Starting phenix.real_space_refine on Mon Mar 11 13:14:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v69_21060/03_2024/6v69_21060.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v69_21060/03_2024/6v69_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v69_21060/03_2024/6v69_21060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v69_21060/03_2024/6v69_21060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v69_21060/03_2024/6v69_21060.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v69_21060/03_2024/6v69_21060.pdb" } 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 Residue "J ARG 272": "NH1" <-> "NH2" Residue "J GLU 381": "OE1" <-> "OE2" Residue "J ARG 405": "NH1" <-> "NH2" Residue "J ARG 428": "NH1" <-> "NH2" Residue "J ARG 432": "NH1" <-> "NH2" Residue "J GLU 467": "OE1" <-> "OE2" Residue "J ARG 715": "NH1" <-> "NH2" Residue "J ARG 724": "NH1" <-> "NH2" Residue "J ARG 887": "NH1" <-> "NH2" Residue "J GLU 912": "OE1" <-> "OE2" Residue "J ARG 944": "NH1" <-> "NH2" Residue "I GLU 108": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "I ARG 271": "NH1" <-> "NH2" Residue "I GLU 472": "OE1" <-> "OE2" Residue "I ARG 501": "NH1" <-> "NH2" Residue "I ARG 515": "NH1" <-> "NH2" Residue "I ARG 517": "NH1" <-> "NH2" Residue "I ARG 606": "NH1" <-> "NH2" Residue "I ARG 647": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.79, per 1000 atoms: 0.81 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 2.4 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: 0.76 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: 2.02 Time building geometry restraints manager: 3.50 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: 100.34 - 107.08: 192 107.08 - 113.81: 4968 113.81 - 120.54: 3510 120.54 - 127.28: 2782 127.28 - 134.01: 92 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 2.440 nonbonded pdb=" OH TYR J 719 " pdb=" O LYS J 804 " model vdw 2.211 2.440 nonbonded pdb=" O TRP J 276 " pdb=" OG SER J 279 " model vdw 2.220 2.440 nonbonded pdb=" O GLU I 141 " pdb=" OG SER I 145 " model vdw 2.285 2.440 nonbonded pdb=" OH TYR I 52 " pdb=" NE ARG I 101 " model vdw 2.288 2.520 ... (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 ========== 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.060 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.730 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.050 ------------------------------------------------------------------------------- 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= 0.170 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.962 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: 0.2115 time to fit residues: 38.8474 Evaluate side-chains 86 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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: 0.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.0870 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 328 GLN ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 818 GLN J 822 ASN J 823 GLN J 830 GLN ** J 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2113 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= 0.192 Angle : 0.605 9.713 11544 Z= 0.313 Chirality : 0.039 0.153 1345 Planarity : 0.004 0.052 1427 Dihedral : 4.167 23.226 1087 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.11 % Allowed : 5.11 % 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: -2.31 (0.25), residues: 991 helix: -1.01 (0.18), residues: 724 sheet: None (None), residues: 0 loop : -2.65 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 190 HIS 0.004 0.001 HIS I 519 PHE 0.024 0.002 PHE I 31 TYR 0.017 0.001 TYR J 739 ARG 0.003 0.000 ARG J 311 *********************** 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 fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 548 MET cc_start: 0.8866 (tmm) cc_final: 0.8554 (tmm) REVERT: J 703 CYS cc_start: 0.7878 (p) cc_final: 0.7426 (p) REVERT: J 992 MET cc_start: 0.7412 (mmt) cc_final: 0.7133 (mmm) REVERT: I 114 ASP cc_start: 0.8702 (t70) cc_final: 0.8334 (t70) REVERT: I 137 MET cc_start: 0.8572 (tpt) cc_final: 0.8357 (tpp) REVERT: I 190 TRP cc_start: 0.8892 (t-100) cc_final: 0.8593 (t-100) REVERT: I 587 ASP cc_start: 0.8988 (p0) cc_final: 0.8779 (t70) REVERT: I 589 CYS cc_start: 0.9030 (m) cc_final: 0.8821 (m) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1800 time to fit residues: 34.2607 Evaluate side-chains 88 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 0.0470 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 915 HIS J 925 GLN J 989 ASN I 528 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2534 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= 0.181 Angle : 0.569 9.821 11544 Z= 0.287 Chirality : 0.039 0.164 1345 Planarity : 0.004 0.048 1427 Dihedral : 4.033 22.636 1087 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.19 % 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: -1.28 (0.27), residues: 991 helix: -0.26 (0.19), residues: 725 sheet: None (None), residues: 0 loop : -2.25 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 190 HIS 0.004 0.001 HIS I 493 PHE 0.015 0.001 PHE J 375 TYR 0.014 0.001 TYR J 739 ARG 0.002 0.000 ARG J 904 *********************** 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 141 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 548 MET cc_start: 0.8875 (tmm) cc_final: 0.8571 (tmm) REVERT: J 703 CYS cc_start: 0.7665 (p) cc_final: 0.7204 (p) REVERT: J 955 MET cc_start: 0.8499 (mmt) cc_final: 0.8144 (mmm) REVERT: J 992 MET cc_start: 0.7374 (mmt) cc_final: 0.7021 (mmm) REVERT: I 104 LEU cc_start: 0.9478 (tp) cc_final: 0.9176 (tp) REVERT: I 114 ASP cc_start: 0.8621 (t70) cc_final: 0.8269 (t0) REVERT: I 190 TRP cc_start: 0.9028 (t-100) cc_final: 0.8637 (t-100) REVERT: I 379 MET cc_start: 0.8577 (ptp) cc_final: 0.8282 (ptm) REVERT: I 490 GLU cc_start: 0.8541 (tt0) cc_final: 0.8098 (tt0) REVERT: I 520 MET cc_start: 0.9098 (mmm) cc_final: 0.8898 (mmm) REVERT: I 558 LEU cc_start: 0.9165 (tp) cc_final: 0.8791 (tt) REVERT: I 589 CYS cc_start: 0.9237 (m) cc_final: 0.8856 (m) REVERT: I 593 CYS cc_start: 0.8988 (m) cc_final: 0.7870 (m) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1718 time to fit residues: 34.7924 Evaluate side-chains 90 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 721 GLN J 822 ASN J 914 GLN J 925 GLN I 397 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8529 Z= 0.242 Angle : 0.599 9.428 11544 Z= 0.301 Chirality : 0.040 0.153 1345 Planarity : 0.004 0.042 1427 Dihedral : 4.143 23.582 1087 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.74 % 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: -0.90 (0.27), residues: 991 helix: 0.03 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -2.17 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 190 HIS 0.004 0.001 HIS I 35 PHE 0.013 0.001 PHE J 375 TYR 0.017 0.002 TYR J 739 ARG 0.007 0.000 ARG J 724 *********************** 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 127 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: J 548 MET cc_start: 0.8830 (tmm) cc_final: 0.8469 (tmm) REVERT: J 703 CYS cc_start: 0.7692 (p) cc_final: 0.7329 (p) REVERT: I 104 LEU cc_start: 0.9516 (tp) cc_final: 0.9191 (tp) REVERT: I 137 MET cc_start: 0.8707 (tpp) cc_final: 0.8469 (tpp) REVERT: I 190 TRP cc_start: 0.9045 (t-100) cc_final: 0.8575 (t-100) REVERT: I 199 GLN cc_start: 0.9042 (mt0) cc_final: 0.8510 (mp-120) REVERT: I 379 MET cc_start: 0.8544 (ptp) cc_final: 0.8265 (ptm) REVERT: I 490 GLU cc_start: 0.8587 (tt0) cc_final: 0.8128 (tt0) REVERT: I 520 MET cc_start: 0.9195 (mmm) cc_final: 0.8815 (mmt) REVERT: I 571 SER cc_start: 0.9226 (m) cc_final: 0.8919 (p) REVERT: I 589 CYS cc_start: 0.9225 (m) cc_final: 0.8889 (m) REVERT: I 593 CYS cc_start: 0.8977 (m) cc_final: 0.7921 (m) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1773 time to fit residues: 32.3585 Evaluate side-chains 87 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 0.0270 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 33 optimal weight: 0.0870 chunk 19 optimal weight: 0.0870 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 822 ASN J 898 HIS J 925 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8529 Z= 0.137 Angle : 0.558 10.471 11544 Z= 0.270 Chirality : 0.037 0.163 1345 Planarity : 0.004 0.069 1427 Dihedral : 3.927 23.460 1087 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % 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: -0.29 (0.27), residues: 991 helix: 0.52 (0.20), residues: 718 sheet: -1.39 (1.15), residues: 12 loop : -2.00 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 190 HIS 0.006 0.001 HIS I 180 PHE 0.025 0.001 PHE J 743 TYR 0.010 0.001 TYR J 699 ARG 0.002 0.000 ARG I 647 *********************** 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 133 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8649 (ppp) cc_final: 0.8352 (ppp) REVERT: J 444 ILE cc_start: 0.9215 (mt) cc_final: 0.8905 (mt) REVERT: J 548 MET cc_start: 0.8874 (tmm) cc_final: 0.8555 (tmm) REVERT: J 703 CYS cc_start: 0.7379 (p) cc_final: 0.7060 (p) REVERT: I 104 LEU cc_start: 0.9494 (tp) cc_final: 0.9195 (tp) REVERT: I 110 GLU cc_start: 0.8585 (tp30) cc_final: 0.8365 (tp30) REVERT: I 137 MET cc_start: 0.8688 (tpp) cc_final: 0.8401 (tpp) REVERT: I 190 TRP cc_start: 0.8998 (t-100) cc_final: 0.8640 (t-100) REVERT: I 199 GLN cc_start: 0.8976 (mt0) cc_final: 0.8476 (mp-120) REVERT: I 490 GLU cc_start: 0.8510 (tt0) cc_final: 0.8029 (tt0) REVERT: I 558 LEU cc_start: 0.9143 (tp) cc_final: 0.8827 (pp) REVERT: I 571 SER cc_start: 0.9155 (m) cc_final: 0.8941 (p) REVERT: I 589 CYS cc_start: 0.9226 (m) cc_final: 0.8878 (m) REVERT: I 593 CYS cc_start: 0.8890 (m) cc_final: 0.7719 (m) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1799 time to fit residues: 34.1653 Evaluate side-chains 91 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 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 57 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 0.0040 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.0270 chunk 56 optimal weight: 0.6980 overall best weight: 0.4650 ------------------------------------------------------------------------------- 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 312 HIS I 378 HIS I 528 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3410 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= 0.153 Angle : 0.564 9.591 11544 Z= 0.275 Chirality : 0.039 0.315 1345 Planarity : 0.004 0.037 1427 Dihedral : 3.829 23.838 1087 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.11 % Allowed : 2.61 % Favored : 97.28 % 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: -0.08 (0.28), residues: 991 helix: 0.68 (0.20), residues: 723 sheet: -0.90 (1.26), residues: 12 loop : -2.04 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 190 HIS 0.004 0.001 HIS I 180 PHE 0.032 0.001 PHE J 743 TYR 0.018 0.001 TYR J 836 ARG 0.003 0.000 ARG I 647 *********************** 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 131 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8611 (ppp) cc_final: 0.8297 (ppp) REVERT: J 829 LEU cc_start: 0.8738 (mt) cc_final: 0.8297 (mt) REVERT: I 104 LEU cc_start: 0.9520 (tp) cc_final: 0.9214 (tp) REVERT: I 190 TRP cc_start: 0.9008 (t-100) cc_final: 0.8582 (t-100) REVERT: I 199 GLN cc_start: 0.8986 (mt0) cc_final: 0.8518 (mp-120) REVERT: I 490 GLU cc_start: 0.8569 (tt0) cc_final: 0.8088 (tt0) REVERT: I 499 MET cc_start: 0.8546 (tpp) cc_final: 0.8316 (tpp) REVERT: I 558 LEU cc_start: 0.9149 (tp) cc_final: 0.8838 (pp) REVERT: I 571 SER cc_start: 0.9185 (m) cc_final: 0.8938 (p) REVERT: I 589 CYS cc_start: 0.9214 (m) cc_final: 0.8893 (m) REVERT: I 593 CYS cc_start: 0.8920 (m) cc_final: 0.7753 (m) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1790 time to fit residues: 33.8038 Evaluate side-chains 89 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 chunk 59 optimal weight: 0.0050 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8529 Z= 0.161 Angle : 0.560 10.128 11544 Z= 0.273 Chirality : 0.038 0.173 1345 Planarity : 0.004 0.049 1427 Dihedral : 3.818 23.755 1087 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 0.15 (0.28), residues: 991 helix: 0.84 (0.20), residues: 723 sheet: -0.82 (1.27), residues: 12 loop : -1.90 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 833 HIS 0.004 0.001 HIS I 180 PHE 0.020 0.001 PHE J 743 TYR 0.014 0.001 TYR I 456 ARG 0.003 0.000 ARG J 724 *********************** 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 129 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8605 (ppp) cc_final: 0.8199 (ppp) REVERT: J 743 PHE cc_start: 0.5727 (m-80) cc_final: 0.5479 (m-80) REVERT: J 833 TRP cc_start: 0.7910 (t-100) cc_final: 0.7492 (t-100) REVERT: I 1 MET cc_start: 0.8944 (tmm) cc_final: 0.8736 (tmm) REVERT: I 104 LEU cc_start: 0.9524 (tp) cc_final: 0.9226 (tp) REVERT: I 137 MET cc_start: 0.8691 (tpp) cc_final: 0.8252 (tpp) REVERT: I 190 TRP cc_start: 0.8985 (t-100) cc_final: 0.8711 (t-100) REVERT: I 199 GLN cc_start: 0.8997 (mt0) cc_final: 0.8536 (mp-120) REVERT: I 490 GLU cc_start: 0.8564 (tt0) cc_final: 0.8088 (tt0) REVERT: I 499 MET cc_start: 0.8542 (tpp) cc_final: 0.8309 (tpp) REVERT: I 558 LEU cc_start: 0.9155 (tp) cc_final: 0.8840 (pp) REVERT: I 589 CYS cc_start: 0.9270 (m) cc_final: 0.8941 (m) REVERT: I 593 CYS cc_start: 0.8996 (m) cc_final: 0.7993 (m) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1835 time to fit residues: 34.1375 Evaluate side-chains 88 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 66 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 413 HIS ** J 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 822 ASN J 925 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8529 Z= 0.161 Angle : 0.569 9.849 11544 Z= 0.275 Chirality : 0.038 0.165 1345 Planarity : 0.003 0.037 1427 Dihedral : 3.809 23.766 1087 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.11 % Allowed : 1.20 % Favored : 98.69 % 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: 0.35 (0.28), residues: 991 helix: 0.98 (0.20), residues: 719 sheet: -0.62 (1.32), residues: 12 loop : -1.80 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 833 HIS 0.003 0.001 HIS J 304 PHE 0.019 0.001 PHE J 743 TYR 0.017 0.001 TYR J 699 ARG 0.002 0.000 ARG I 647 *********************** 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 127 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 365 MET cc_start: 0.8529 (ppp) cc_final: 0.8083 (ppp) REVERT: J 833 TRP cc_start: 0.8075 (t-100) cc_final: 0.7622 (t-100) REVERT: I 31 PHE cc_start: 0.7333 (m-80) cc_final: 0.7132 (m-10) REVERT: I 104 LEU cc_start: 0.9518 (tp) cc_final: 0.9220 (tp) REVERT: I 137 MET cc_start: 0.8689 (tpp) cc_final: 0.8221 (tpp) REVERT: I 190 TRP cc_start: 0.8992 (t-100) cc_final: 0.8693 (t-100) REVERT: I 199 GLN cc_start: 0.8998 (mt0) cc_final: 0.8536 (mp-120) REVERT: I 490 GLU cc_start: 0.8563 (tt0) cc_final: 0.8092 (tt0) REVERT: I 499 MET cc_start: 0.8612 (tpp) cc_final: 0.8382 (tpp) REVERT: I 558 LEU cc_start: 0.9145 (tp) cc_final: 0.8837 (pp) REVERT: I 589 CYS cc_start: 0.9269 (m) cc_final: 0.8949 (m) REVERT: I 593 CYS cc_start: 0.8999 (m) cc_final: 0.7983 (m) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1761 time to fit residues: 32.3584 Evaluate side-chains 89 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8529 Z= 0.162 Angle : 0.582 10.055 11544 Z= 0.282 Chirality : 0.038 0.164 1345 Planarity : 0.003 0.037 1427 Dihedral : 3.840 23.523 1087 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.11 % Allowed : 0.76 % Favored : 99.13 % 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: 0.43 (0.28), residues: 991 helix: 1.04 (0.20), residues: 717 sheet: -0.55 (1.34), residues: 12 loop : -1.75 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 833 HIS 0.003 0.001 HIS I 180 PHE 0.036 0.001 PHE J 743 TYR 0.018 0.001 TYR J 836 ARG 0.004 0.000 ARG I 647 *********************** 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 127 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 833 TRP cc_start: 0.8445 (t-100) cc_final: 0.7587 (t60) REVERT: I 31 PHE cc_start: 0.7301 (m-80) cc_final: 0.7048 (m-10) REVERT: I 104 LEU cc_start: 0.9497 (tp) cc_final: 0.9182 (tp) REVERT: I 137 MET cc_start: 0.8693 (tpp) cc_final: 0.8228 (tpp) REVERT: I 190 TRP cc_start: 0.8996 (t-100) cc_final: 0.8707 (t-100) REVERT: I 199 GLN cc_start: 0.8995 (mt0) cc_final: 0.8537 (mp-120) REVERT: I 490 GLU cc_start: 0.8568 (tt0) cc_final: 0.8089 (tt0) REVERT: I 499 MET cc_start: 0.8619 (tpp) cc_final: 0.8390 (tpp) REVERT: I 558 LEU cc_start: 0.9137 (tp) cc_final: 0.8837 (pp) REVERT: I 589 CYS cc_start: 0.9274 (m) cc_final: 0.8950 (m) REVERT: I 593 CYS cc_start: 0.9000 (m) cc_final: 0.7975 (m) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1730 time to fit residues: 32.1430 Evaluate side-chains 91 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 925 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8529 Z= 0.156 Angle : 0.577 9.977 11544 Z= 0.280 Chirality : 0.038 0.159 1345 Planarity : 0.003 0.037 1427 Dihedral : 3.839 23.127 1087 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 0.52 (0.28), residues: 991 helix: 1.11 (0.20), residues: 717 sheet: -0.48 (1.36), residues: 12 loop : -1.69 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 190 HIS 0.003 0.001 HIS I 180 PHE 0.016 0.001 PHE J 993 TYR 0.022 0.001 TYR J 739 ARG 0.005 0.000 ARG I 647 ********************** 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 131 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: J 743 PHE cc_start: 0.5300 (m-80) cc_final: 0.4415 (m-80) REVERT: J 833 TRP cc_start: 0.8381 (t-100) cc_final: 0.7774 (t-100) REVERT: I 31 PHE cc_start: 0.7298 (m-80) cc_final: 0.7072 (m-10) REVERT: I 104 LEU cc_start: 0.9513 (tp) cc_final: 0.9228 (tp) REVERT: I 183 MET cc_start: 0.9318 (tmm) cc_final: 0.9083 (tmm) REVERT: I 190 TRP cc_start: 0.8968 (t-100) cc_final: 0.8709 (t-100) REVERT: I 199 GLN cc_start: 0.8993 (mt0) cc_final: 0.8585 (mp-120) REVERT: I 379 MET cc_start: 0.8483 (ptp) cc_final: 0.8061 (ptp) REVERT: I 490 GLU cc_start: 0.8569 (tt0) cc_final: 0.8087 (tt0) REVERT: I 558 LEU cc_start: 0.9134 (tp) cc_final: 0.8836 (pp) REVERT: I 589 CYS cc_start: 0.9275 (m) cc_final: 0.8953 (m) REVERT: I 593 CYS cc_start: 0.8997 (m) cc_final: 0.7963 (m) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1778 time to fit residues: 33.6955 Evaluate side-chains 94 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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 925 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.078390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.064527 restraints weight = 63701.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066741 restraints weight = 30100.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.068223 restraints weight = 17971.135| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8529 Z= 0.163 Angle : 0.586 10.005 11544 Z= 0.285 Chirality : 0.038 0.159 1345 Planarity : 0.003 0.037 1427 Dihedral : 3.841 23.009 1087 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.56 % 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: 0.56 (0.28), residues: 991 helix: 1.14 (0.20), residues: 717 sheet: -0.48 (1.32), residues: 12 loop : -1.68 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 833 HIS 0.003 0.001 HIS I 180 PHE 0.019 0.001 PHE J 287 TYR 0.023 0.001 TYR J 699 ARG 0.002 0.000 ARG I 647 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1856.52 seconds wall clock time: 34 minutes 26.26 seconds (2066.26 seconds total)