.95e+01 angle pdb=" N VAL J 555 " pdb=" CA VAL J 555 " pdb=" C VAL J 555 " ideal model delta sigma weight residual 113.20 109.28 3.92 9.60e-01 1.09e+00 1.67e+01 angle pdb=" N LYS J 712 " pdb=" CA LYS J 712 " pdb=" C LYS J 712 " ideal model delta sigma weight residual 109.95 105.59 4.36 1.44e+00 4.82e-01 9.16e+00 angle pdb=" CA LEU I 410 " pdb=" CB LEU I 410 " pdb=" CG LEU I 410 " ideal model delta sigma weight residual 116.30 125.20 -8.90 3.50e+00 8.16e-02 6.47e+00 angle pdb=" C LEU J 305 " pdb=" N THR J 306 " pdb=" CA THR J 306 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.40e+00 ... (remaining 11539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4579 17.40 - 34.80: 405 34.80 - 52.20: 71 52.20 - 69.59: 10 69.59 - 86.99: 1 Dihedral angle restraints: 5066 sinusoidal: 2029 harmonic: 3037 Sorted by residual: dihedral pdb=" CA ASP J 713 " pdb=" C ASP J 713 " pdb=" N TYR J 714 " pdb=" CA TYR J 714 " ideal model delta harmonic sigma weight residual 180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ASP I 534 " pdb=" C ASP I 534 " pdb=" N VAL I 535 " pdb=" CA VAL I 535 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE J 726 " pdb=" C PHE J 726 " pdb=" N PHE J 727 " pdb=" CA PHE J 727 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 959 0.035 - 0.071: 310 0.071 - 0.106: 66 0.106 - 0.141: 9 0.141 - 0.177: 1 Chirality restraints: 1345 Sorted by residual: chirality pdb=" CG LEU I 531 " pdb=" CB LEU I 531 " pdb=" CD1 LEU I 531 " pdb=" CD2 LEU I 531 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CA THR J 306 " pdb=" N THR J 306 " pdb=" C THR J 306 " pdb=" CB THR J 306 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE J 393 " pdb=" N ILE J 393 " pdb=" C ILE J 393 " pdb=" CB ILE J 393 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1342 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR J 692 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO J 693 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO J 693 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 693 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU I 165 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO I 166 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO I 166 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 166 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 467 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO I 468 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO I 468 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 468 " 0.017 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 909 2.74 - 3.28: 8977 3.28 - 3.82: 12413 3.82 - 4.36: 15038 4.36 - 4.90: 24087 Nonbonded interactions: 61424 Sorted by model distance: nonbonded pdb=" O TYR I 480 " pdb=" OG SER I 483 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR J 719 " pdb=" O LYS J 804 " model vdw 2.211 3.040 nonbonded pdb=" O TRP J 276 " pdb=" OG SER J 279 " model vdw 2.220 3.040 nonbonded pdb=" O GLU I 141 " pdb=" OG SER I 145 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR I 52 " pdb=" NE ARG I 101 " model vdw 2.288 3.120 ... (remaining 61419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.000 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.590 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 : 0.003 0.027 8529 Z= 0.124 Angle : 0.515 8.900 11544 Z= 0.286 Chirality : 0.036 0.177 1345 Planarity : 0.003 0.041 1427 Dihedral : 13.159 86.994 3076 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.22 % Allowed : 5.01 % Favored : 94.78 % 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: -4.11 (0.22), residues: 991 helix: -2.67 (0.15), residues: 681 sheet: None (None), residues: 0 loop : -2.36 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 486 HIS 0.003 0.001 HIS I 35 PHE 0.016 0.001 PHE J 727 TYR 0.009 0.001 TYR I 653 ARG 0.003 0.000 ARG I 517 Details of bonding type rmsd hydrogen bonds : bond 0.31137 ( 438) hydrogen bonds : angle 9.44116 ( 1297) covalent geometry : bond 0.00265 ( 8529) covalent geometry : angle 0.51485 (11544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8734 (ppp) cc_final: 0.8442 (ppp) REVERT: J 963 MET cc_start: 0.8431 (mtp) cc_final: 0.8229 (mtt) REVERT: J 992 MET cc_start: 0.7327 (mmt) cc_final: 0.7118 (mmm) REVERT: I 137 MET cc_start: 0.8713 (tpt) cc_final: 0.8302 (tpp) REVERT: I 344 MET cc_start: 0.9172 (tpp) cc_final: 0.8906 (tpp) REVERT: I 355 LYS cc_start: 0.8797 (tppt) cc_final: 0.8546 (tppt) REVERT: I 379 MET cc_start: 0.8605 (ptp) cc_final: 0.8160 (ptm) REVERT: I 520 MET cc_start: 0.9428 (mmt) cc_final: 0.9196 (mmm) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2161 time to fit residues: 39.8085 Evaluate side-chains 86 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.0470 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.0010 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 overall best weight: 0.4284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 328 GLN ** J 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 818 GLN J 822 ASN J 823 GLN J 830 GLN J 925 GLN ** J 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 938 HIS I 26 GLN I 193 HIS I 393 ASN I 498 GLN I 518 ASN I 539 GLN I 542 GLN I 560 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.063785 restraints weight = 51931.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.065855 restraints weight = 25398.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.067253 restraints weight = 15484.996| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8529 Z= 0.141 Angle : 0.618 10.339 11544 Z= 0.316 Chirality : 0.039 0.156 1345 Planarity : 0.004 0.051 1427 Dihedral : 4.190 23.228 1087 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.99 % 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: -2.27 (0.25), residues: 991 helix: -1.01 (0.18), residues: 721 sheet: None (None), residues: 0 loop : -2.53 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 190 HIS 0.004 0.001 HIS I 590 PHE 0.024 0.002 PHE I 31 TYR 0.019 0.001 TYR J 739 ARG 0.003 0.000 ARG J 311 Details of bonding type rmsd hydrogen bonds : bond 0.06126 ( 438) hydrogen bonds : angle 4.94489 ( 1297) covalent geometry : bond 0.00277 ( 8529) covalent geometry : angle 0.61806 (11544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 548 MET cc_start: 0.8873 (tmm) cc_final: 0.8595 (tmm) REVERT: J 561 MET cc_start: 0.7975 (ttp) cc_final: 0.7727 (ttp) REVERT: J 699 TYR cc_start: 0.8084 (t80) cc_final: 0.7681 (t80) REVERT: J 703 CYS cc_start: 0.7792 (p) cc_final: 0.7293 (p) REVERT: J 992 MET cc_start: 0.7303 (mmt) cc_final: 0.7083 (mmm) REVERT: I 137 MET cc_start: 0.8545 (tpt) cc_final: 0.8321 (tpp) REVERT: I 199 GLN cc_start: 0.8858 (mt0) cc_final: 0.8382 (mp-120) REVERT: I 525 ASP cc_start: 0.8942 (t0) cc_final: 0.8713 (t0) REVERT: I 558 LEU cc_start: 0.9202 (tp) cc_final: 0.8778 (pp) REVERT: I 587 ASP cc_start: 0.8952 (p0) cc_final: 0.8740 (t70) REVERT: I 589 CYS cc_start: 0.9085 (m) cc_final: 0.8881 (m) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2087 time to fit residues: 40.8109 Evaluate side-chains 92 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 77 optimal weight: 0.0770 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 721 GLN J 822 ASN J 914 GLN J 915 HIS J 925 GLN J 989 ASN I 3 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.078427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.064065 restraints weight = 76676.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.066471 restraints weight = 32345.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.068158 restraints weight = 18582.235| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8529 Z= 0.119 Angle : 0.552 10.375 11544 Z= 0.277 Chirality : 0.038 0.146 1345 Planarity : 0.004 0.043 1427 Dihedral : 3.912 22.554 1087 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.30 % 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: -1.22 (0.26), residues: 991 helix: -0.23 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -2.16 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 190 HIS 0.003 0.001 HIS I 463 PHE 0.015 0.001 PHE J 375 TYR 0.014 0.001 TYR J 739 ARG 0.004 0.000 ARG J 724 Details of bonding type rmsd hydrogen bonds : bond 0.05020 ( 438) hydrogen bonds : angle 4.32379 ( 1297) covalent geometry : bond 0.00230 ( 8529) covalent geometry : angle 0.55216 (11544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8544 (ppp) cc_final: 0.8270 (ppp) REVERT: J 548 MET cc_start: 0.8864 (tmm) cc_final: 0.8554 (tmm) REVERT: J 699 TYR cc_start: 0.8286 (t80) cc_final: 0.7799 (t80) REVERT: J 703 CYS cc_start: 0.7531 (p) cc_final: 0.7158 (p) REVERT: J 902 MET cc_start: 0.8625 (mmm) cc_final: 0.8392 (mmm) REVERT: J 955 MET cc_start: 0.8490 (mmt) cc_final: 0.8158 (mmm) REVERT: J 992 MET cc_start: 0.7353 (mmt) cc_final: 0.7080 (mmm) REVERT: I 199 GLN cc_start: 0.8821 (mt0) cc_final: 0.8457 (mp-120) REVERT: I 379 MET cc_start: 0.8625 (ptp) cc_final: 0.8372 (ptm) REVERT: I 490 GLU cc_start: 0.8443 (tt0) cc_final: 0.8011 (tt0) REVERT: I 558 LEU cc_start: 0.9254 (tp) cc_final: 0.8708 (pp) REVERT: I 571 SER cc_start: 0.9243 (m) cc_final: 0.8904 (p) REVERT: I 589 CYS cc_start: 0.9201 (m) cc_final: 0.8876 (m) REVERT: I 593 CYS cc_start: 0.8899 (m) cc_final: 0.7646 (m) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2762 time to fit residues: 55.9097 Evaluate side-chains 93 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 413 HIS ** J 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 822 ASN J 925 GLN I 528 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.076666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.063186 restraints weight = 61486.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.065330 restraints weight = 29206.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.066793 restraints weight = 17506.162| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8529 Z= 0.153 Angle : 0.592 9.987 11544 Z= 0.295 Chirality : 0.039 0.148 1345 Planarity : 0.004 0.039 1427 Dihedral : 4.027 23.422 1087 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.11 % Allowed : 3.05 % Favored : 96.84 % 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: -0.82 (0.27), residues: 991 helix: 0.09 (0.19), residues: 721 sheet: None (None), residues: 0 loop : -2.09 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 190 HIS 0.009 0.001 HIS I 180 PHE 0.012 0.001 PHE J 375 TYR 0.018 0.001 TYR J 699 ARG 0.003 0.000 ARG J 688 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 438) hydrogen bonds : angle 4.25234 ( 1297) covalent geometry : bond 0.00339 ( 8529) covalent geometry : angle 0.59191 (11544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 332 ASP cc_start: 0.8578 (t0) cc_final: 0.8368 (t0) REVERT: J 365 MET cc_start: 0.8602 (ppp) cc_final: 0.8290 (ppp) REVERT: J 548 MET cc_start: 0.8891 (tmm) cc_final: 0.8547 (tmm) REVERT: J 703 CYS cc_start: 0.7347 (p) cc_final: 0.7075 (p) REVERT: J 817 CYS cc_start: 0.8602 (m) cc_final: 0.8327 (m) REVERT: J 955 MET cc_start: 0.8474 (mmt) cc_final: 0.8145 (mmm) REVERT: I 104 LEU cc_start: 0.9443 (tp) cc_final: 0.9151 (tp) REVERT: I 137 MET cc_start: 0.8593 (tpp) cc_final: 0.8353 (tpp) REVERT: I 190 TRP cc_start: 0.8953 (t-100) cc_final: 0.8695 (t-100) REVERT: I 199 GLN cc_start: 0.8810 (mt0) cc_final: 0.8460 (mp-120) REVERT: I 379 MET cc_start: 0.8614 (ptp) cc_final: 0.8344 (ptm) REVERT: I 490 GLU cc_start: 0.8431 (tt0) cc_final: 0.7984 (tt0) REVERT: I 558 LEU cc_start: 0.9146 (tp) cc_final: 0.8777 (tt) REVERT: I 571 SER cc_start: 0.9230 (m) cc_final: 0.8930 (p) REVERT: I 589 CYS cc_start: 0.9179 (m) cc_final: 0.8874 (m) REVERT: I 593 CYS cc_start: 0.8827 (m) cc_final: 0.7618 (m) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2362 time to fit residues: 42.7977 Evaluate side-chains 91 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 98 optimal weight: 0.0870 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 413 HIS ** J 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 822 ASN J 925 GLN I 98 GLN I 312 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.077929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.064242 restraints weight = 63373.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.066517 restraints weight = 29023.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.068041 restraints weight = 17034.160| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8529 Z= 0.115 Angle : 0.568 10.372 11544 Z= 0.278 Chirality : 0.038 0.150 1345 Planarity : 0.003 0.038 1427 Dihedral : 3.930 23.638 1087 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.11 % Allowed : 2.72 % Favored : 97.17 % 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: -0.41 (0.27), residues: 991 helix: 0.42 (0.20), residues: 718 sheet: -1.39 (1.15), residues: 12 loop : -2.03 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 190 HIS 0.004 0.001 HIS I 180 PHE 0.021 0.001 PHE J 743 TYR 0.012 0.001 TYR J 699 ARG 0.004 0.000 ARG I 647 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 438) hydrogen bonds : angle 4.00348 ( 1297) covalent geometry : bond 0.00240 ( 8529) covalent geometry : angle 0.56808 (11544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8656 (ppp) cc_final: 0.8274 (ppp) REVERT: J 548 MET cc_start: 0.9001 (tmm) cc_final: 0.8758 (tmm) REVERT: J 703 CYS cc_start: 0.7266 (p) cc_final: 0.6977 (p) REVERT: I 31 PHE cc_start: 0.7246 (m-80) cc_final: 0.7028 (m-10) REVERT: I 104 LEU cc_start: 0.9433 (tp) cc_final: 0.9146 (tp) REVERT: I 137 MET cc_start: 0.8679 (tpp) cc_final: 0.8375 (tpp) REVERT: I 199 GLN cc_start: 0.8863 (mt0) cc_final: 0.8478 (mp-120) REVERT: I 379 MET cc_start: 0.8590 (ptp) cc_final: 0.8312 (ptm) REVERT: I 490 GLU cc_start: 0.8455 (tt0) cc_final: 0.7985 (tt0) REVERT: I 558 LEU cc_start: 0.9208 (tp) cc_final: 0.8683 (pp) REVERT: I 571 SER cc_start: 0.9221 (m) cc_final: 0.8959 (p) REVERT: I 589 CYS cc_start: 0.9229 (m) cc_final: 0.8903 (m) REVERT: I 593 CYS cc_start: 0.8874 (m) cc_final: 0.7767 (m) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2255 time to fit residues: 43.3036 Evaluate side-chains 89 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 413 HIS ** J 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 822 ASN J 925 GLN I 397 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.077444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.063418 restraints weight = 73495.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.065797 restraints weight = 31865.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.067405 restraints weight = 18280.082| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8529 Z= 0.125 Angle : 0.566 10.222 11544 Z= 0.279 Chirality : 0.038 0.135 1345 Planarity : 0.004 0.037 1427 Dihedral : 3.892 23.910 1087 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.11 % Allowed : 3.05 % Favored : 96.84 % 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 (0.27), residues: 991 helix: 0.59 (0.20), residues: 721 sheet: -0.92 (1.26), residues: 12 loop : -1.94 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 833 HIS 0.003 0.001 HIS I 312 PHE 0.036 0.001 PHE J 743 TYR 0.020 0.001 TYR J 836 ARG 0.003 0.000 ARG I 647 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 438) hydrogen bonds : angle 3.93230 ( 1297) covalent geometry : bond 0.00269 ( 8529) covalent geometry : angle 0.56609 (11544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8514 (ppp) cc_final: 0.8203 (ppp) REVERT: J 381 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7821 (tm-30) REVERT: J 383 GLU cc_start: 0.8485 (tt0) cc_final: 0.8001 (tp30) REVERT: J 703 CYS cc_start: 0.7310 (p) cc_final: 0.7047 (p) REVERT: I 199 GLN cc_start: 0.8886 (mt0) cc_final: 0.8520 (mp-120) REVERT: I 379 MET cc_start: 0.8587 (ptp) cc_final: 0.8309 (ptm) REVERT: I 490 GLU cc_start: 0.8427 (tt0) cc_final: 0.7980 (tt0) REVERT: I 520 MET cc_start: 0.9085 (mmm) cc_final: 0.8867 (mmt) REVERT: I 558 LEU cc_start: 0.9109 (tp) cc_final: 0.8734 (pp) REVERT: I 571 SER cc_start: 0.9193 (m) cc_final: 0.8961 (p) REVERT: I 582 LEU cc_start: 0.9596 (mt) cc_final: 0.9346 (pp) REVERT: I 589 CYS cc_start: 0.9235 (m) cc_final: 0.8932 (m) REVERT: I 593 CYS cc_start: 0.8898 (m) cc_final: 0.7825 (m) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1944 time to fit residues: 35.1306 Evaluate side-chains 88 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 99 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 413 HIS J 822 ASN J 914 GLN J 925 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.077630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.063920 restraints weight = 62835.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.066166 restraints weight = 28866.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.067677 restraints weight = 17017.622| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8529 Z= 0.126 Angle : 0.578 10.271 11544 Z= 0.283 Chirality : 0.039 0.160 1345 Planarity : 0.004 0.058 1427 Dihedral : 3.929 24.063 1087 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.11 % Allowed : 1.52 % Favored : 98.37 % 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: 0.05 (0.28), residues: 991 helix: 0.76 (0.20), residues: 720 sheet: -0.84 (1.27), residues: 12 loop : -1.89 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 833 HIS 0.003 0.001 HIS I 180 PHE 0.019 0.001 PHE J 743 TYR 0.010 0.001 TYR J 739 ARG 0.003 0.000 ARG I 647 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 438) hydrogen bonds : angle 3.91329 ( 1297) covalent geometry : bond 0.00275 ( 8529) covalent geometry : angle 0.57769 (11544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8542 (ppp) cc_final: 0.8083 (ppp) REVERT: J 381 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7793 (tm-30) REVERT: J 703 CYS cc_start: 0.7025 (p) cc_final: 0.6699 (p) REVERT: I 31 PHE cc_start: 0.7370 (m-80) cc_final: 0.7124 (m-10) REVERT: I 104 LEU cc_start: 0.9432 (tp) cc_final: 0.9172 (tp) REVERT: I 137 MET cc_start: 0.8629 (tpp) cc_final: 0.8204 (tpp) REVERT: I 199 GLN cc_start: 0.8897 (mt0) cc_final: 0.8549 (mp-120) REVERT: I 379 MET cc_start: 0.8599 (ptp) cc_final: 0.8310 (ptm) REVERT: I 490 GLU cc_start: 0.8440 (tt0) cc_final: 0.8015 (tt0) REVERT: I 520 MET cc_start: 0.9096 (mmm) cc_final: 0.8864 (mmt) REVERT: I 558 LEU cc_start: 0.9157 (tp) cc_final: 0.8681 (pp) REVERT: I 571 SER cc_start: 0.9142 (m) cc_final: 0.8935 (p) REVERT: I 582 LEU cc_start: 0.9611 (mt) cc_final: 0.9321 (pp) REVERT: I 589 CYS cc_start: 0.9211 (m) cc_final: 0.8855 (m) REVERT: I 593 CYS cc_start: 0.8888 (m) cc_final: 0.7811 (m) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2220 time to fit residues: 43.0506 Evaluate side-chains 88 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 413 HIS ** J 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 914 GLN J 925 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.064676 restraints weight = 48920.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.066615 restraints weight = 25072.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.067940 restraints weight = 15674.973| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8529 Z= 0.133 Angle : 0.591 9.949 11544 Z= 0.290 Chirality : 0.039 0.155 1345 Planarity : 0.004 0.037 1427 Dihedral : 3.936 24.179 1087 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.11 % Allowed : 1.63 % Favored : 98.26 % 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: 0.15 (0.28), residues: 991 helix: 0.82 (0.20), residues: 719 sheet: -0.56 (1.34), residues: 12 loop : -1.82 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP J 833 HIS 0.003 0.001 HIS I 180 PHE 0.014 0.001 PHE J 743 TYR 0.019 0.001 TYR J 699 ARG 0.002 0.000 ARG J 688 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 438) hydrogen bonds : angle 3.92152 ( 1297) covalent geometry : bond 0.00293 ( 8529) covalent geometry : angle 0.59112 (11544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8490 (ppp) cc_final: 0.8038 (ppp) REVERT: J 381 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7753 (tm-30) REVERT: J 383 GLU cc_start: 0.8283 (tt0) cc_final: 0.7943 (tp30) REVERT: J 703 CYS cc_start: 0.6757 (p) cc_final: 0.6444 (p) REVERT: I 31 PHE cc_start: 0.7329 (m-80) cc_final: 0.7089 (m-10) REVERT: I 199 GLN cc_start: 0.8842 (mt0) cc_final: 0.8521 (mp-120) REVERT: I 379 MET cc_start: 0.8584 (ptp) cc_final: 0.8299 (ptm) REVERT: I 490 GLU cc_start: 0.8464 (tt0) cc_final: 0.8048 (tt0) REVERT: I 520 MET cc_start: 0.9128 (mmm) cc_final: 0.8868 (mmt) REVERT: I 558 LEU cc_start: 0.9139 (tp) cc_final: 0.8678 (pp) REVERT: I 571 SER cc_start: 0.9175 (m) cc_final: 0.8951 (p) REVERT: I 582 LEU cc_start: 0.9618 (mt) cc_final: 0.9315 (pp) REVERT: I 589 CYS cc_start: 0.9185 (m) cc_final: 0.8845 (m) REVERT: I 593 CYS cc_start: 0.8861 (m) cc_final: 0.7763 (m) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2520 time to fit residues: 47.4063 Evaluate side-chains 95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.0040 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 413 HIS ** J 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 914 GLN J 925 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063805 restraints weight = 78055.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.066250 restraints weight = 33133.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.067894 restraints weight = 18796.387| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8529 Z= 0.117 Angle : 0.581 10.405 11544 Z= 0.284 Chirality : 0.038 0.182 1345 Planarity : 0.003 0.038 1427 Dihedral : 3.907 24.013 1087 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.11 % Allowed : 0.65 % Favored : 99.24 % 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: 0.28 (0.28), residues: 991 helix: 0.89 (0.20), residues: 719 sheet: -0.40 (1.36), residues: 12 loop : -1.68 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 833 HIS 0.003 0.001 HIS I 463 PHE 0.030 0.001 PHE J 743 TYR 0.015 0.001 TYR J 699 ARG 0.004 0.000 ARG I 647 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 438) hydrogen bonds : angle 3.85809 ( 1297) covalent geometry : bond 0.00250 ( 8529) covalent geometry : angle 0.58052 (11544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8586 (ppp) cc_final: 0.8089 (ppp) REVERT: J 381 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7773 (tm-30) REVERT: J 383 GLU cc_start: 0.8293 (tt0) cc_final: 0.7935 (tp30) REVERT: I 31 PHE cc_start: 0.7413 (m-80) cc_final: 0.7138 (m-10) REVERT: I 104 LEU cc_start: 0.9398 (tp) cc_final: 0.9125 (tp) REVERT: I 137 MET cc_start: 0.8642 (tpp) cc_final: 0.8185 (tpp) REVERT: I 199 GLN cc_start: 0.8873 (mt0) cc_final: 0.8541 (mp-120) REVERT: I 379 MET cc_start: 0.8574 (ptp) cc_final: 0.8290 (ptm) REVERT: I 490 GLU cc_start: 0.8469 (tt0) cc_final: 0.8046 (tt0) REVERT: I 520 MET cc_start: 0.9121 (mmm) cc_final: 0.8850 (mmt) REVERT: I 558 LEU cc_start: 0.9158 (tp) cc_final: 0.8675 (pp) REVERT: I 582 LEU cc_start: 0.9622 (mt) cc_final: 0.9302 (pp) REVERT: I 589 CYS cc_start: 0.9231 (m) cc_final: 0.8884 (m) REVERT: I 593 CYS cc_start: 0.8902 (m) cc_final: 0.7786 (m) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2650 time to fit residues: 52.1161 Evaluate side-chains 96 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 0.0570 chunk 99 optimal weight: 0.9980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 413 HIS ** J 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 914 GLN J 915 HIS J 925 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.064417 restraints weight = 73153.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.066833 restraints weight = 31879.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068453 restraints weight = 18284.768| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 8529 Z= 0.117 Angle : 0.598 10.369 11544 Z= 0.293 Chirality : 0.038 0.151 1345 Planarity : 0.004 0.038 1427 Dihedral : 3.906 23.730 1087 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.11 % Allowed : 0.65 % Favored : 99.24 % 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 (0.28), residues: 991 helix: 1.03 (0.20), residues: 716 sheet: -0.28 (1.39), residues: 12 loop : -1.63 (0.41), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 833 HIS 0.003 0.001 HIS I 180 PHE 0.019 0.001 PHE J 375 TYR 0.049 0.002 TYR J 739 ARG 0.004 0.000 ARG I 647 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 438) hydrogen bonds : angle 3.86381 ( 1297) covalent geometry : bond 0.00258 ( 8529) covalent geometry : angle 0.59802 (11544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 381 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7801 (tm-30) REVERT: J 383 GLU cc_start: 0.8327 (tt0) cc_final: 0.7962 (tp30) REVERT: J 921 LYS cc_start: 0.5986 (mmtt) cc_final: 0.5053 (mmtm) REVERT: I 31 PHE cc_start: 0.7422 (m-80) cc_final: 0.7148 (m-10) REVERT: I 104 LEU cc_start: 0.9409 (tp) cc_final: 0.9137 (tp) REVERT: I 199 GLN cc_start: 0.8884 (mt0) cc_final: 0.8547 (mp-120) REVERT: I 379 MET cc_start: 0.8559 (ptp) cc_final: 0.8278 (ptm) REVERT: I 490 GLU cc_start: 0.8508 (tt0) cc_final: 0.8069 (tt0) REVERT: I 520 MET cc_start: 0.9078 (mmm) cc_final: 0.8821 (mmt) REVERT: I 558 LEU cc_start: 0.9171 (tp) cc_final: 0.8678 (pp) REVERT: I 582 LEU cc_start: 0.9625 (mt) cc_final: 0.9296 (mt) REVERT: I 589 CYS cc_start: 0.9263 (m) cc_final: 0.8922 (m) REVERT: I 593 CYS cc_start: 0.8904 (m) cc_final: 0.7772 (m) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1804 time to fit residues: 35.1227 Evaluate side-chains 93 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 413 HIS ** J 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 914 GLN J 915 HIS J 925 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.077958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.064056 restraints weight = 67217.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.066356 restraints weight = 30580.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.067907 restraints weight = 17873.535| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8529 Z= 0.134 Angle : 0.606 10.204 11544 Z= 0.298 Chirality : 0.039 0.153 1345 Planarity : 0.004 0.037 1427 Dihedral : 3.919 23.668 1087 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.11 % Allowed : 0.44 % Favored : 99.46 % 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 (0.28), residues: 991 helix: 1.04 (0.20), residues: 718 sheet: -0.35 (1.42), residues: 12 loop : -1.52 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP J 833 HIS 0.003 0.001 HIS I 180 PHE 0.041 0.001 PHE J 743 TYR 0.032 0.002 TYR J 739 ARG 0.002 0.000 ARG I 647 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 438) hydrogen bonds : angle 3.90673 ( 1297) covalent geometry : bond 0.00299 ( 8529) covalent geometry : angle 0.60595 (11544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3728.00 seconds wall clock time: 69 minutes 35.68 seconds (4175.68 seconds total)