Starting phenix.real_space_refine on Sun Jun 15 08:04:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xsr_33432/06_2025/7xsr_33432.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xsr_33432/06_2025/7xsr_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/cci-nas-00/data/ceres_data/7xsr_33432/06_2025/7xsr_33432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xsr_33432/06_2025/7xsr_33432.map" model { file = "/net/cci-nas-00/data/ceres_data/7xsr_33432/06_2025/7xsr_33432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xsr_33432/06_2025/7xsr_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.43, per 1000 atoms: 0.56 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: 3.89 Conformation dependent library (CDL) restraints added in 2.0 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: 5.70 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: 7.50 Time building geometry restraints manager: 4.66 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: 1.350 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: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 46.730 Find NCS groups from input model: 0.190 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:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.650 ------------------------------------------------------------------------------- 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 : 0.010 0.486 17399 Z= 0.481 Angle : 1.027 27.530 23688 Z= 0.572 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 Details of bonding type rmsd hydrogen bonds : bond 0.16205 ( 645) hydrogen bonds : angle 5.80955 ( 1914) metal coordination : bond 0.25129 ( 15) metal coordination : angle 13.65040 ( 15) covalent geometry : bond 0.00742 (17384) covalent geometry : angle 0.96864 (23673) *********************** 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 : 1.848 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: 1.3711 time to fit residues: 706.3854 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 : 1.806 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108297 restraints weight = 23500.661| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.95 r_work: 0.3181 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 17399 Z= 0.120 Angle : 0.574 11.827 23688 Z= 0.301 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 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 645) hydrogen bonds : angle 4.20667 ( 1914) metal coordination : bond 0.01094 ( 15) metal coordination : angle 2.89951 ( 15) covalent geometry : bond 0.00261 (17384) covalent geometry : angle 0.56937 (23673) *********************** 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 : 1.961 Fit side-chains revert: symmetry clash REVERT: B 174 SER cc_start: 0.8594 (t) cc_final: 0.8355 (m) REVERT: B 315 GLU cc_start: 0.8336 (tt0) cc_final: 0.8044 (mt-10) REVERT: B 348 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: B 351 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8382 (tttt) REVERT: B 453 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6874 (p0) REVERT: B 454 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7160 (mm-30) REVERT: B 509 MET cc_start: 0.8788 (mmm) cc_final: 0.8512 (mmp) REVERT: B 547 ASP cc_start: 0.8186 (p0) cc_final: 0.7930 (p0) REVERT: B 581 GLU cc_start: 0.7643 (pt0) cc_final: 0.7384 (pt0) REVERT: B 624 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7600 (mm-30) REVERT: B 651 PHE cc_start: 0.8564 (m-80) cc_final: 0.8331 (m-80) REVERT: B 698 ASP cc_start: 0.7477 (m-30) cc_final: 0.7266 (m-30) REVERT: B 807 THR cc_start: 0.8522 (p) cc_final: 0.8294 (m) REVERT: B 918 LYS cc_start: 0.6117 (mptt) cc_final: 0.5185 (mppt) REVERT: B 932 LYS cc_start: 0.8063 (ptmm) cc_final: 0.7852 (pttp) REVERT: B 1436 TYR cc_start: 0.8572 (t80) cc_final: 0.8329 (t80) REVERT: B 1640 GLU cc_start: 0.8061 (pt0) cc_final: 0.7668 (pm20) REVERT: B 1660 ASP cc_start: 0.7555 (m-30) cc_final: 0.7261 (m-30) REVERT: B 1665 LYS cc_start: 0.8491 (mtpt) cc_final: 0.8266 (mtpt) REVERT: B 1666 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8277 (mp) REVERT: C 102 GLU cc_start: 0.7454 (tt0) cc_final: 0.7136 (tt0) REVERT: C 155 LYS cc_start: 0.6426 (tmmt) cc_final: 0.6183 (tmtt) REVERT: C 174 CYS cc_start: 0.7660 (m) cc_final: 0.7298 (p) REVERT: C 217 ASP cc_start: 0.7521 (t0) cc_final: 0.7264 (t0) REVERT: C 267 LYS cc_start: 0.8023 (tttm) cc_final: 0.7756 (tttt) REVERT: C 286 ASP cc_start: 0.7107 (m-30) cc_final: 0.6894 (m-30) REVERT: C 323 ARG cc_start: 0.8375 (mpt180) cc_final: 0.8067 (mtt90) REVERT: C 393 LEU cc_start: 0.8734 (mm) cc_final: 0.8431 (mt) REVERT: C 483 ASP cc_start: 0.8211 (m-30) cc_final: 0.7613 (m-30) outliers start: 63 outliers final: 22 residues processed: 394 average time/residue: 1.3723 time to fit residues: 597.3723 Evaluate side-chains 362 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 337 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 453 ASN 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 99 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 193 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 453 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106928 restraints weight = 23358.485| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.95 r_work: 0.3155 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17399 Z= 0.134 Angle : 0.565 10.867 23688 Z= 0.295 Chirality : 0.041 0.200 2563 Planarity : 0.005 0.069 2873 Dihedral : 14.910 176.861 2889 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 4.29 % Allowed : 21.86 % Favored : 73.86 % 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: -0.33 (0.18), residues: 1951 helix: 1.41 (0.20), residues: 698 sheet: 0.47 (0.31), residues: 254 loop : -1.69 (0.17), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 278 HIS 0.011 0.001 HIS B 908 PHE 0.016 0.001 PHE B 546 TYR 0.014 0.001 TYR C 607 ARG 0.006 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 645) hydrogen bonds : angle 4.04192 ( 1914) metal coordination : bond 0.00315 ( 15) metal coordination : angle 2.42971 ( 15) covalent geometry : bond 0.00310 (17384) covalent geometry : angle 0.56169 (23673) *********************** 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 431 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 357 time to evaluate : 2.025 Fit side-chains revert: symmetry clash REVERT: B 15 PHE cc_start: 0.8886 (m-80) cc_final: 0.8404 (m-80) REVERT: B 229 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7941 (mtmp) REVERT: B 313 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8265 (mtmm) REVERT: B 315 GLU cc_start: 0.8398 (tt0) cc_final: 0.7993 (mt-10) REVERT: B 348 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: B 454 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 547 ASP cc_start: 0.8179 (p0) cc_final: 0.7941 (p0) REVERT: B 622 ILE cc_start: 0.8309 (mm) cc_final: 0.8089 (mt) REVERT: B 624 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7660 (mm-30) REVERT: B 651 PHE cc_start: 0.8597 (m-80) cc_final: 0.8376 (m-80) REVERT: B 666 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8348 (tttm) REVERT: B 918 LYS cc_start: 0.6188 (mptt) cc_final: 0.5214 (mppt) REVERT: B 932 LYS cc_start: 0.8136 (ptmm) cc_final: 0.7917 (pttp) REVERT: B 1436 TYR cc_start: 0.8570 (t80) cc_final: 0.8341 (t80) REVERT: B 1444 ILE cc_start: 0.8229 (mm) cc_final: 0.7980 (mp) REVERT: B 1504 GLU cc_start: 0.7734 (mp0) cc_final: 0.7493 (mp0) REVERT: B 1565 ASP cc_start: 0.7961 (t0) cc_final: 0.7431 (m-30) REVERT: B 1596 GLN cc_start: 0.7985 (mt0) cc_final: 0.7776 (mm110) REVERT: B 1660 ASP cc_start: 0.7660 (m-30) cc_final: 0.7334 (m-30) REVERT: B 1665 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8355 (mtpt) REVERT: C 42 LYS cc_start: 0.7384 (mttt) cc_final: 0.7112 (mtpp) REVERT: C 102 GLU cc_start: 0.7355 (tt0) cc_final: 0.7022 (tt0) REVERT: C 151 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: C 155 LYS cc_start: 0.6319 (tmmt) cc_final: 0.5962 (tmtt) REVERT: C 174 CYS cc_start: 0.7852 (m) cc_final: 0.7508 (p) REVERT: C 217 ASP cc_start: 0.7509 (t0) cc_final: 0.7233 (t0) REVERT: C 224 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7855 (tmmm) REVERT: C 234 ASP cc_start: 0.7606 (t70) cc_final: 0.7166 (t0) REVERT: C 286 ASP cc_start: 0.7101 (m-30) cc_final: 0.6882 (m-30) REVERT: C 318 ASP cc_start: 0.8194 (t70) cc_final: 0.7916 (t0) REVERT: C 323 ARG cc_start: 0.8344 (mpt180) cc_final: 0.7877 (mtt-85) REVERT: C 393 LEU cc_start: 0.8742 (mm) cc_final: 0.8479 (mt) REVERT: C 413 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7801 (tpt) REVERT: C 508 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7983 (tptm) REVERT: C 569 ASP cc_start: 0.7685 (t0) cc_final: 0.7357 (m-30) outliers start: 74 outliers final: 32 residues processed: 394 average time/residue: 1.4502 time to fit residues: 630.2682 Evaluate side-chains 386 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 348 time to evaluate : 1.779 ------------------------------------------------------------------------------- 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 229 LYS Chi-restraints excluded: chain B residue 308 GLU 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 426 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL 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 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 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 224 LYS 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 413 MET Chi-restraints excluded: chain C residue 475 ASP 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 142 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 181 optimal weight: 0.0970 chunk 27 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 673 GLN B 908 HIS B 919 ASN B1617 HIS C 46 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS C 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.126169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104803 restraints weight = 23515.865| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.96 r_work: 0.3118 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17399 Z= 0.179 Angle : 0.610 12.649 23688 Z= 0.316 Chirality : 0.044 0.222 2563 Planarity : 0.005 0.068 2873 Dihedral : 14.871 176.318 2883 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 4.93 % Allowed : 22.55 % Favored : 72.52 % 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: -0.17 (0.18), residues: 1951 helix: 1.61 (0.20), residues: 697 sheet: 0.40 (0.31), residues: 266 loop : -1.61 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 278 HIS 0.010 0.002 HIS B 908 PHE 0.018 0.002 PHE B 546 TYR 0.016 0.002 TYR B 149 ARG 0.007 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 645) hydrogen bonds : angle 4.11960 ( 1914) metal coordination : bond 0.00357 ( 15) metal coordination : angle 2.31536 ( 15) covalent geometry : bond 0.00430 (17384) covalent geometry : angle 0.60730 (23673) *********************** 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 441 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 356 time to evaluate : 2.053 Fit side-chains REVERT: B 7 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7442 (m110) REVERT: B 55 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7917 (ptpt) REVERT: B 91 SER cc_start: 0.8593 (p) cc_final: 0.8309 (t) REVERT: B 202 TYR cc_start: 0.8799 (m-80) cc_final: 0.8547 (m-80) REVERT: B 313 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8278 (mtpp) REVERT: B 315 GLU cc_start: 0.8397 (tt0) cc_final: 0.8055 (mt-10) REVERT: B 454 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7143 (mm-30) REVERT: B 547 ASP cc_start: 0.8190 (p0) cc_final: 0.7941 (p0) REVERT: B 624 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 651 PHE cc_start: 0.8663 (m-80) cc_final: 0.8425 (m-80) REVERT: B 666 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8420 (tttm) REVERT: B 705 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7911 (mtp85) REVERT: B 727 HIS cc_start: 0.6469 (OUTLIER) cc_final: 0.5803 (p90) REVERT: B 836 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7809 (mt) REVERT: B 879 MET cc_start: 0.7036 (mtp) cc_final: 0.6814 (mtt) REVERT: B 918 LYS cc_start: 0.6322 (mptt) cc_final: 0.5471 (mppt) REVERT: B 932 LYS cc_start: 0.8253 (ptmm) cc_final: 0.7993 (ptmm) REVERT: B 1436 TYR cc_start: 0.8717 (t80) cc_final: 0.8388 (t80) REVERT: B 1444 ILE cc_start: 0.8398 (mm) cc_final: 0.8173 (mp) REVERT: B 1459 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7380 (pt) REVERT: B 1491 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8090 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7860 (mp0) cc_final: 0.7519 (mp0) REVERT: B 1565 ASP cc_start: 0.7941 (t0) cc_final: 0.7501 (m-30) REVERT: B 1660 ASP cc_start: 0.7749 (m-30) cc_final: 0.7542 (m-30) REVERT: B 1665 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8350 (mtpm) REVERT: C 42 LYS cc_start: 0.7398 (mttt) cc_final: 0.7131 (mtpp) REVERT: C 102 GLU cc_start: 0.7387 (tt0) cc_final: 0.7123 (mt-10) REVERT: C 151 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: C 174 CYS cc_start: 0.7824 (m) cc_final: 0.7539 (p) REVERT: C 197 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: C 217 ASP cc_start: 0.7490 (t0) cc_final: 0.7241 (t0) REVERT: C 234 ASP cc_start: 0.7580 (t70) cc_final: 0.7144 (t0) REVERT: C 286 ASP cc_start: 0.7163 (m-30) cc_final: 0.6942 (m-30) REVERT: C 318 ASP cc_start: 0.8224 (t70) cc_final: 0.7951 (t0) REVERT: C 323 ARG cc_start: 0.8403 (mpt180) cc_final: 0.7939 (mtt-85) REVERT: C 393 LEU cc_start: 0.8754 (mm) cc_final: 0.8538 (mt) REVERT: C 413 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7838 (tpt) REVERT: C 472 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7820 (pp) REVERT: C 569 ASP cc_start: 0.7709 (t0) cc_final: 0.7475 (m-30) outliers start: 85 outliers final: 43 residues processed: 399 average time/residue: 1.4469 time to fit residues: 636.2791 Evaluate side-chains 395 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 340 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 190 ASP Chi-restraints excluded: chain B residue 201 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 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 612 TRP Chi-restraints excluded: chain B residue 636 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 727 HIS 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 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 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1675 LYS 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 197 GLN 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 413 MET Chi-restraints excluded: chain C residue 472 LEU 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 104 optimal weight: 0.0000 chunk 158 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 106 optimal weight: 0.0470 chunk 147 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.5086 ------------------------------------------------------------------------------- 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 453 ASN B 615 ASN B 908 HIS B 919 ASN B 986 ASN B1544 ASN B1584 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107138 restraints weight = 23621.254| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.96 r_work: 0.3158 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17399 Z= 0.108 Angle : 0.542 12.101 23688 Z= 0.281 Chirality : 0.040 0.180 2563 Planarity : 0.004 0.066 2873 Dihedral : 14.775 177.581 2883 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.87 % Favored : 95.08 % Rotamer: Outliers : 4.46 % Allowed : 23.54 % Favored : 72.00 % 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: 0.07 (0.18), residues: 1951 helix: 1.90 (0.20), residues: 694 sheet: 0.41 (0.30), residues: 274 loop : -1.51 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 443 HIS 0.012 0.001 HIS B 908 PHE 0.012 0.001 PHE B 824 TYR 0.014 0.001 TYR C 428 ARG 0.008 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 645) hydrogen bonds : angle 3.95097 ( 1914) metal coordination : bond 0.00219 ( 15) metal coordination : angle 2.03277 ( 15) covalent geometry : bond 0.00240 (17384) covalent geometry : angle 0.53931 (23673) *********************** 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 423 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 346 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: B 7 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7442 (m110) REVERT: B 91 SER cc_start: 0.8576 (p) cc_final: 0.8298 (t) REVERT: B 202 TYR cc_start: 0.8793 (m-80) cc_final: 0.8582 (m-80) REVERT: B 313 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8195 (mtpp) REVERT: B 351 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8195 (tttt) REVERT: B 453 ASN cc_start: 0.7082 (OUTLIER) cc_final: 0.6671 (p0) REVERT: B 454 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7072 (mm-30) REVERT: B 547 ASP cc_start: 0.8165 (p0) cc_final: 0.7936 (p0) REVERT: B 624 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 651 PHE cc_start: 0.8614 (m-80) cc_final: 0.8405 (m-80) REVERT: B 666 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8348 (tttm) REVERT: B 705 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7843 (mtp85) REVERT: B 788 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7976 (p0) REVERT: B 918 LYS cc_start: 0.6287 (mptt) cc_final: 0.5393 (mppt) REVERT: B 932 LYS cc_start: 0.8241 (ptmm) cc_final: 0.8009 (pttp) REVERT: B 1436 TYR cc_start: 0.8518 (t80) cc_final: 0.8268 (t80) REVERT: B 1444 ILE cc_start: 0.8321 (mm) cc_final: 0.8072 (mp) REVERT: B 1458 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8197 (t) REVERT: B 1459 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7268 (pt) REVERT: B 1504 GLU cc_start: 0.7846 (mp0) cc_final: 0.7471 (mp0) REVERT: B 1565 ASP cc_start: 0.7911 (t0) cc_final: 0.7386 (m-30) REVERT: B 1665 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8305 (mtpm) REVERT: B 1666 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8188 (mp) REVERT: B 1668 ASP cc_start: 0.5845 (OUTLIER) cc_final: 0.5419 (t70) REVERT: B 1691 PHE cc_start: 0.7936 (t80) cc_final: 0.7500 (t80) REVERT: C 42 LYS cc_start: 0.7379 (mttt) cc_final: 0.7123 (mtpp) REVERT: C 102 GLU cc_start: 0.7358 (tt0) cc_final: 0.7112 (mt-10) REVERT: C 151 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: C 174 CYS cc_start: 0.7777 (m) cc_final: 0.7531 (p) REVERT: C 217 ASP cc_start: 0.7476 (t0) cc_final: 0.7229 (t0) REVERT: C 224 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7849 (tmmm) REVERT: C 234 ASP cc_start: 0.7545 (t70) cc_final: 0.7102 (t0) REVERT: C 286 ASP cc_start: 0.7098 (m-30) cc_final: 0.6865 (m-30) REVERT: C 318 ASP cc_start: 0.8201 (t70) cc_final: 0.7935 (t0) REVERT: C 323 ARG cc_start: 0.8285 (mpt180) cc_final: 0.7888 (mtt-85) REVERT: C 393 LEU cc_start: 0.8733 (mm) cc_final: 0.8521 (mt) REVERT: C 413 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7823 (tpt) REVERT: C 424 ASN cc_start: 0.8338 (t0) cc_final: 0.8037 (t0) REVERT: C 569 ASP cc_start: 0.7683 (t0) cc_final: 0.7430 (m-30) outliers start: 77 outliers final: 43 residues processed: 388 average time/residue: 1.4173 time to fit residues: 606.3715 Evaluate side-chains 393 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 338 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 636 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 788 ASP 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 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU 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 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 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 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 287 MET Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 413 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 610 ILE Chi-restraints excluded: chain C residue 683 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 2 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 GLN B 453 ASN B 498 GLN B 615 ASN B 871 ASN B 908 HIS B 919 ASN B1596 GLN C 46 ASN C 357 GLN C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101102 restraints weight = 23534.943| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.95 r_work: 0.3104 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17399 Z= 0.222 Angle : 0.644 12.701 23688 Z= 0.332 Chirality : 0.046 0.249 2563 Planarity : 0.005 0.065 2873 Dihedral : 14.923 176.509 2883 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 4.87 % Allowed : 24.23 % Favored : 70.90 % 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: -0.09 (0.18), residues: 1951 helix: 1.70 (0.20), residues: 698 sheet: 0.52 (0.31), residues: 266 loop : -1.62 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1530 HIS 0.016 0.002 HIS B 908 PHE 0.019 0.002 PHE B 557 TYR 0.018 0.002 TYR B 149 ARG 0.008 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 645) hydrogen bonds : angle 4.14021 ( 1914) metal coordination : bond 0.00493 ( 15) metal coordination : angle 2.34465 ( 15) covalent geometry : bond 0.00543 (17384) covalent geometry : angle 0.64109 (23673) *********************** 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 432 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 348 time to evaluate : 1.938 Fit side-chains REVERT: B 7 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7499 (m110) REVERT: B 55 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7971 (ptpt) REVERT: B 313 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8223 (mtmm) REVERT: B 315 GLU cc_start: 0.8452 (tt0) cc_final: 0.8035 (mt-10) REVERT: B 453 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7447 (p0) REVERT: B 454 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7331 (mm-30) REVERT: B 547 ASP cc_start: 0.8171 (p0) cc_final: 0.7931 (p0) REVERT: B 624 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 651 PHE cc_start: 0.8663 (m-80) cc_final: 0.8429 (m-80) REVERT: B 666 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8423 (tttm) REVERT: B 705 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7892 (mtp85) REVERT: B 836 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7840 (mt) REVERT: B 918 LYS cc_start: 0.6479 (mptt) cc_final: 0.5572 (mppt) REVERT: B 932 LYS cc_start: 0.8313 (ptmm) cc_final: 0.8059 (ptmm) REVERT: B 1436 TYR cc_start: 0.8746 (t80) cc_final: 0.8394 (t80) REVERT: B 1444 ILE cc_start: 0.8456 (mm) cc_final: 0.8219 (mp) REVERT: B 1491 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8235 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7937 (mp0) cc_final: 0.7579 (mp0) REVERT: B 1565 ASP cc_start: 0.7990 (t0) cc_final: 0.7577 (m-30) REVERT: B 1660 ASP cc_start: 0.7803 (m-30) cc_final: 0.7583 (m-30) REVERT: B 1665 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8211 (mtmt) REVERT: B 1666 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 1668 ASP cc_start: 0.5965 (OUTLIER) cc_final: 0.5497 (t70) REVERT: C 42 LYS cc_start: 0.7471 (mttt) cc_final: 0.7160 (mtpp) REVERT: C 102 GLU cc_start: 0.7435 (tt0) cc_final: 0.7201 (mt-10) REVERT: C 151 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: C 174 CYS cc_start: 0.7904 (m) cc_final: 0.7572 (p) REVERT: C 175 GLU cc_start: 0.7767 (tt0) cc_final: 0.7538 (mt-10) REVERT: C 217 ASP cc_start: 0.7522 (t0) cc_final: 0.7277 (t0) REVERT: C 224 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7830 (tmmm) REVERT: C 234 ASP cc_start: 0.7603 (t70) cc_final: 0.7137 (t0) REVERT: C 286 ASP cc_start: 0.7194 (m-30) cc_final: 0.6988 (m-30) REVERT: C 318 ASP cc_start: 0.8183 (t70) cc_final: 0.7913 (t0) REVERT: C 323 ARG cc_start: 0.8434 (mpt180) cc_final: 0.8136 (mtt90) REVERT: C 393 LEU cc_start: 0.8737 (mm) cc_final: 0.8534 (mt) REVERT: C 424 ASN cc_start: 0.8456 (t0) cc_final: 0.8116 (t0) REVERT: C 569 ASP cc_start: 0.7727 (t0) cc_final: 0.7517 (m-30) outliers start: 84 outliers final: 50 residues processed: 387 average time/residue: 1.4393 time to fit residues: 612.4701 Evaluate side-chains 400 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 339 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 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 453 ASN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 581 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 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 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 1474 GLU Chi-restraints excluded: chain B residue 1490 ILE Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 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 B residue 1675 LYS 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 224 LYS 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 413 MET 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 652 ILE Chi-restraints excluded: chain C residue 683 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN B 498 GLN B 615 ASN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN 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 = 0.3532 r_free = 0.3532 target = 0.121825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.100640 restraints weight = 23421.653| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.95 r_work: 0.3096 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17399 Z= 0.242 Angle : 0.661 12.534 23688 Z= 0.343 Chirality : 0.047 0.206 2563 Planarity : 0.005 0.065 2873 Dihedral : 15.019 176.335 2883 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.05 % Favored : 93.90 % Rotamer: Outliers : 4.87 % Allowed : 24.87 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 1951 helix: 1.56 (0.19), residues: 699 sheet: 0.50 (0.31), residues: 266 loop : -1.70 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1530 HIS 0.021 0.002 HIS B 908 PHE 0.019 0.002 PHE B 546 TYR 0.018 0.002 TYR B 149 ARG 0.009 0.001 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.05177 ( 645) hydrogen bonds : angle 4.19823 ( 1914) metal coordination : bond 0.00596 ( 15) metal coordination : angle 2.31033 ( 15) covalent geometry : bond 0.00595 (17384) covalent geometry : angle 0.65855 (23673) *********************** 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 431 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 347 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: B 7 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7450 (m110) REVERT: B 55 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7980 (ptpt) REVERT: B 202 TYR cc_start: 0.8705 (m-80) cc_final: 0.8495 (m-80) REVERT: B 313 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8206 (mtmm) REVERT: B 315 GLU cc_start: 0.8454 (tt0) cc_final: 0.8048 (mt-10) REVERT: B 454 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7376 (mm-30) REVERT: B 547 ASP cc_start: 0.8179 (p0) cc_final: 0.7940 (p0) REVERT: B 627 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7963 (mtp) REVERT: B 651 PHE cc_start: 0.8664 (m-80) cc_final: 0.8397 (m-80) REVERT: B 666 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8421 (tttm) REVERT: B 705 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7892 (mtp85) REVERT: B 788 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7989 (p0) REVERT: B 836 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7784 (mt) REVERT: B 908 HIS cc_start: 0.8428 (t-170) cc_final: 0.8193 (t70) REVERT: B 918 LYS cc_start: 0.6547 (mptt) cc_final: 0.5544 (mppt) REVERT: B 932 LYS cc_start: 0.8331 (ptmm) cc_final: 0.8090 (ptmm) REVERT: B 985 LYS cc_start: 0.8410 (mttp) cc_final: 0.8184 (mttm) REVERT: B 1436 TYR cc_start: 0.8772 (t80) cc_final: 0.8344 (t80) REVERT: B 1491 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8210 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7960 (mp0) cc_final: 0.7565 (mp0) REVERT: B 1565 ASP cc_start: 0.7977 (t0) cc_final: 0.7553 (m-30) REVERT: B 1666 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8383 (mp) REVERT: C 42 LYS cc_start: 0.7508 (mttt) cc_final: 0.7192 (mtpp) REVERT: C 102 GLU cc_start: 0.7426 (tt0) cc_final: 0.7189 (mt-10) REVERT: C 151 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: C 174 CYS cc_start: 0.7884 (m) cc_final: 0.7536 (p) REVERT: C 175 GLU cc_start: 0.7773 (tt0) cc_final: 0.7530 (mt-10) REVERT: C 217 ASP cc_start: 0.7502 (t0) cc_final: 0.7272 (t0) REVERT: C 224 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7796 (tmmm) REVERT: C 234 ASP cc_start: 0.7581 (t70) cc_final: 0.7158 (t0) REVERT: C 286 ASP cc_start: 0.7170 (m-30) cc_final: 0.6965 (m-30) REVERT: C 318 ASP cc_start: 0.8182 (t70) cc_final: 0.7921 (t0) REVERT: C 323 ARG cc_start: 0.8419 (mpt180) cc_final: 0.8149 (mtt90) outliers start: 84 outliers final: 53 residues processed: 386 average time/residue: 1.4559 time to fit residues: 618.3188 Evaluate side-chains 399 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 335 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 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 553 GLU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 627 MET 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 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 975 LEU Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1454 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 1497 ILE Chi-restraints excluded: chain B residue 1514 LYS 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 1672 LEU Chi-restraints excluded: chain B residue 1675 LYS 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 148 LEU Chi-restraints excluded: chain C residue 151 GLU 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 287 MET 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 413 MET 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 628 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 40 optimal weight: 0.0070 chunk 86 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 453 ASN B 498 GLN B 615 ASN B 871 ASN B 908 HIS B 919 ASN B1596 GLN B1671 ASN C 46 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103941 restraints weight = 23347.858| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.95 r_work: 0.3151 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17399 Z= 0.117 Angle : 0.561 12.556 23688 Z= 0.292 Chirality : 0.041 0.187 2563 Planarity : 0.005 0.064 2873 Dihedral : 14.857 177.847 2883 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 3.59 % Allowed : 26.09 % Favored : 70.32 % 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: 1.91 (0.20), residues: 696 sheet: 0.54 (0.31), residues: 264 loop : -1.60 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 443 HIS 0.012 0.001 HIS B 908 PHE 0.014 0.001 PHE B 824 TYR 0.016 0.001 TYR C 428 ARG 0.010 0.000 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 645) hydrogen bonds : angle 3.98930 ( 1914) metal coordination : bond 0.00199 ( 15) metal coordination : angle 2.04905 ( 15) covalent geometry : bond 0.00264 (17384) covalent geometry : angle 0.55876 (23673) *********************** 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 403 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 341 time to evaluate : 1.722 Fit side-chains revert: symmetry clash REVERT: B 7 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7470 (m110) REVERT: B 200 GLU cc_start: 0.7537 (mp0) cc_final: 0.7293 (mp0) REVERT: B 313 LYS cc_start: 0.8417 (mtpt) cc_final: 0.8189 (mtmm) REVERT: B 315 GLU cc_start: 0.8453 (tt0) cc_final: 0.8041 (mt-10) REVERT: B 454 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7319 (mm-30) REVERT: B 547 ASP cc_start: 0.8153 (p0) cc_final: 0.7934 (p0) REVERT: B 651 PHE cc_start: 0.8608 (m-80) cc_final: 0.8339 (m-80) REVERT: B 666 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8343 (tttm) REVERT: B 705 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7877 (mtp85) REVERT: B 788 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7997 (p0) REVERT: B 918 LYS cc_start: 0.6428 (mptt) cc_final: 0.5493 (mppt) REVERT: B 932 LYS cc_start: 0.8322 (ptmm) cc_final: 0.8064 (ptmm) REVERT: B 985 LYS cc_start: 0.8285 (mttp) cc_final: 0.8082 (mttm) REVERT: B 1025 ASP cc_start: 0.7209 (p0) cc_final: 0.6995 (p0) REVERT: B 1436 TYR cc_start: 0.8609 (t80) cc_final: 0.8325 (t80) REVERT: B 1491 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8190 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7920 (mp0) cc_final: 0.7541 (mp0) REVERT: B 1565 ASP cc_start: 0.7927 (t0) cc_final: 0.7428 (m-30) REVERT: B 1666 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8236 (mp) REVERT: C 102 GLU cc_start: 0.7383 (tt0) cc_final: 0.7129 (mt-10) REVERT: C 151 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: C 174 CYS cc_start: 0.7818 (m) cc_final: 0.7528 (p) REVERT: C 217 ASP cc_start: 0.7464 (t0) cc_final: 0.7231 (t0) REVERT: C 224 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7774 (tmmm) REVERT: C 234 ASP cc_start: 0.7536 (t70) cc_final: 0.7065 (t0) REVERT: C 286 ASP cc_start: 0.7084 (m-30) cc_final: 0.6882 (m-30) REVERT: C 318 ASP cc_start: 0.8154 (t70) cc_final: 0.7894 (t0) REVERT: C 323 ARG cc_start: 0.8277 (mpt180) cc_final: 0.7975 (mtt90) REVERT: C 424 ASN cc_start: 0.8410 (t0) cc_final: 0.8096 (t0) outliers start: 62 outliers final: 39 residues processed: 367 average time/residue: 1.4639 time to fit residues: 592.3679 Evaluate side-chains 382 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 335 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 79 ASN 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 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 581 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 788 ASP 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 975 LEU Chi-restraints excluded: chain B residue 1454 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 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU 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 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 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 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 189 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 179 optimal weight: 0.0060 chunk 186 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN B 498 GLN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1573 ASN 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 = 0.3548 r_free = 0.3548 target = 0.122999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101658 restraints weight = 23563.537| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.95 r_work: 0.3113 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17399 Z= 0.194 Angle : 0.636 12.515 23688 Z= 0.328 Chirality : 0.044 0.199 2563 Planarity : 0.005 0.064 2873 Dihedral : 14.903 176.857 2883 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 4.00 % Allowed : 25.80 % 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: -0.03 (0.18), residues: 1951 helix: 1.78 (0.20), residues: 699 sheet: 0.68 (0.31), residues: 261 loop : -1.64 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1530 HIS 0.021 0.002 HIS B 908 PHE 0.017 0.002 PHE B 546 TYR 0.016 0.002 TYR B 149 ARG 0.011 0.001 ARG C 260 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 645) hydrogen bonds : angle 4.07264 ( 1914) metal coordination : bond 0.00477 ( 15) metal coordination : angle 2.24194 ( 15) covalent geometry : bond 0.00473 (17384) covalent geometry : angle 0.63334 (23673) *********************** 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 412 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 343 time to evaluate : 1.751 Fit side-chains revert: symmetry clash REVERT: B 7 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7457 (m110) REVERT: B 200 GLU cc_start: 0.7550 (mp0) cc_final: 0.7253 (mp0) REVERT: B 313 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8188 (mtmm) REVERT: B 315 GLU cc_start: 0.8449 (tt0) cc_final: 0.8059 (mt-10) REVERT: B 454 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7331 (mm-30) REVERT: B 547 ASP cc_start: 0.8151 (p0) cc_final: 0.7920 (p0) REVERT: B 651 PHE cc_start: 0.8650 (m-80) cc_final: 0.8407 (m-80) REVERT: B 666 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8410 (tttm) REVERT: B 705 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7872 (mtp85) REVERT: B 788 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7995 (p0) REVERT: B 836 LEU cc_start: 0.8117 (mm) cc_final: 0.7823 (mt) REVERT: B 918 LYS cc_start: 0.6429 (mptt) cc_final: 0.5474 (mppt) REVERT: B 932 LYS cc_start: 0.8323 (ptmm) cc_final: 0.8070 (ptmm) REVERT: B 1025 ASP cc_start: 0.7216 (p0) cc_final: 0.7015 (p0) REVERT: B 1436 TYR cc_start: 0.8722 (t80) cc_final: 0.8409 (t80) REVERT: B 1491 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8223 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7952 (mp0) cc_final: 0.7571 (mp0) REVERT: B 1565 ASP cc_start: 0.7967 (t0) cc_final: 0.7514 (m-30) REVERT: B 1666 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8270 (mp) REVERT: C 102 GLU cc_start: 0.7424 (tt0) cc_final: 0.7178 (mt-10) REVERT: C 151 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: C 155 LYS cc_start: 0.6186 (tmmt) cc_final: 0.5654 (tmtt) REVERT: C 174 CYS cc_start: 0.7847 (m) cc_final: 0.7527 (p) REVERT: C 217 ASP cc_start: 0.7500 (t0) cc_final: 0.7271 (t0) REVERT: C 224 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7822 (tmmm) REVERT: C 234 ASP cc_start: 0.7548 (t70) cc_final: 0.7083 (t0) REVERT: C 318 ASP cc_start: 0.8147 (t70) cc_final: 0.7892 (t0) REVERT: C 424 ASN cc_start: 0.8454 (t0) cc_final: 0.8138 (t0) outliers start: 69 outliers final: 47 residues processed: 369 average time/residue: 1.6526 time to fit residues: 673.7041 Evaluate side-chains 393 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 338 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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 79 ASN Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 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 475 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 581 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 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 975 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 1573 ASN 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 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS Chi-restraints excluded: chain C residue 45 ILE 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 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 287 MET 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 652 ILE Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain C residue 699 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0887 > 50: distance: 66 - 83: 14.190 distance: 70 - 91: 6.536 distance: 76 - 99: 8.998 distance: 79 - 83: 16.960 distance: 80 - 108: 9.304 distance: 83 - 84: 7.916 distance: 84 - 85: 16.116 distance: 84 - 87: 14.210 distance: 85 - 91: 18.852 distance: 86 - 114: 13.878 distance: 87 - 88: 13.245 distance: 88 - 89: 16.068 distance: 88 - 90: 11.469 distance: 91 - 92: 11.511 distance: 92 - 93: 12.446 distance: 92 - 95: 14.977 distance: 93 - 94: 13.225 distance: 93 - 99: 19.953 distance: 94 - 122: 19.700 distance: 95 - 96: 3.972 distance: 96 - 97: 18.951 distance: 96 - 98: 14.010 distance: 99 - 100: 4.040 distance: 100 - 101: 9.307 distance: 100 - 103: 9.118 distance: 101 - 102: 12.027 distance: 101 - 108: 5.894 distance: 103 - 104: 6.346 distance: 104 - 105: 4.829 distance: 105 - 106: 12.493 distance: 105 - 107: 17.240 distance: 108 - 109: 10.669 distance: 109 - 110: 6.002 distance: 110 - 111: 16.712 distance: 110 - 114: 14.130 distance: 112 - 113: 15.688 distance: 114 - 115: 6.405 distance: 115 - 116: 16.764 distance: 115 - 118: 12.174 distance: 116 - 117: 17.657 distance: 116 - 122: 14.075 distance: 118 - 119: 7.601 distance: 119 - 120: 30.250 distance: 119 - 121: 29.796 distance: 122 - 123: 12.304 distance: 123 - 124: 25.429 distance: 123 - 126: 16.379 distance: 124 - 125: 27.450 distance: 124 - 130: 20.569 distance: 126 - 127: 19.846 distance: 127 - 128: 6.677 distance: 130 - 131: 14.203 distance: 130 - 136: 16.308 distance: 131 - 132: 25.127 distance: 131 - 134: 36.025 distance: 132 - 133: 25.596 distance: 132 - 137: 23.740 distance: 134 - 135: 30.653 distance: 135 - 136: 7.850 distance: 137 - 138: 8.749 distance: 138 - 139: 21.774 distance: 139 - 140: 19.616 distance: 139 - 141: 22.286 distance: 141 - 142: 28.662 distance: 142 - 143: 18.284 distance: 142 - 145: 25.956 distance: 143 - 144: 17.526 distance: 143 - 150: 5.319 distance: 145 - 146: 24.198 distance: 146 - 147: 15.134 distance: 147 - 148: 5.310 distance: 148 - 149: 17.354 distance: 150 - 151: 5.049 distance: 151 - 152: 14.851 distance: 151 - 154: 16.891 distance: 152 - 153: 22.214 distance: 152 - 158: 12.072 distance: 154 - 155: 6.175 distance: 155 - 156: 14.109 distance: 155 - 157: 6.067