Starting phenix.real_space_refine on Mon Nov 18 17:48:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/11_2024/7xsr_33432.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/11_2024/7xsr_33432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/11_2024/7xsr_33432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/11_2024/7xsr_33432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/11_2024/7xsr_33432.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsr_33432/11_2024/7xsr_33432.cif" } resolution = 2.97 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= 0.003 sd= 0.044 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 49 5.49 5 S 57 5.16 5 C 10558 2.51 5 N 2934 2.21 5 O 3305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16907 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 10378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1287, 10378 Classifications: {'peptide': 1287} Link IDs: {'PTRANS': 60, 'TRANS': 1226} Chain breaks: 3 Chain: "C" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5482 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain breaks: 1 Chain: "A" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 14} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 676 SG CYS B 88 90.553 35.311 38.173 1.00 33.30 S ATOM 947 SG CYS B 121 94.678 33.022 37.660 1.00 41.85 S ATOM 993 SG CYS B 127 94.923 36.292 40.080 1.00 31.93 S ATOM 1017 SG CYS B 130 92.866 33.583 41.273 1.00 29.20 S ATOM 3755 SG CYS B 491 64.651 52.396 51.436 1.00 34.19 S ATOM 3837 SG CYS B 503 66.139 54.198 48.666 1.00 31.01 S ATOM 3859 SG CYS B 506 69.366 52.378 51.448 1.00 29.73 S ATOM 5830 SG CYS B 750 41.081 64.124 69.071 1.00 47.55 S ATOM 5843 SG CYS B 752 42.051 68.235 68.440 1.00 40.60 S ATOM 5865 SG CYS B 755 44.819 66.200 69.641 1.00 34.26 S ATOM 7868 SG CYS B1018 35.862 82.640 102.441 1.00 31.62 S ATOM 8039 SG CYS B1406 35.145 79.400 100.591 1.00 35.05 S ATOM 8090 SG CYS B1414 33.705 83.417 98.992 1.00 31.82 S ATOM 8107 SG CYS B1417 37.109 82.215 98.694 1.00 28.08 S Time building chain proxies: 9.72, per 1000 atoms: 0.57 Number of scatterers: 16907 At special positions: 0 Unit cell: (118.845, 136.8, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 57 16.00 P 49 15.00 O 3305 8.00 N 2934 7.00 C 10558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.16 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 130 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 88 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 506 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 503 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 491 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 752 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 755 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1406 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1417 " Number of angles added : 15 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 20 sheets defined 39.3% alpha, 17.3% beta 5 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 6.11 Creating SS restraints... Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.786A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.871A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.331A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 354 through 375 removed outlier: 3.508A pdb=" N PHE B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 488 removed outlier: 3.614A pdb=" N LEU B 475 " --> pdb=" O PRO B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.792A pdb=" N LEU B 634 " --> pdb=" O LYS B 630 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.724A pdb=" N LEU B 658 " --> pdb=" O ARG B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.770A pdb=" N HIS B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 759 Processing helix chain 'B' and resid 831 through 848 Processing helix chain 'B' and resid 855 through 859 Processing helix chain 'B' and resid 873 through 883 Processing helix chain 'B' and resid 999 through 1015 removed outlier: 3.802A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1404 removed outlier: 3.720A pdb=" N HIS B1404 " --> pdb=" O LYS B1401 " (cutoff:3.500A) Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 4.212A pdb=" N SER B1467 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1493 removed outlier: 3.942A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1499 Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.505A pdb=" N ILE B1587 " --> pdb=" O PRO B1583 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 removed outlier: 3.659A pdb=" N VAL B1618 " --> pdb=" O GLN B1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1615 through 1618' Processing helix chain 'B' and resid 1619 through 1629 Processing helix chain 'B' and resid 1673 through 1683 removed outlier: 3.570A pdb=" N THR B1683 " --> pdb=" O LYS B1679 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 33 Processing helix chain 'C' and resid 37 through 59 Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.757A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 109 removed outlier: 3.811A pdb=" N LYS C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 136 Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 163 through 177 removed outlier: 4.107A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 230 through 246 removed outlier: 4.258A pdb=" N ASP C 234 " --> pdb=" O HIS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.982A pdb=" N ILE C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 302 through 322 removed outlier: 3.845A pdb=" N LYS C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 340 through 362 removed outlier: 3.975A pdb=" N TYR C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 451 removed outlier: 3.517A pdb=" N PHE C 437 " --> pdb=" O TYR C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 490 through 494 Processing helix chain 'C' and resid 509 through 513 removed outlier: 3.688A pdb=" N GLU C 512 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 513 " --> pdb=" O PHE C 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 509 through 513' Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 547 through 552 Processing helix chain 'C' and resid 566 through 571 Processing helix chain 'C' and resid 592 through 596 removed outlier: 3.710A pdb=" N SER C 596 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 613 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.851A pdb=" N ALA C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 679 removed outlier: 3.849A pdb=" N THR C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 691 removed outlier: 4.032A pdb=" N TRP C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.718A pdb=" N PHE C 703 " --> pdb=" O HIS C 699 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.748A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 19 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP B 44 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 21 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N TRP B 46 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 13.887A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP B 190 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 192 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.922A pdb=" N LEU B 167 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR B 9 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.627A pdb=" N VAL B 85 " --> pdb=" O TRP B 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.355A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.753A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY B 600 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.753A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.693A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AB1, first strand: chain 'B' and resid 533 through 534 removed outlier: 3.726A pdb=" N THR B 539 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 703 through 704 removed outlier: 3.542A pdb=" N ARG B 719 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 703 through 704 removed outlier: 3.542A pdb=" N ARG B 719 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 699 through 700 removed outlier: 6.942A pdb=" N ALA B 699 " --> pdb=" O TYR B 808 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 803 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.975A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.975A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU B 950 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS B 957 " --> pdb=" O ILE B1564 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE B1564 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU B 959 " --> pdb=" O ILE B1562 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE B1562 " --> pdb=" O GLU B 959 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 985 through 986 removed outlier: 6.469A pdb=" N LYS B 985 " --> pdb=" O THR B1508 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 425 through 431 removed outlier: 3.588A pdb=" N PHE C 405 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 562 through 563 removed outlier: 7.961A pdb=" N LYS C 562 " --> pdb=" O TYR C 536 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU C 538 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR C 660 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 586 through 587 666 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 7.06 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3255 1.33 - 1.45: 4542 1.45 - 1.57: 9445 1.57 - 1.69: 62 1.69 - 1.81: 80 Bond restraints: 17384 Sorted by residual: bond pdb=" O3' G A 27 " pdb=" P C A 28 " ideal model delta sigma weight residual 1.607 1.475 0.132 1.50e-02 4.44e+03 7.70e+01 bond pdb=" O3' C D 9 " pdb=" P U D 10 " ideal model delta sigma weight residual 1.607 1.481 0.126 1.50e-02 4.44e+03 7.03e+01 bond pdb=" O3' U D 8 " pdb=" P C D 9 " ideal model delta sigma weight residual 1.607 1.488 0.119 1.50e-02 4.44e+03 6.31e+01 bond pdb=" O3' U D -2 " pdb=" P A D -1 " ideal model delta sigma weight residual 1.607 1.491 0.116 1.50e-02 4.44e+03 6.03e+01 bond pdb=" O3' G D -9 " pdb=" P U D -8 " ideal model delta sigma weight residual 1.607 1.493 0.114 1.50e-02 4.44e+03 5.77e+01 ... (remaining 17379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 23409 3.76 - 7.52: 236 7.52 - 11.29: 23 11.29 - 15.05: 2 15.05 - 18.81: 3 Bond angle restraints: 23673 Sorted by residual: angle pdb=" O3' C D 13 " pdb=" C3' C D 13 " pdb=" C2' C D 13 " ideal model delta sigma weight residual 113.70 132.27 -18.57 1.50e+00 4.44e-01 1.53e+02 angle pdb=" O2' C D 1 " pdb=" C2' C D 1 " pdb=" C1' C D 1 " ideal model delta sigma weight residual 108.40 91.70 16.70 1.50e+00 4.44e-01 1.24e+02 angle pdb=" O2' U D -2 " pdb=" C2' U D -2 " pdb=" C1' U D -2 " ideal model delta sigma weight residual 111.80 100.28 11.52 1.50e+00 4.44e-01 5.89e+01 angle pdb=" O4' A D -1 " pdb=" C1' A D -1 " pdb=" C2' A D -1 " ideal model delta sigma weight residual 105.80 99.29 6.51 1.00e+00 1.00e+00 4.23e+01 angle pdb=" O2' C D -7 " pdb=" C2' C D -7 " pdb=" C1' C D -7 " ideal model delta sigma weight residual 108.40 117.85 -9.45 1.50e+00 4.44e-01 3.97e+01 ... (remaining 23668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 10009 33.72 - 67.43: 471 67.43 - 101.15: 38 101.15 - 134.87: 2 134.87 - 168.58: 4 Dihedral angle restraints: 10524 sinusoidal: 4865 harmonic: 5659 Sorted by residual: dihedral pdb=" O4' U D -13 " pdb=" C1' U D -13 " pdb=" N1 U D -13 " pdb=" C2 U D -13 " ideal model delta sinusoidal sigma weight residual -160.00 5.71 -165.71 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 50.53 149.47 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U D -8 " pdb=" C1' U D -8 " pdb=" N1 U D -8 " pdb=" C2 U D -8 " ideal model delta sinusoidal sigma weight residual -128.00 40.58 -168.58 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 10521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2518 0.181 - 0.363: 40 0.363 - 0.544: 3 0.544 - 0.725: 1 0.725 - 0.907: 1 Chirality restraints: 2563 Sorted by residual: chirality pdb=" C3' C D 13 " pdb=" C4' C D 13 " pdb=" O3' C D 13 " pdb=" C2' C D 13 " both_signs ideal model delta sigma weight residual False -2.48 -1.57 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" C2' C D -7 " pdb=" C3' C D -7 " pdb=" O2' C D -7 " pdb=" C1' C D -7 " both_signs ideal model delta sigma weight residual False -2.75 -2.19 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C2' C D 13 " pdb=" C3' C D 13 " pdb=" O2' C D 13 " pdb=" C1' C D 13 " both_signs ideal model delta sigma weight residual False -2.75 -2.32 -0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 2560 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D -1 " 0.093 2.00e-02 2.50e+03 4.23e-02 4.93e+01 pdb=" N9 A D -1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 A D -1 " 0.008 2.00e-02 2.50e+03 pdb=" N7 A D -1 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D -1 " -0.010 2.00e-02 2.50e+03 pdb=" C6 A D -1 " 0.029 2.00e-02 2.50e+03 pdb=" N6 A D -1 " 0.013 2.00e-02 2.50e+03 pdb=" N1 A D -1 " 0.020 2.00e-02 2.50e+03 pdb=" C2 A D -1 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A D -1 " -0.021 2.00e-02 2.50e+03 pdb=" C4 A D -1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 34 " 0.077 2.00e-02 2.50e+03 3.25e-02 2.90e+01 pdb=" N9 A A 34 " -0.048 2.00e-02 2.50e+03 pdb=" C8 A A 34 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A A 34 " -0.009 2.00e-02 2.50e+03 pdb=" C5 A A 34 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A A 34 " 0.017 2.00e-02 2.50e+03 pdb=" N6 A A 34 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A 34 " 0.027 2.00e-02 2.50e+03 pdb=" C2 A A 34 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A A 34 " -0.032 2.00e-02 2.50e+03 pdb=" C4 A A 34 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 442 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C LYS B 442 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS B 442 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU B 443 " -0.023 2.00e-02 2.50e+03 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4099 2.79 - 3.32: 13688 3.32 - 3.85: 26543 3.85 - 4.37: 30891 4.37 - 4.90: 54969 Nonbonded interactions: 130190 Sorted by model distance: nonbonded pdb=" OG SER B 378 " pdb=" OD1 ASN B 453 " model vdw 2.268 3.040 nonbonded pdb=" O ASN B 179 " pdb=" O2' G D -3 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR B1645 " pdb=" OP1 C D 14 " model vdw 2.328 3.040 nonbonded pdb=" O THR C 702 " pdb=" OG SER C 706 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR B 191 " pdb=" OD1 ASP B 386 " model vdw 2.333 3.040 ... (remaining 130185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.120 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 46.150 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.007 0.132 17384 Z= 0.464 Angle : 0.969 18.809 23673 Z= 0.568 Chirality : 0.066 0.907 2563 Planarity : 0.008 0.088 2873 Dihedral : 18.284 168.585 6888 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 3.94 % Allowed : 12.64 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.57 (0.15), residues: 1951 helix: -1.57 (0.15), residues: 692 sheet: 0.06 (0.31), residues: 267 loop : -2.35 (0.15), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 443 HIS 0.006 0.001 HIS B 924 PHE 0.025 0.002 PHE B 805 TYR 0.022 0.002 TYR C 75 ARG 0.013 0.001 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 414 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: B 184 ASP cc_start: 0.7111 (m-30) cc_final: 0.6910 (m-30) REVERT: B 315 GLU cc_start: 0.7349 (tt0) cc_final: 0.7135 (mt-10) REVERT: B 318 ASP cc_start: 0.6903 (t0) cc_final: 0.6654 (t0) REVERT: B 351 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8234 (tttt) REVERT: B 401 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 516 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6715 (p0) REVERT: B 547 ASP cc_start: 0.7473 (p0) cc_final: 0.7230 (p0) REVERT: B 651 PHE cc_start: 0.8405 (m-80) cc_final: 0.8188 (m-80) REVERT: B 698 ASP cc_start: 0.7080 (m-30) cc_final: 0.6834 (m-30) REVERT: B 807 THR cc_start: 0.8431 (p) cc_final: 0.8181 (m) REVERT: B 918 LYS cc_start: 0.5955 (mptt) cc_final: 0.5167 (mppt) REVERT: B 1400 ASP cc_start: 0.7527 (m-30) cc_final: 0.7319 (m-30) REVERT: B 1436 TYR cc_start: 0.8182 (t80) cc_final: 0.7922 (t80) REVERT: B 1565 ASP cc_start: 0.7212 (t0) cc_final: 0.6915 (m-30) REVERT: B 1660 ASP cc_start: 0.6454 (m-30) cc_final: 0.6123 (m-30) REVERT: B 1665 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7685 (mtpt) REVERT: B 1666 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 167 ILE cc_start: 0.8093 (mt) cc_final: 0.7789 (mt) REVERT: C 267 LYS cc_start: 0.7937 (tttm) cc_final: 0.7646 (tttt) REVERT: C 352 CYS cc_start: 0.6977 (m) cc_final: 0.6451 (m) REVERT: C 483 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: C 613 SER cc_start: 0.7965 (m) cc_final: 0.7742 (m) outliers start: 68 outliers final: 15 residues processed: 466 average time/residue: 1.4051 time to fit residues: 724.1616 Evaluate side-chains 365 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 346 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 680 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN B 434 GLN B 453 ASN B 881 ASN B 900 ASN B 908 HIS B 917 ASN B 919 ASN B1404 HIS B1596 GLN B1604 ASN C 147 ASN C 183 HIS C 513 ASN C 552 ASN C 572 ASN C 592 ASN C 602 ASN C 642 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17384 Z= 0.166 Angle : 0.569 11.827 23673 Z= 0.300 Chirality : 0.041 0.214 2563 Planarity : 0.005 0.071 2873 Dihedral : 15.131 177.920 2912 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 3.65 % Allowed : 21.04 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 1951 helix: 0.61 (0.19), residues: 697 sheet: 0.31 (0.31), residues: 257 loop : -1.89 (0.16), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 278 HIS 0.006 0.001 HIS C 183 PHE 0.016 0.001 PHE B 546 TYR 0.013 0.001 TYR C 607 ARG 0.004 0.000 ARG B1644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 356 time to evaluate : 2.110 Fit side-chains revert: symmetry clash REVERT: B 315 GLU cc_start: 0.7450 (tt0) cc_final: 0.7216 (mt-10) REVERT: B 348 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: B 351 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8227 (tttt) REVERT: B 509 MET cc_start: 0.8568 (mmm) cc_final: 0.8316 (mmp) REVERT: B 651 PHE cc_start: 0.8387 (m-80) cc_final: 0.8169 (m-80) REVERT: B 807 THR cc_start: 0.8468 (p) cc_final: 0.8191 (m) REVERT: B 918 LYS cc_start: 0.5803 (mptt) cc_final: 0.4887 (mppt) REVERT: B 1436 TYR cc_start: 0.8181 (t80) cc_final: 0.7934 (t80) REVERT: B 1660 ASP cc_start: 0.6462 (m-30) cc_final: 0.6225 (m-30) REVERT: B 1666 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8309 (mp) REVERT: C 102 GLU cc_start: 0.6796 (tt0) cc_final: 0.6518 (tt0) REVERT: C 155 LYS cc_start: 0.6478 (tmmt) cc_final: 0.6191 (tmtt) REVERT: C 217 ASP cc_start: 0.6948 (t0) cc_final: 0.6743 (t0) REVERT: C 393 LEU cc_start: 0.8762 (mm) cc_final: 0.8446 (mt) REVERT: C 483 ASP cc_start: 0.7620 (m-30) cc_final: 0.7037 (m-30) outliers start: 63 outliers final: 22 residues processed: 394 average time/residue: 1.4602 time to fit residues: 637.7100 Evaluate side-chains 361 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 337 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 683 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 0.0010 chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 181 optimal weight: 0.0050 chunk 195 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 908 HIS B 919 ASN B 924 HIS B 986 ASN B1573 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17384 Z= 0.223 Angle : 0.585 10.912 23673 Z= 0.306 Chirality : 0.043 0.199 2563 Planarity : 0.005 0.068 2873 Dihedral : 14.912 176.454 2889 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.46 % Rotamer: Outliers : 4.99 % Allowed : 21.28 % Favored : 73.74 % 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: -0.37 (0.18), residues: 1951 helix: 1.34 (0.20), residues: 701 sheet: 0.47 (0.31), residues: 255 loop : -1.69 (0.17), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 278 HIS 0.006 0.001 HIS B 908 PHE 0.018 0.002 PHE B 546 TYR 0.015 0.002 TYR C 607 ARG 0.012 0.001 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 360 time to evaluate : 1.860 Fit side-chains revert: symmetry clash REVERT: B 15 PHE cc_start: 0.8661 (m-80) cc_final: 0.8267 (m-80) REVERT: B 174 SER cc_start: 0.8346 (m) cc_final: 0.8134 (t) REVERT: B 315 GLU cc_start: 0.7559 (tt0) cc_final: 0.7226 (mt-10) REVERT: B 348 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6907 (mp10) REVERT: B 651 PHE cc_start: 0.8432 (m-80) cc_final: 0.8177 (m-80) REVERT: B 666 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7987 (tttm) REVERT: B 918 LYS cc_start: 0.5878 (mptt) cc_final: 0.5139 (mppt) REVERT: B 1430 LYS cc_start: 0.8263 (mtmm) cc_final: 0.8038 (mttt) REVERT: B 1436 TYR cc_start: 0.8247 (t80) cc_final: 0.8025 (t80) REVERT: B 1444 ILE cc_start: 0.8172 (mm) cc_final: 0.7952 (mp) REVERT: B 1491 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7865 (ttp-170) REVERT: B 1565 ASP cc_start: 0.7249 (t0) cc_final: 0.7002 (m-30) REVERT: C 102 GLU cc_start: 0.6723 (tt0) cc_final: 0.6463 (mt-10) REVERT: C 151 GLU cc_start: 0.6879 (mp0) cc_final: 0.6550 (mp0) REVERT: C 217 ASP cc_start: 0.6993 (t0) cc_final: 0.6770 (t0) REVERT: C 224 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7774 (tmmm) REVERT: C 234 ASP cc_start: 0.6997 (t70) cc_final: 0.6647 (t0) REVERT: C 267 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7801 (ptmm) REVERT: C 393 LEU cc_start: 0.8779 (mm) cc_final: 0.8521 (mt) REVERT: C 472 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7714 (pp) outliers start: 86 outliers final: 33 residues processed: 405 average time/residue: 1.4559 time to fit residues: 650.5326 Evaluate side-chains 385 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 346 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1573 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 652 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 GLN B 498 GLN B 673 GLN B 908 HIS B 919 ASN B1584 GLN B1596 GLN B1617 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17384 Z= 0.345 Angle : 0.652 12.571 23673 Z= 0.339 Chirality : 0.046 0.237 2563 Planarity : 0.005 0.068 2873 Dihedral : 14.976 176.597 2883 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 4.99 % Allowed : 23.19 % Favored : 71.83 % 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: -0.29 (0.18), residues: 1951 helix: 1.44 (0.20), residues: 698 sheet: 0.43 (0.31), residues: 266 loop : -1.66 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1530 HIS 0.011 0.002 HIS B 908 PHE 0.020 0.002 PHE B 546 TYR 0.018 0.002 TYR B 149 ARG 0.006 0.001 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 357 time to evaluate : 1.956 Fit side-chains REVERT: B 7 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.7025 (m110) REVERT: B 55 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7798 (ptpt) REVERT: B 91 SER cc_start: 0.8276 (p) cc_final: 0.7995 (t) REVERT: B 131 ILE cc_start: 0.8382 (pt) cc_final: 0.8150 (pt) REVERT: B 315 GLU cc_start: 0.7585 (tt0) cc_final: 0.7258 (mt-10) REVERT: B 666 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8028 (tttm) REVERT: B 687 THR cc_start: 0.7719 (m) cc_final: 0.7379 (p) REVERT: B 836 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7828 (mt) REVERT: B 918 LYS cc_start: 0.6092 (mptt) cc_final: 0.5426 (mppt) REVERT: B 1430 LYS cc_start: 0.8279 (mtmm) cc_final: 0.8058 (mttt) REVERT: B 1436 TYR cc_start: 0.8418 (t80) cc_final: 0.8052 (t80) REVERT: B 1444 ILE cc_start: 0.8338 (mm) cc_final: 0.8078 (mp) REVERT: B 1459 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7491 (pt) REVERT: B 1491 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7927 (ttp-170) REVERT: B 1640 GLU cc_start: 0.7099 (pm20) cc_final: 0.6893 (pm20) REVERT: B 1660 ASP cc_start: 0.6639 (m-30) cc_final: 0.6325 (m-30) REVERT: B 1665 LYS cc_start: 0.8085 (mtpm) cc_final: 0.7517 (mtpt) REVERT: B 1666 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8443 (mp) REVERT: B 1668 ASP cc_start: 0.5210 (OUTLIER) cc_final: 0.4857 (t70) REVERT: C 102 GLU cc_start: 0.6765 (tt0) cc_final: 0.6497 (mt-10) REVERT: C 151 GLU cc_start: 0.6898 (mp0) cc_final: 0.6608 (mp0) REVERT: C 234 ASP cc_start: 0.6959 (t70) cc_final: 0.6628 (t0) outliers start: 86 outliers final: 47 residues processed: 405 average time/residue: 1.5091 time to fit residues: 674.2364 Evaluate side-chains 396 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 341 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1490 ILE Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1675 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 652 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 2 optimal weight: 0.0270 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 615 ASN B 908 HIS B 919 ASN B 986 ASN B1596 GLN B1617 HIS ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17384 Z= 0.188 Angle : 0.558 12.213 23673 Z= 0.292 Chirality : 0.041 0.197 2563 Planarity : 0.005 0.065 2873 Dihedral : 14.845 177.594 2883 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.07 % Favored : 94.82 % Rotamer: Outliers : 4.52 % Allowed : 24.35 % Favored : 71.13 % 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: -0.05 (0.18), residues: 1951 helix: 1.75 (0.20), residues: 698 sheet: 0.47 (0.31), residues: 266 loop : -1.58 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.011 0.001 HIS B 908 PHE 0.013 0.001 PHE B1570 TYR 0.014 0.001 TYR C 607 ARG 0.007 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 347 time to evaluate : 2.035 Fit side-chains REVERT: B 7 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6982 (m110) REVERT: B 91 SER cc_start: 0.8260 (p) cc_final: 0.8003 (t) REVERT: B 174 SER cc_start: 0.8319 (m) cc_final: 0.8112 (t) REVERT: B 452 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7769 (mt) REVERT: B 666 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7962 (tttm) REVERT: B 836 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7732 (mt) REVERT: B 918 LYS cc_start: 0.6056 (mptt) cc_final: 0.5373 (mppt) REVERT: B 1430 LYS cc_start: 0.8247 (mtmm) cc_final: 0.8033 (mttt) REVERT: B 1436 TYR cc_start: 0.8280 (t80) cc_final: 0.8032 (t80) REVERT: B 1444 ILE cc_start: 0.8159 (mm) cc_final: 0.7939 (mp) REVERT: B 1458 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8036 (t) REVERT: B 1459 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7355 (pt) REVERT: B 1491 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.8024 (ttp-170) REVERT: B 1640 GLU cc_start: 0.7138 (pm20) cc_final: 0.6893 (pm20) REVERT: B 1660 ASP cc_start: 0.6645 (m-30) cc_final: 0.6238 (m-30) REVERT: B 1665 LYS cc_start: 0.7976 (mtpm) cc_final: 0.7424 (mtpt) REVERT: B 1668 ASP cc_start: 0.5086 (OUTLIER) cc_final: 0.4782 (t70) REVERT: C 102 GLU cc_start: 0.6702 (tt0) cc_final: 0.6460 (mt-10) REVERT: C 151 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: C 224 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7703 (tmmm) REVERT: C 234 ASP cc_start: 0.6915 (t70) cc_final: 0.6537 (t0) REVERT: C 424 ASN cc_start: 0.8152 (t0) cc_final: 0.7834 (t0) outliers start: 78 outliers final: 42 residues processed: 392 average time/residue: 1.4674 time to fit residues: 636.3745 Evaluate side-chains 390 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 338 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1514 LYS Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 698 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 159 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 453 ASN B 615 ASN B 871 ASN B 908 HIS B 919 ASN B1596 GLN C 295 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17384 Z= 0.212 Angle : 0.573 12.422 23673 Z= 0.298 Chirality : 0.042 0.191 2563 Planarity : 0.005 0.064 2873 Dihedral : 14.824 177.517 2883 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 4.41 % Allowed : 24.99 % Favored : 70.61 % 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: 0.01 (0.18), residues: 1951 helix: 1.81 (0.20), residues: 698 sheet: 0.49 (0.31), residues: 266 loop : -1.54 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 443 HIS 0.015 0.001 HIS B 908 PHE 0.014 0.001 PHE B 546 TYR 0.016 0.001 TYR B1595 ARG 0.008 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 346 time to evaluate : 2.255 Fit side-chains REVERT: B 7 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6991 (m110) REVERT: B 55 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7792 (ptpt) REVERT: B 91 SER cc_start: 0.8244 (p) cc_final: 0.8002 (t) REVERT: B 174 SER cc_start: 0.8333 (m) cc_final: 0.8118 (t) REVERT: B 315 GLU cc_start: 0.7594 (tt0) cc_final: 0.7325 (mt-10) REVERT: B 452 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7684 (mt) REVERT: B 666 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7930 (tttm) REVERT: B 801 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6503 (t70) REVERT: B 836 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7748 (mt) REVERT: B 918 LYS cc_start: 0.6075 (mptt) cc_final: 0.5383 (mppt) REVERT: B 1430 LYS cc_start: 0.8248 (mtmm) cc_final: 0.8028 (mttt) REVERT: B 1436 TYR cc_start: 0.8286 (t80) cc_final: 0.8023 (t80) REVERT: B 1444 ILE cc_start: 0.8224 (mm) cc_final: 0.7993 (mp) REVERT: B 1458 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.8043 (t) REVERT: B 1491 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7998 (ttp-170) REVERT: B 1640 GLU cc_start: 0.7115 (pm20) cc_final: 0.6852 (pm20) REVERT: B 1660 ASP cc_start: 0.6675 (m-30) cc_final: 0.6276 (m-30) REVERT: B 1665 LYS cc_start: 0.7967 (mtpm) cc_final: 0.7489 (mtpt) REVERT: B 1666 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8120 (mp) REVERT: B 1668 ASP cc_start: 0.5065 (OUTLIER) cc_final: 0.4760 (t70) REVERT: C 102 GLU cc_start: 0.6707 (tt0) cc_final: 0.6443 (mt-10) REVERT: C 151 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6560 (mp0) REVERT: C 224 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7711 (tmmm) REVERT: C 234 ASP cc_start: 0.6886 (t70) cc_final: 0.6529 (t0) outliers start: 76 outliers final: 47 residues processed: 384 average time/residue: 1.5340 time to fit residues: 648.3518 Evaluate side-chains 402 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 343 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1514 LYS Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 0.0020 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 140 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.5366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 615 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1544 ASN B1596 GLN C 357 GLN C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17384 Z= 0.161 Angle : 0.548 12.518 23673 Z= 0.286 Chirality : 0.040 0.188 2563 Planarity : 0.004 0.063 2873 Dihedral : 14.742 178.041 2883 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 4.29 % Allowed : 25.51 % Favored : 70.20 % 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: 0.14 (0.18), residues: 1951 helix: 1.95 (0.20), residues: 696 sheet: 0.54 (0.31), residues: 266 loop : -1.49 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.018 0.001 HIS B 908 PHE 0.013 0.001 PHE B 824 TYR 0.017 0.001 TYR B1595 ARG 0.008 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 342 time to evaluate : 1.974 Fit side-chains REVERT: B 7 ASN cc_start: 0.7224 (OUTLIER) cc_final: 0.6980 (m110) REVERT: B 91 SER cc_start: 0.8236 (p) cc_final: 0.7986 (t) REVERT: B 174 SER cc_start: 0.8293 (m) cc_final: 0.8083 (t) REVERT: B 315 GLU cc_start: 0.7609 (tt0) cc_final: 0.7335 (mt-10) REVERT: B 452 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7566 (mt) REVERT: B 666 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7904 (tttm) REVERT: B 705 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7271 (ttp-170) REVERT: B 836 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7689 (mt) REVERT: B 918 LYS cc_start: 0.6043 (mptt) cc_final: 0.5342 (mppt) REVERT: B 1430 LYS cc_start: 0.8245 (mtmm) cc_final: 0.8015 (mttt) REVERT: B 1444 ILE cc_start: 0.8177 (mm) cc_final: 0.7966 (mp) REVERT: B 1458 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7991 (t) REVERT: B 1491 ARG cc_start: 0.8287 (ttp-170) cc_final: 0.8009 (ttp-170) REVERT: B 1640 GLU cc_start: 0.7079 (pm20) cc_final: 0.6820 (pm20) REVERT: B 1660 ASP cc_start: 0.6666 (m-30) cc_final: 0.6282 (m-30) REVERT: B 1665 LYS cc_start: 0.7952 (mtpm) cc_final: 0.7479 (mtpt) REVERT: B 1666 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8078 (mp) REVERT: B 1668 ASP cc_start: 0.5093 (OUTLIER) cc_final: 0.4779 (t70) REVERT: C 102 GLU cc_start: 0.6701 (tt0) cc_final: 0.6431 (mt-10) REVERT: C 151 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: C 224 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7683 (tmmm) REVERT: C 234 ASP cc_start: 0.6876 (t70) cc_final: 0.6528 (t0) outliers start: 74 outliers final: 44 residues processed: 380 average time/residue: 1.5071 time to fit residues: 634.5274 Evaluate side-chains 390 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 336 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1471 ASP Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1544 ASN Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1671 ASN Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 683 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 534 ASN B 871 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1544 ASN B1596 GLN B1671 ASN C 197 GLN C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17384 Z= 0.310 Angle : 0.640 12.550 23673 Z= 0.331 Chirality : 0.045 0.188 2563 Planarity : 0.005 0.063 2873 Dihedral : 14.840 176.912 2883 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.05 % Rotamer: Outliers : 4.52 % Allowed : 25.91 % Favored : 69.57 % 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: -0.01 (0.18), residues: 1951 helix: 1.77 (0.20), residues: 698 sheet: 0.50 (0.31), residues: 266 loop : -1.56 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1530 HIS 0.020 0.002 HIS B 908 PHE 0.018 0.002 PHE B 557 TYR 0.016 0.002 TYR B 149 ARG 0.010 0.001 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 343 time to evaluate : 1.952 Fit side-chains REVERT: B 7 ASN cc_start: 0.7278 (OUTLIER) cc_final: 0.7019 (m110) REVERT: B 55 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7832 (ptpt) REVERT: B 91 SER cc_start: 0.8238 (p) cc_final: 0.8016 (t) REVERT: B 131 ILE cc_start: 0.8424 (pt) cc_final: 0.8175 (pt) REVERT: B 315 GLU cc_start: 0.7603 (tt0) cc_final: 0.7325 (mt-10) REVERT: B 452 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7747 (mt) REVERT: B 666 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7980 (tttm) REVERT: B 705 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7300 (ttp-170) REVERT: B 918 LYS cc_start: 0.6166 (mptt) cc_final: 0.5402 (mppt) REVERT: B 1430 LYS cc_start: 0.8259 (mtmm) cc_final: 0.8038 (mttt) REVERT: B 1444 ILE cc_start: 0.8290 (mm) cc_final: 0.8066 (mp) REVERT: B 1491 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8044 (ttp-170) REVERT: B 1640 GLU cc_start: 0.7106 (pm20) cc_final: 0.6846 (pm20) REVERT: B 1660 ASP cc_start: 0.6647 (m-30) cc_final: 0.6201 (m-30) REVERT: B 1665 LYS cc_start: 0.7947 (mtpm) cc_final: 0.7477 (mtpt) REVERT: B 1666 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8218 (mp) REVERT: B 1668 ASP cc_start: 0.5177 (OUTLIER) cc_final: 0.4852 (t70) REVERT: C 102 GLU cc_start: 0.6722 (tt0) cc_final: 0.6460 (mt-10) REVERT: C 151 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6529 (mp0) REVERT: C 224 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7682 (tmmm) REVERT: C 234 ASP cc_start: 0.6884 (t70) cc_final: 0.6537 (t0) outliers start: 78 outliers final: 52 residues processed: 384 average time/residue: 1.4807 time to fit residues: 626.8996 Evaluate side-chains 400 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 338 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1471 ASP Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1514 LYS Chi-restraints excluded: chain B residue 1544 ASN Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1675 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 107 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN B 498 GLN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1544 ASN B1596 GLN B1671 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17384 Z= 0.173 Angle : 0.579 12.554 23673 Z= 0.299 Chirality : 0.041 0.195 2563 Planarity : 0.005 0.063 2873 Dihedral : 14.779 177.626 2883 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 3.65 % Allowed : 26.43 % Favored : 69.91 % 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: 0.11 (0.18), residues: 1951 helix: 1.92 (0.20), residues: 698 sheet: 0.52 (0.31), residues: 256 loop : -1.49 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.015 0.001 HIS B 908 PHE 0.015 0.001 PHE C 254 TYR 0.017 0.001 TYR C 428 ARG 0.011 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 337 time to evaluate : 1.954 Fit side-chains REVERT: B 7 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.7016 (m110) REVERT: B 55 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7798 (ptpt) REVERT: B 91 SER cc_start: 0.8285 (p) cc_final: 0.8043 (t) REVERT: B 315 GLU cc_start: 0.7599 (tt0) cc_final: 0.7312 (mt-10) REVERT: B 378 SER cc_start: 0.6301 (OUTLIER) cc_final: 0.6083 (p) REVERT: B 452 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7717 (mt) REVERT: B 666 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7922 (tttm) REVERT: B 705 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7266 (ttp-170) REVERT: B 918 LYS cc_start: 0.6121 (mptt) cc_final: 0.5418 (mppt) REVERT: B 1430 LYS cc_start: 0.8250 (mtmm) cc_final: 0.8035 (mttt) REVERT: B 1491 ARG cc_start: 0.8286 (ttp-170) cc_final: 0.8025 (ttp-170) REVERT: B 1640 GLU cc_start: 0.7081 (pm20) cc_final: 0.6849 (pm20) REVERT: B 1660 ASP cc_start: 0.6619 (m-30) cc_final: 0.6186 (m-30) REVERT: B 1665 LYS cc_start: 0.7926 (mtpm) cc_final: 0.7458 (mtpt) REVERT: B 1666 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8092 (mp) REVERT: B 1668 ASP cc_start: 0.5117 (OUTLIER) cc_final: 0.4814 (t70) REVERT: C 102 GLU cc_start: 0.6707 (tt0) cc_final: 0.6463 (mt-10) REVERT: C 151 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: C 224 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7668 (tmmm) REVERT: C 234 ASP cc_start: 0.6873 (t70) cc_final: 0.6523 (t0) outliers start: 63 outliers final: 37 residues processed: 367 average time/residue: 1.4782 time to fit residues: 597.9967 Evaluate side-chains 381 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 334 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1544 ASN Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 182 optimal weight: 0.0870 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 434 GLN B 453 ASN B 498 GLN B 871 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1544 ASN B1596 GLN B1671 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17384 Z= 0.323 Angle : 0.663 12.515 23673 Z= 0.341 Chirality : 0.045 0.191 2563 Planarity : 0.005 0.064 2873 Dihedral : 14.883 176.558 2883 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.05 % Favored : 93.90 % Rotamer: Outliers : 3.59 % Allowed : 26.72 % Favored : 69.68 % 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: -0.04 (0.18), residues: 1951 helix: 1.71 (0.20), residues: 701 sheet: 0.62 (0.31), residues: 261 loop : -1.59 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B1530 HIS 0.008 0.002 HIS B 727 PHE 0.018 0.002 PHE B 557 TYR 0.017 0.002 TYR B 149 ARG 0.012 0.001 ARG C 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 342 time to evaluate : 2.040 Fit side-chains REVERT: B 7 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.7009 (m110) REVERT: B 36 MET cc_start: 0.8647 (mmm) cc_final: 0.8446 (mmt) REVERT: B 55 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7832 (ptpt) REVERT: B 91 SER cc_start: 0.8271 (p) cc_final: 0.8053 (t) REVERT: B 131 ILE cc_start: 0.8419 (pt) cc_final: 0.8179 (pt) REVERT: B 315 GLU cc_start: 0.7619 (tt0) cc_final: 0.7320 (mt-10) REVERT: B 378 SER cc_start: 0.6304 (OUTLIER) cc_final: 0.6060 (p) REVERT: B 452 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7860 (mt) REVERT: B 666 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7994 (tttm) REVERT: B 705 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7305 (ttp-170) REVERT: B 836 LEU cc_start: 0.8086 (mm) cc_final: 0.7793 (mt) REVERT: B 918 LYS cc_start: 0.6220 (mptt) cc_final: 0.5381 (mppt) REVERT: B 1430 LYS cc_start: 0.8295 (mtmm) cc_final: 0.8059 (mttt) REVERT: B 1491 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8076 (ttp-170) REVERT: B 1640 GLU cc_start: 0.7145 (pm20) cc_final: 0.6905 (pm20) REVERT: B 1666 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 1668 ASP cc_start: 0.5334 (OUTLIER) cc_final: 0.4965 (t70) REVERT: C 102 GLU cc_start: 0.6739 (tt0) cc_final: 0.6474 (mt-10) REVERT: C 151 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: C 155 LYS cc_start: 0.6289 (tmmt) cc_final: 0.5793 (tmtt) REVERT: C 224 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7707 (tmmm) REVERT: C 234 ASP cc_start: 0.6893 (t70) cc_final: 0.6532 (t0) REVERT: C 318 ASP cc_start: 0.7469 (t70) cc_final: 0.7257 (t0) REVERT: C 424 ASN cc_start: 0.8204 (t0) cc_final: 0.7891 (t0) outliers start: 62 outliers final: 41 residues processed: 374 average time/residue: 1.5135 time to fit residues: 626.0612 Evaluate side-chains 389 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 337 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 348 GLN B 498 GLN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1596 GLN B1671 ASN C 197 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105174 restraints weight = 23536.838| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.94 r_work: 0.3130 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17384 Z= 0.219 Angle : 0.613 12.793 23673 Z= 0.317 Chirality : 0.042 0.192 2563 Planarity : 0.005 0.062 2873 Dihedral : 14.834 177.167 2883 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 3.48 % Allowed : 26.72 % Favored : 69.80 % 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: 0.03 (0.18), residues: 1951 helix: 1.79 (0.20), residues: 701 sheet: 0.62 (0.31), residues: 261 loop : -1.55 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 443 HIS 0.010 0.001 HIS B 328 PHE 0.017 0.001 PHE C 254 TYR 0.018 0.001 TYR B1595 ARG 0.012 0.000 ARG C 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8958.59 seconds wall clock time: 160 minutes 18.79 seconds (9618.79 seconds total)