Starting phenix.real_space_refine on Sat Dec 9 21:21:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/12_2023/7yuy_34115_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/12_2023/7yuy_34115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/12_2023/7yuy_34115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/12_2023/7yuy_34115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/12_2023/7yuy_34115_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuy_34115/12_2023/7yuy_34115_neut_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 72 5.16 5 C 8140 2.51 5 N 2035 2.21 5 O 2143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 166": "OD1" <-> "OD2" Residue "F PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 381": "OE1" <-> "OE2" Residue "F ASP 391": "OD1" <-> "OD2" Residue "F GLU 416": "OE1" <-> "OE2" Residue "F GLU 421": "OE1" <-> "OE2" Residue "F ASP 433": "OD1" <-> "OD2" Residue "F PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 514": "OE1" <-> "OE2" Residue "F PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 816": "OE1" <-> "OE2" Residue "F GLU 859": "OE1" <-> "OE2" Residue "F GLU 974": "OE1" <-> "OE2" Residue "F GLU 984": "OE1" <-> "OE2" Residue "F PHE 1000": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1041": "OE1" <-> "OE2" Residue "F GLU 1044": "OE1" <-> "OE2" Residue "F TYR 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1141": "OE1" <-> "OE2" Residue "F PHE 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1497": "OE1" <-> "OE2" Residue "F ASP 1498": "OD1" <-> "OD2" Residue "F TYR 1506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1736": "OE1" <-> "OE2" Residue "F PHE 1841": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12391 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 12063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1503, 12063 Classifications: {'peptide': 1503} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 66, 'TRANS': 1436} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 107 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'BGC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 255 Unusual residues: {'C14': 1, 'D10': 6, 'D12': 3, 'DD9': 7, 'HP6': 7, 'XKP': 1} Classifications: {'undetermined': 25} Link IDs: {None: 24} Time building chain proxies: 6.86, per 1000 atoms: 0.55 Number of scatterers: 12391 At special positions: 0 Unit cell: (101.2, 115, 135.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 1 15.00 O 2143 8.00 N 2035 7.00 C 8140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 658 " - pdb=" SG CYS F 669 " distance=1.77 Simple disulfide: pdb=" SG CYS F1328 " - pdb=" SG CYS F1345 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BGC C 1 " - " BGC C 2 " " BGC C 2 " - " BGC C 3 " " BGC C 3 " - " BGC C 4 " BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F1849 " Time building additional restraints: 4.81 Conformation dependent library (CDL) restraints added in 2.2 seconds 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 4 sheets defined 53.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'F' and resid 161 through 175 removed outlier: 4.118A pdb=" N ILE F 167 " --> pdb=" O GLN F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 195 removed outlier: 3.952A pdb=" N ASP F 187 " --> pdb=" O ARG F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 213 removed outlier: 3.733A pdb=" N LEU F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 228 removed outlier: 3.546A pdb=" N ALA F 227 " --> pdb=" O LYS F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 242 Processing helix chain 'F' and resid 283 through 295 removed outlier: 4.207A pdb=" N ARG F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 312 removed outlier: 3.645A pdb=" N VAL F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS F 304 " --> pdb=" O GLU F 300 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 307 " --> pdb=" O ARG F 303 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR F 308 " --> pdb=" O HIS F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 336 Processing helix chain 'F' and resid 340 through 343 No H-bonds generated for 'chain 'F' and resid 340 through 343' Processing helix chain 'F' and resid 352 through 356 Processing helix chain 'F' and resid 359 through 368 Processing helix chain 'F' and resid 390 through 393 No H-bonds generated for 'chain 'F' and resid 390 through 393' Processing helix chain 'F' and resid 395 through 398 removed outlier: 3.647A pdb=" N TRP F 398 " --> pdb=" O GLN F 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 395 through 398' Processing helix chain 'F' and resid 400 through 405 removed outlier: 4.766A pdb=" N LYS F 405 " --> pdb=" O GLU F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 422 No H-bonds generated for 'chain 'F' and resid 420 through 422' Processing helix chain 'F' and resid 424 through 427 removed outlier: 4.148A pdb=" N GLY F 427 " --> pdb=" O LEU F 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 424 through 427' Processing helix chain 'F' and resid 445 through 451 removed outlier: 3.962A pdb=" N VAL F 449 " --> pdb=" O TRP F 445 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR F 450 " --> pdb=" O LEU F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 469 removed outlier: 3.888A pdb=" N MET F 465 " --> pdb=" O SER F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 516 removed outlier: 4.595A pdb=" N GLY F 499 " --> pdb=" O SER F 495 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY F 500 " --> pdb=" O CYS F 496 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR F 501 " --> pdb=" O ALA F 497 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL F 502 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 503 " --> pdb=" O GLY F 499 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN F 507 " --> pdb=" O ALA F 503 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR F 511 " --> pdb=" O GLN F 507 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER F 516 " --> pdb=" O LEU F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 550 removed outlier: 3.801A pdb=" N TRP F 533 " --> pdb=" O SER F 529 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE F 534 " --> pdb=" O ARG F 530 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE F 537 " --> pdb=" O TRP F 533 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE F 538 " --> pdb=" O PHE F 534 " (cutoff:3.500A) Proline residue: F 545 - end of helix removed outlier: 3.634A pdb=" N PHE F 548 " --> pdb=" O GLY F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 581 removed outlier: 4.147A pdb=" N VAL F 564 " --> pdb=" O THR F 560 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL F 565 " --> pdb=" O ALA F 561 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET F 569 " --> pdb=" O VAL F 565 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 570 " --> pdb=" O ALA F 566 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE F 571 " --> pdb=" O ALA F 567 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL F 574 " --> pdb=" O PHE F 570 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA F 575 " --> pdb=" O PHE F 571 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE F 577 " --> pdb=" O ALA F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 587 No H-bonds generated for 'chain 'F' and resid 585 through 587' Processing helix chain 'F' and resid 617 through 635 removed outlier: 4.103A pdb=" N TYR F 622 " --> pdb=" O ARG F 618 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU F 623 " --> pdb=" O TRP F 619 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 624 " --> pdb=" O MET F 620 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TRP F 625 " --> pdb=" O SER F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 644 No H-bonds generated for 'chain 'F' and resid 642 through 644' Processing helix chain 'F' and resid 646 through 651 Processing helix chain 'F' and resid 672 through 684 Processing helix chain 'F' and resid 687 through 710 removed outlier: 4.009A pdb=" N ASP F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR F 692 " --> pdb=" O PHE F 688 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR F 693 " --> pdb=" O PHE F 689 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE F 697 " --> pdb=" O TYR F 693 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 698 " --> pdb=" O LEU F 694 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE F 703 " --> pdb=" O VAL F 699 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F 704 " --> pdb=" O ASN F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 722 No H-bonds generated for 'chain 'F' and resid 719 through 722' Processing helix chain 'F' and resid 727 through 733 removed outlier: 3.578A pdb=" N SER F 732 " --> pdb=" O LYS F 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 763 removed outlier: 3.632A pdb=" N MET F 761 " --> pdb=" O ILE F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 769 through 774 removed outlier: 3.952A pdb=" N GLN F 773 " --> pdb=" O ILE F 769 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS F 774 " --> pdb=" O ASP F 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 769 through 774' Processing helix chain 'F' and resid 794 through 796 No H-bonds generated for 'chain 'F' and resid 794 through 796' Processing helix chain 'F' and resid 810 through 812 No H-bonds generated for 'chain 'F' and resid 810 through 812' Processing helix chain 'F' and resid 814 through 826 removed outlier: 4.044A pdb=" N LEU F 826 " --> pdb=" O PHE F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 858 through 861 No H-bonds generated for 'chain 'F' and resid 858 through 861' Processing helix chain 'F' and resid 872 through 879 Processing helix chain 'F' and resid 883 through 895 Processing helix chain 'F' and resid 933 through 945 Processing helix chain 'F' and resid 951 through 971 removed outlier: 5.144A pdb=" N ASN F 959 " --> pdb=" O SER F 955 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR F 960 " --> pdb=" O GLY F 956 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER F 961 " --> pdb=" O PHE F 957 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG F 962 " --> pdb=" O MET F 958 " (cutoff:3.500A) Processing helix chain 'F' and resid 974 through 979 removed outlier: 4.328A pdb=" N PHE F 979 " --> pdb=" O ILE F 975 " (cutoff:3.500A) Processing helix chain 'F' and resid 983 through 994 Processing helix chain 'F' and resid 1007 through 1009 No H-bonds generated for 'chain 'F' and resid 1007 through 1009' Processing helix chain 'F' and resid 1012 through 1024 removed outlier: 3.768A pdb=" N GLU F1016 " --> pdb=" O PRO F1012 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN F1017 " --> pdb=" O HIS F1013 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA F1018 " --> pdb=" O GLU F1014 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F1022 " --> pdb=" O ALA F1018 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG F1023 " --> pdb=" O GLU F1019 " (cutoff:3.500A) Processing helix chain 'F' and resid 1083 through 1088 Processing helix chain 'F' and resid 1110 through 1112 No H-bonds generated for 'chain 'F' and resid 1110 through 1112' Processing helix chain 'F' and resid 1115 through 1120 removed outlier: 3.757A pdb=" N LEU F1119 " --> pdb=" O ILE F1115 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA F1120 " --> pdb=" O ARG F1116 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1115 through 1120' Processing helix chain 'F' and resid 1169 through 1186 Processing helix chain 'F' and resid 1201 through 1205 Processing helix chain 'F' and resid 1224 through 1228 Processing helix chain 'F' and resid 1274 through 1279 Processing helix chain 'F' and resid 1284 through 1291 Processing helix chain 'F' and resid 1295 through 1319 removed outlier: 3.603A pdb=" N ASN F1301 " --> pdb=" O PHE F1297 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F1302 " --> pdb=" O HIS F1298 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE F1303 " --> pdb=" O LEU F1299 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN F1305 " --> pdb=" O ASN F1301 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN F1309 " --> pdb=" O GLN F1305 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET F1310 " --> pdb=" O LEU F1306 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE F1311 " --> pdb=" O SER F1307 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET F1312 " --> pdb=" O LEU F1308 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F1313 " --> pdb=" O GLN F1309 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F1316 " --> pdb=" O MET F1312 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN F1317 " --> pdb=" O LEU F1313 " (cutoff:3.500A) Processing helix chain 'F' and resid 1349 through 1364 removed outlier: 3.620A pdb=" N TRP F1354 " --> pdb=" O PRO F1350 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL F1355 " --> pdb=" O ALA F1351 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG F1356 " --> pdb=" O VAL F1352 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG F1357 " --> pdb=" O ASP F1353 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU F1360 " --> pdb=" O ARG F1356 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER F1361 " --> pdb=" O ARG F1357 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F1363 " --> pdb=" O THR F1359 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F1364 " --> pdb=" O LEU F1360 " (cutoff:3.500A) Processing helix chain 'F' and resid 1371 through 1378 Processing helix chain 'F' and resid 1383 through 1393 Processing helix chain 'F' and resid 1399 through 1405 Processing helix chain 'F' and resid 1408 through 1417 Processing helix chain 'F' and resid 1438 through 1445 removed outlier: 3.854A pdb=" N PHE F1445 " --> pdb=" O LEU F1441 " (cutoff:3.500A) Processing helix chain 'F' and resid 1451 through 1466 removed outlier: 3.788A pdb=" N ARG F1455 " --> pdb=" O TYR F1451 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET F1459 " --> pdb=" O ARG F1455 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F1460 " --> pdb=" O SER F1456 " (cutoff:3.500A) Processing helix chain 'F' and resid 1470 through 1480 removed outlier: 4.152A pdb=" N LEU F1473 " --> pdb=" O ALA F1470 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TRP F1474 " --> pdb=" O PRO F1471 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA F1477 " --> pdb=" O TRP F1474 " (cutoff:3.500A) Processing helix chain 'F' and resid 1498 through 1511 Processing helix chain 'F' and resid 1566 through 1583 removed outlier: 3.547A pdb=" N TYR F1571 " --> pdb=" O PRO F1567 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA F1572 " --> pdb=" O CYS F1568 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS F1575 " --> pdb=" O TYR F1571 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F1578 " --> pdb=" O GLY F1574 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE F1582 " --> pdb=" O ALA F1578 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN F1583 " --> pdb=" O PHE F1579 " (cutoff:3.500A) Processing helix chain 'F' and resid 1599 through 1625 removed outlier: 3.529A pdb=" N ILE F1603 " --> pdb=" O VAL F1599 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA F1608 " --> pdb=" O ILE F1604 " (cutoff:3.500A) Proline residue: F1609 - end of helix Processing helix chain 'F' and resid 1639 through 1664 removed outlier: 3.536A pdb=" N HIS F1654 " --> pdb=" O ALA F1650 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET F1661 " --> pdb=" O PHE F1657 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP F1662 " --> pdb=" O PHE F1658 " (cutoff:3.500A) Processing helix chain 'F' and resid 1670 through 1696 removed outlier: 3.937A pdb=" N ILE F1674 " --> pdb=" O VAL F1670 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY F1675 " --> pdb=" O ARG F1671 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR F1678 " --> pdb=" O ILE F1674 " (cutoff:3.500A) Processing helix chain 'F' and resid 1725 through 1752 removed outlier: 3.802A pdb=" N LYS F1733 " --> pdb=" O GLU F1729 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA F1741 " --> pdb=" O LEU F1737 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA F1742 " --> pdb=" O SER F1738 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY F1747 " --> pdb=" O ASP F1743 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS F1748 " --> pdb=" O PHE F1744 " (cutoff:3.500A) Processing helix chain 'F' and resid 1755 through 1757 No H-bonds generated for 'chain 'F' and resid 1755 through 1757' Processing helix chain 'F' and resid 1764 through 1774 Processing helix chain 'F' and resid 1787 through 1820 removed outlier: 4.046A pdb=" N SER F1802 " --> pdb=" O LYS F1798 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU F1803 " --> pdb=" O LYS F1799 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F1808 " --> pdb=" O TYR F1804 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA F1809 " --> pdb=" O PHE F1805 " (cutoff:3.500A) Proline residue: F1818 - end of helix Processing sheet with id= A, first strand: chain 'F' and resid 779 through 781 Processing sheet with id= B, first strand: chain 'F' and resid 999 through 1004 removed outlier: 6.726A pdb=" N TYR F1097 " --> pdb=" O THR F 843 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU F 845 " --> pdb=" O TYR F1097 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN F1099 " --> pdb=" O LEU F 845 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 1030 through 1032 removed outlier: 3.878A pdb=" N PHE F1068 " --> pdb=" O LEU F1051 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 1148 through 1152 removed outlier: 7.341A pdb=" N ARG F1235 " --> pdb=" O ALA F1149 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL F1151 " --> pdb=" O ARG F1235 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LYS F1237 " --> pdb=" O VAL F1151 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 433 hydrogen bonds defined for protein. 1263 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: 3.95 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2020 1.32 - 1.44: 3475 1.44 - 1.57: 7069 1.57 - 1.69: 3 1.69 - 1.81: 115 Bond restraints: 12682 Sorted by residual: bond pdb=" C17 XKP F1925 " pdb=" C22 XKP F1925 " ideal model delta sigma weight residual 1.524 1.306 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C8 XKP F1925 " pdb=" O2 XKP F1925 " ideal model delta sigma weight residual 1.409 1.451 -0.042 2.00e-02 2.50e+03 4.51e+00 bond pdb=" O5 XKP F1925 " pdb=" P XKP F1925 " ideal model delta sigma weight residual 1.647 1.606 0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C3 XKP F1925 " pdb=" C4 XKP F1925 " ideal model delta sigma weight residual 1.535 1.495 0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C LEU F 642 " pdb=" N PRO F 643 " ideal model delta sigma weight residual 1.334 1.349 -0.015 8.40e-03 1.42e+04 3.33e+00 ... (remaining 12677 not shown) Histogram of bond angle deviations from ideal: 96.68 - 104.16: 188 104.16 - 111.64: 5517 111.64 - 119.13: 4665 119.13 - 126.61: 6526 126.61 - 134.09: 220 Bond angle restraints: 17116 Sorted by residual: angle pdb=" N VAL F 318 " pdb=" CA VAL F 318 " pdb=" C VAL F 318 " ideal model delta sigma weight residual 112.90 104.78 8.12 9.60e-01 1.09e+00 7.15e+01 angle pdb=" C ARG F 869 " pdb=" CA ARG F 869 " pdb=" CB ARG F 869 " ideal model delta sigma weight residual 116.54 108.36 8.18 1.15e+00 7.56e-01 5.06e+01 angle pdb=" CA ARG F 869 " pdb=" C ARG F 869 " pdb=" N VAL F 870 " ideal model delta sigma weight residual 119.52 115.38 4.14 7.90e-01 1.60e+00 2.74e+01 angle pdb=" N ILE F 734 " pdb=" CA ILE F 734 " pdb=" C ILE F 734 " ideal model delta sigma weight residual 113.71 109.08 4.63 9.50e-01 1.11e+00 2.37e+01 angle pdb=" C SER F 281 " pdb=" CA SER F 281 " pdb=" CB SER F 281 " ideal model delta sigma weight residual 115.79 110.49 5.30 1.19e+00 7.06e-01 1.98e+01 ... (remaining 17111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.79: 7191 28.79 - 57.57: 306 57.57 - 86.35: 22 86.35 - 115.14: 3 115.14 - 143.92: 5 Dihedral angle restraints: 7527 sinusoidal: 3110 harmonic: 4417 Sorted by residual: dihedral pdb=" CB CYS F1328 " pdb=" SG CYS F1328 " pdb=" SG CYS F1345 " pdb=" CB CYS F1345 " ideal model delta sinusoidal sigma weight residual 93.00 134.43 -41.43 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CB CYS F 658 " pdb=" SG CYS F 658 " pdb=" SG CYS F 669 " pdb=" CB CYS F 669 " ideal model delta sinusoidal sigma weight residual -86.00 -126.36 40.36 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA PHE F1657 " pdb=" C PHE F1657 " pdb=" N PHE F1658 " pdb=" CA PHE F1658 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 7524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 1890 0.216 - 0.432: 3 0.432 - 0.649: 0 0.649 - 0.865: 0 0.865 - 1.081: 1 Chirality restraints: 1894 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F1849 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.48 1.08 2.00e-01 2.50e+01 2.92e+01 chirality pdb=" C1 BGC C 3 " pdb=" O3 BGC C 2 " pdb=" C2 BGC C 3 " pdb=" O5 BGC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.58e+01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.19e+01 ... (remaining 1891 not shown) Planarity restraints: 2123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.278 2.00e-02 2.50e+03 2.33e-01 6.77e+02 pdb=" C7 NAG A 1 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.393 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.136 2.00e-02 2.50e+03 1.12e-01 1.56e+02 pdb=" C7 NAG A 2 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.179 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F1849 " 0.063 2.00e-02 2.50e+03 5.99e-02 4.49e+01 pdb=" CG ASN F1849 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN F1849 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN F1849 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG A 1 " 0.070 2.00e-02 2.50e+03 ... (remaining 2120 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 159 2.64 - 3.21: 11300 3.21 - 3.77: 16859 3.77 - 4.34: 22945 4.34 - 4.90: 38423 Nonbonded interactions: 89686 Sorted by model distance: nonbonded pdb=" O4 BGC C 3 " pdb=" O5 BGC C 4 " model vdw 2.081 2.440 nonbonded pdb=" O3 NAG A 2 " pdb=" O7 NAG A 2 " model vdw 2.103 2.440 nonbonded pdb=" O2 BGC C 1 " pdb=" O2 BGC C 2 " model vdw 2.139 2.440 nonbonded pdb=" O MET F 458 " pdb=" OH TYR F 633 " model vdw 2.227 2.440 nonbonded pdb=" NH1 ARG F 344 " pdb=" O GLU F 346 " model vdw 2.231 2.520 ... (remaining 89681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 3.660 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.010 Find NCS groups from input model: 0.320 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.006 0.218 12682 Z= 0.389 Angle : 0.873 11.334 17116 Z= 0.504 Chirality : 0.054 1.081 1894 Planarity : 0.007 0.233 2122 Dihedral : 15.147 143.924 4663 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.66 % Favored : 90.14 % Rotamer: Outliers : 0.32 % Allowed : 0.47 % Favored : 99.21 % 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: -2.51 (0.22), residues: 1481 helix: -0.61 (0.18), residues: 842 sheet: -2.90 (0.69), residues: 56 loop : -3.15 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 625 HIS 0.011 0.001 HIS F 384 PHE 0.025 0.002 PHE F 796 TYR 0.019 0.001 TYR F1093 ARG 0.005 0.000 ARG F 940 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.362 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 169 average time/residue: 0.2795 time to fit residues: 66.1745 Evaluate side-chains 131 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.256 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2575 time to fit residues: 2.3904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 316 ASN F1107 ASN F1238 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12682 Z= 0.164 Angle : 0.600 6.415 17116 Z= 0.299 Chirality : 0.041 0.171 1894 Planarity : 0.004 0.045 2122 Dihedral : 8.981 117.711 1875 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.91 % Favored : 90.88 % Rotamer: Outliers : 1.26 % Allowed : 8.04 % Favored : 90.70 % 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: -1.90 (0.22), residues: 1481 helix: -0.04 (0.19), residues: 830 sheet: -1.44 (0.93), residues: 41 loop : -3.06 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 625 HIS 0.007 0.001 HIS F1238 PHE 0.017 0.001 PHE F1766 TYR 0.022 0.001 TYR F 875 ARG 0.004 0.000 ARG F 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.481 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 161 average time/residue: 0.2977 time to fit residues: 67.9302 Evaluate side-chains 141 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1149 time to fit residues: 3.7228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 147 optimal weight: 30.0000 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 779 GLN F1107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12682 Z= 0.251 Angle : 0.595 9.178 17116 Z= 0.296 Chirality : 0.042 0.179 1894 Planarity : 0.003 0.034 2122 Dihedral : 8.085 108.288 1875 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.72 % Favored : 90.07 % Rotamer: Outliers : 0.95 % Allowed : 12.45 % Favored : 86.60 % 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: -1.71 (0.22), residues: 1481 helix: 0.18 (0.19), residues: 825 sheet: -2.46 (0.68), residues: 61 loop : -2.96 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 625 HIS 0.005 0.001 HIS F 384 PHE 0.015 0.001 PHE F 796 TYR 0.016 0.001 TYR F1330 ARG 0.003 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.343 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 146 average time/residue: 0.2941 time to fit residues: 60.2472 Evaluate side-chains 133 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.411 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1179 time to fit residues: 2.9233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1088 HIS F1107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12682 Z= 0.173 Angle : 0.571 14.642 17116 Z= 0.279 Chirality : 0.041 0.183 1894 Planarity : 0.003 0.041 2122 Dihedral : 7.375 102.745 1875 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.98 % Favored : 90.82 % Rotamer: Outliers : 1.58 % Allowed : 14.66 % Favored : 83.77 % 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: -1.46 (0.23), residues: 1481 helix: 0.42 (0.19), residues: 822 sheet: -2.14 (0.70), residues: 58 loop : -2.91 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 625 HIS 0.005 0.001 HIS F 384 PHE 0.012 0.001 PHE F 796 TYR 0.015 0.001 TYR F1330 ARG 0.004 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.374 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 152 average time/residue: 0.2954 time to fit residues: 62.6352 Evaluate side-chains 143 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.383 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1167 time to fit residues: 4.0543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 0.0050 chunk 59 optimal weight: 30.0000 chunk 123 optimal weight: 0.2980 chunk 100 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 130 optimal weight: 50.0000 chunk 36 optimal weight: 7.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1104 ASN F1107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12682 Z= 0.204 Angle : 0.574 11.799 17116 Z= 0.282 Chirality : 0.042 0.173 1894 Planarity : 0.003 0.038 2122 Dihedral : 7.054 103.824 1875 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.91 % Favored : 90.88 % Rotamer: Outliers : 1.42 % Allowed : 15.52 % Favored : 83.06 % 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: -1.33 (0.23), residues: 1481 helix: 0.50 (0.19), residues: 827 sheet: -2.08 (0.70), residues: 58 loop : -2.84 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 625 HIS 0.005 0.001 HIS F 384 PHE 0.021 0.001 PHE F 887 TYR 0.016 0.001 TYR F1330 ARG 0.007 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.453 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 147 average time/residue: 0.3298 time to fit residues: 68.7045 Evaluate side-chains 131 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1264 time to fit residues: 3.6211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 50.0000 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 chunk 145 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12682 Z= 0.280 Angle : 0.603 10.263 17116 Z= 0.298 Chirality : 0.043 0.196 1894 Planarity : 0.004 0.041 2122 Dihedral : 7.186 108.347 1875 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.59 % Favored : 90.21 % Rotamer: Outliers : 1.73 % Allowed : 17.10 % Favored : 81.17 % 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: -1.27 (0.23), residues: 1481 helix: 0.53 (0.19), residues: 831 sheet: -1.91 (0.75), residues: 55 loop : -2.82 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 625 HIS 0.004 0.001 HIS F 384 PHE 0.016 0.001 PHE F 796 TYR 0.028 0.001 TYR F 875 ARG 0.007 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.577 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 146 average time/residue: 0.3131 time to fit residues: 64.4671 Evaluate side-chains 136 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1207 time to fit residues: 3.9711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12682 Z= 0.329 Angle : 0.622 10.028 17116 Z= 0.310 Chirality : 0.044 0.211 1894 Planarity : 0.004 0.041 2122 Dihedral : 7.380 111.570 1875 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.66 % Favored : 90.14 % Rotamer: Outliers : 1.10 % Allowed : 17.89 % Favored : 81.01 % 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 (0.23), residues: 1481 helix: 0.53 (0.19), residues: 830 sheet: -1.94 (0.75), residues: 55 loop : -2.84 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 625 HIS 0.004 0.001 HIS F 384 PHE 0.017 0.002 PHE F 796 TYR 0.022 0.001 TYR F 875 ARG 0.005 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.524 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 136 average time/residue: 0.3244 time to fit residues: 61.5018 Evaluate side-chains 132 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1368 time to fit residues: 3.8291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 113 optimal weight: 30.0000 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12682 Z= 0.278 Angle : 0.604 9.723 17116 Z= 0.300 Chirality : 0.043 0.190 1894 Planarity : 0.004 0.041 2122 Dihedral : 7.347 111.893 1875 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.59 % Favored : 90.21 % Rotamer: Outliers : 0.95 % Allowed : 18.99 % Favored : 80.06 % 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: -1.24 (0.23), residues: 1481 helix: 0.61 (0.19), residues: 828 sheet: -1.86 (0.76), residues: 55 loop : -2.89 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 625 HIS 0.005 0.001 HIS F 384 PHE 0.017 0.001 PHE F 887 TYR 0.023 0.001 TYR F 875 ARG 0.005 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.388 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 138 average time/residue: 0.3005 time to fit residues: 58.1238 Evaluate side-chains 130 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1207 time to fit residues: 2.7652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12682 Z= 0.246 Angle : 0.609 10.958 17116 Z= 0.301 Chirality : 0.043 0.180 1894 Planarity : 0.003 0.041 2122 Dihedral : 7.243 111.607 1875 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.45 % Favored : 90.34 % Rotamer: Outliers : 0.47 % Allowed : 19.31 % Favored : 80.22 % 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: -1.16 (0.23), residues: 1481 helix: 0.70 (0.19), residues: 828 sheet: -1.87 (0.75), residues: 55 loop : -2.89 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 445 HIS 0.005 0.001 HIS F 384 PHE 0.016 0.001 PHE F 548 TYR 0.022 0.001 TYR F 875 ARG 0.006 0.000 ARG F1154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.532 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 131 average time/residue: 0.3129 time to fit residues: 57.6858 Evaluate side-chains 131 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1219 time to fit residues: 2.6733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 0.0030 chunk 126 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12682 Z= 0.154 Angle : 0.575 14.214 17116 Z= 0.279 Chirality : 0.041 0.172 1894 Planarity : 0.003 0.040 2122 Dihedral : 6.704 107.594 1875 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.51 % Favored : 91.29 % Rotamer: Outliers : 0.16 % Allowed : 20.02 % Favored : 79.83 % 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: -0.96 (0.23), residues: 1481 helix: 0.88 (0.19), residues: 832 sheet: -1.86 (0.72), residues: 58 loop : -2.85 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 445 HIS 0.006 0.001 HIS F 384 PHE 0.019 0.001 PHE F 887 TYR 0.022 0.001 TYR F 875 ARG 0.007 0.000 ARG F1154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.394 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.3224 time to fit residues: 59.9641 Evaluate side-chains 127 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.156579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.098012 restraints weight = 17966.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100680 restraints weight = 13777.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100331 restraints weight = 10554.612| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12682 Z= 0.159 Angle : 0.577 14.150 17116 Z= 0.279 Chirality : 0.041 0.171 1894 Planarity : 0.003 0.041 2122 Dihedral : 6.459 107.151 1875 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.71 % Favored : 91.09 % Rotamer: Outliers : 0.24 % Allowed : 20.09 % Favored : 79.67 % 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: -0.80 (0.23), residues: 1481 helix: 1.00 (0.19), residues: 834 sheet: -1.36 (0.83), residues: 48 loop : -2.81 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 445 HIS 0.006 0.001 HIS F 384 PHE 0.016 0.001 PHE F 548 TYR 0.021 0.001 TYR F 875 ARG 0.007 0.000 ARG F1154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.25 seconds wall clock time: 42 minutes 16.13 seconds (2536.13 seconds total)