Starting phenix.real_space_refine on Sat Sep 12 15:40:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xsq_33431/09_2026/7xsq_33431.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xsq_33431/09_2026/7xsq_33431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xsq_33431/09_2026/7xsq_33431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xsq_33431/09_2026/7xsq_33431.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xsq_33431/09_2026/7xsq_33431.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xsq_33431/09_2026/7xsq_33431.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xsq_33431/09_2026/7xsq_33431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xsq_33431/09_2026/7xsq_33431.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.043 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 34 5.49 5 S 58 5.16 5 C 10416 2.51 5 N 2871 2.21 5 O 3190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16573 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1289, 10360 Classifications: {'peptide': 1289} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1228} Chain breaks: 4 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 5497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5497 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 20, 'TRANS': 657} Chain breaks: 1 Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 4, 'rna3p_pyr': 12} Link IDs: {'rna2p': 18, 'rna3p': 15} Chain: "A" 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 A 88 73.809 53.222 16.483 1.00 45.82 S ATOM 947 SG CYS A 121 76.522 51.899 14.048 1.00 61.32 S ATOM 993 SG CYS A 127 76.225 56.086 15.747 1.00 45.94 S ATOM 1017 SG CYS A 130 77.046 53.458 18.103 1.00 42.70 S ATOM 3719 SG CYS A 491 52.437 61.408 42.912 1.00 46.51 S ATOM 3787 SG CYS A 501 53.083 59.323 39.953 1.00 44.14 S ATOM 3801 SG CYS A 503 51.299 62.610 39.196 1.00 43.50 S ATOM 3823 SG CYS A 506 54.777 63.351 39.866 1.00 41.76 S ATOM 5794 SG CYS A 750 39.273 68.362 70.149 1.00 58.43 S ATOM 5807 SG CYS A 752 37.664 71.672 69.253 1.00 50.96 S ATOM 5829 SG CYS A 755 41.156 71.793 68.251 1.00 44.65 S ATOM 7828 SG CYS A1018 41.571 94.247 99.201 1.00 43.48 S ATOM 8053 SG CYS A1406 41.983 90.729 97.844 1.00 47.50 S ATOM 8104 SG CYS A1414 38.207 92.683 97.500 1.00 40.99 S ATOM 8121 SG CYS A1417 40.861 93.151 95.074 1.00 36.65 S Time building chain proxies: 3.03, per 1000 atoms: 0.18 Number of scatterers: 16573 At special positions: 0 Unit cell: (107.73, 149.625, 134.235, 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 58 16.00 P 34 15.00 O 3190 8.00 N 2871 7.00 C 10416 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: 1.26 Conformation dependent library (CDL) restraints added in 714.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 121 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " Number of angles added : 21 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3646 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 21 sheets defined 40.0% alpha, 16.4% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.748A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 267 through 287 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.493A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 removed outlier: 5.776A pdb=" N GLY A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 350 through 353 removed outlier: 3.918A pdb=" N ILE A 353 " --> pdb=" O ASN A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 354 through 375 removed outlier: 3.520A pdb=" N PHE A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.532A pdb=" N LEU A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 569 through 580 removed outlier: 3.741A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.630A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 631 through 636' Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.641A pdb=" N CYS A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 658 " --> pdb=" O ARG A 655 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 658' Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 723 through 739 removed outlier: 3.669A pdb=" N HIS A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 758 Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 873 through 882 Processing helix chain 'A' and resid 909 through 914 removed outlier: 4.330A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.801A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 removed outlier: 3.884A pdb=" N LEU A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1404 Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1463 through 1467 removed outlier: 3.628A pdb=" N PHE A1466 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.756A pdb=" N LYS A1493 " --> pdb=" O ILE A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1499 removed outlier: 3.613A pdb=" N ILE A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A1499 " --> pdb=" O LEU A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 Processing helix chain 'A' and resid 1583 through 1603 removed outlier: 3.519A pdb=" N ILE A1587 " --> pdb=" O PRO A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.614A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1673 through 1683 removed outlier: 3.513A pdb=" N ARG A1677 " --> pdb=" O PRO A1673 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 32 Processing helix chain 'B' and resid 37 through 59 removed outlier: 4.231A pdb=" N LYS B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.842A pdb=" N PHE B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.870A pdb=" N LYS B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 136 Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.583A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 190 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 208 through 224 removed outlier: 3.640A pdb=" N ALA B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 246 removed outlier: 4.354A pdb=" N ASP B 234 " --> pdb=" O HIS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.810A pdb=" N ILE B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 297 removed outlier: 3.547A pdb=" N LEU B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 322 Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 340 through 362 removed outlier: 4.081A pdb=" N TYR B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 451 removed outlier: 3.587A pdb=" N PHE B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 Processing helix chain 'B' and resid 470 through 474 removed outlier: 3.807A pdb=" N PHE B 473 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 509 through 513 removed outlier: 3.611A pdb=" N GLU B 512 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 513 " --> pdb=" O PHE B 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 509 through 513' Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 547 through 552 Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.566A pdb=" N LEU B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 596 removed outlier: 3.808A pdb=" N SER B 596 " --> pdb=" O PRO B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 644 through 653 removed outlier: 3.936A pdb=" N ALA B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.868A pdb=" N THR B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 691 removed outlier: 3.972A pdb=" N TRP B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.554A pdb=" N PHE B 703 " --> pdb=" O HIS B 699 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.857A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 18 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP A 195 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 13.759A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 4.113A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 158 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR A 9 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.302A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 7.154A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.601A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.601A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.866A pdb=" N VAL A 432 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB2, first strand: chain 'A' and resid 533 through 534 removed outlier: 3.838A pdb=" N THR A 539 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.979A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.979A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB6, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.884A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.884A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS A 957 " --> pdb=" O ILE A1564 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE A1564 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLU A 959 " --> pdb=" O ILE A1562 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A1562 " --> pdb=" O GLU A 959 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 985 through 986 removed outlier: 6.679A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 425 through 431 Processing sheet with id=AC2, first strand: chain 'B' and resid 536 through 540 removed outlier: 5.193A pdb=" N THR B 660 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA B 626 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 585 through 587 removed outlier: 4.390A pdb=" N HIS B 585 " --> pdb=" O LYS B 599 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1854 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 2709 1.26 - 1.40: 4287 1.40 - 1.54: 9626 1.54 - 1.67: 308 1.67 - 1.81: 81 Bond restraints: 17011 Sorted by residual: bond pdb=" C PRO A1687 " pdb=" O PRO A1687 " ideal model delta sigma weight residual 1.233 1.125 0.108 1.19e-02 7.06e+03 8.21e+01 bond pdb=" C TRP A1688 " pdb=" O TRP A1688 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.33e-02 5.65e+03 1.73e+01 bond pdb=" C TYR A 921 " pdb=" N TYR A 922 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.07e-02 2.33e+03 1.10e+01 bond pdb=" N PRO A1690 " pdb=" CD PRO A1690 " ideal model delta sigma weight residual 1.474 1.430 0.044 1.40e-02 5.10e+03 9.94e+00 bond pdb=" N PHE A1691 " pdb=" CA PHE A1691 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.34e-02 5.57e+03 6.43e+00 ... (remaining 17006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 21920 1.96 - 3.92: 940 3.92 - 5.88: 182 5.88 - 7.84: 41 7.84 - 9.80: 14 Bond angle restraints: 23097 Sorted by residual: angle pdb=" C PRO A1687 " pdb=" CA PRO A1687 " pdb=" CB PRO A1687 " ideal model delta sigma weight residual 111.23 102.89 8.34 1.28e+00 6.10e-01 4.24e+01 angle pdb=" N PRO A1690 " pdb=" CD PRO A1690 " pdb=" CG PRO A1690 " ideal model delta sigma weight residual 103.80 97.07 6.73 1.20e+00 6.94e-01 3.15e+01 angle pdb=" N PRO A1687 " pdb=" CA PRO A1687 " pdb=" C PRO A1687 " ideal model delta sigma weight residual 111.21 118.89 -7.68 1.59e+00 3.96e-01 2.33e+01 angle pdb=" C SER A 396 " pdb=" N GLU A 397 " pdb=" CA GLU A 397 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" CA ASN A1649 " pdb=" CB ASN A1649 " pdb=" CG ASN A1649 " ideal model delta sigma weight residual 112.60 117.07 -4.47 1.00e+00 1.00e+00 2.00e+01 ... (remaining 23092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 8814 17.96 - 35.93: 957 35.93 - 53.89: 266 53.89 - 71.86: 102 71.86 - 89.82: 24 Dihedral angle restraints: 10163 sinusoidal: 4491 harmonic: 5672 Sorted by residual: dihedral pdb=" C4' C D 14 " pdb=" C3' C D 14 " pdb=" C2' C D 14 " pdb=" C1' C D 14 " ideal model delta sinusoidal sigma weight residual 36.34 -38.65 75.00 1 3.10e+00 1.04e-01 7.40e+02 dihedral pdb=" C4' C D 15 " pdb=" C3' C D 15 " pdb=" C2' C D 15 " pdb=" C1' C D 15 " ideal model delta sinusoidal sigma weight residual 36.34 -37.60 73.95 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' A D -6 " pdb=" C3' A D -6 " pdb=" C2' A D -6 " pdb=" C1' A D -6 " ideal model delta sinusoidal sigma weight residual 36.34 -37.49 73.83 1 3.10e+00 1.04e-01 7.21e+02 ... (remaining 10160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1941 0.069 - 0.138: 404 0.138 - 0.208: 76 0.208 - 0.277: 54 0.277 - 0.346: 18 Chirality restraints: 2493 Sorted by residual: chirality pdb=" C3' U D 5 " pdb=" C4' U D 5 " pdb=" O3' U D 5 " pdb=" C2' U D 5 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C3' A D -1 " pdb=" C4' A D -1 " pdb=" O3' A D -1 " pdb=" C2' A D -1 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C2' G D -3 " pdb=" C3' G D -3 " pdb=" O2' G D -3 " pdb=" C1' G D -3 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 2490 not shown) Planarity restraints: 2854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 962 " -0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO A 963 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 963 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 963 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 297 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ALA A 297 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA A 297 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 298 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 700 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.95e+00 pdb=" N PRO B 701 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 701 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 701 " 0.045 5.00e-02 4.00e+02 ... (remaining 2851 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 574 2.71 - 3.25: 14512 3.25 - 3.80: 24888 3.80 - 4.35: 31649 4.35 - 4.90: 54924 Nonbonded interactions: 126547 Sorted by model distance: nonbonded pdb=" O SER A 449 " pdb=" OG SER A 449 " model vdw 2.157 3.040 nonbonded pdb=" O THR B 87 " pdb=" OG1 THR B 87 " model vdw 2.266 3.040 nonbonded pdb=" O ASN A 179 " pdb=" O2' G D -3 " model vdw 2.268 3.040 nonbonded pdb=" O THR A 969 " pdb=" OG1 THR A 969 " model vdw 2.269 3.040 nonbonded pdb=" O PHE A 104 " pdb=" O2' G D -9 " model vdw 2.318 3.040 ... (remaining 126542 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 0.228 17027 Z= 0.400 Angle : 1.048 22.746 23118 Z= 0.532 Chirality : 0.072 0.346 2493 Planarity : 0.008 0.089 2854 Dihedral : 17.289 89.819 6517 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 2.74 % Allowed : 11.42 % Favored : 85.85 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.15), residues: 1953 helix: -1.78 (0.15), residues: 686 sheet: -0.49 (0.31), residues: 248 loop : -2.41 (0.15), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 16 TYR 0.029 0.003 TYR B 607 PHE 0.034 0.003 PHE B 324 TRP 0.021 0.003 TRP A 612 HIS 0.018 0.002 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00868 / 0.37 (17011) covalent geometry : angle 0.97988 / 0.53 (23097) hydrogen bonds : bond 0.17052 / 11.22 ( 625) hydrogen bonds : angle 5.80984 / 3.98 ( 1854) metal coordination : bond 0.13659 / 7.83 ( 16) metal coordination : angle 12.36578 / 7.65 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 414 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASN cc_start: 0.7618 (t0) cc_final: 0.7401 (t0) REVERT: A 708 ASN cc_start: 0.6887 (t0) cc_final: 0.6610 (t0) REVERT: A 784 GLU cc_start: 0.6149 (mt-10) cc_final: 0.5929 (mt-10) REVERT: A 938 ASP cc_start: 0.7148 (p0) cc_final: 0.6858 (p0) REVERT: A 1504 GLU cc_start: 0.5849 (tp30) cc_final: 0.5628 (tp30) REVERT: A 1570 PHE cc_start: 0.7967 (p90) cc_final: 0.7601 (p90) REVERT: B 16 ARG cc_start: 0.7210 (ptp90) cc_final: 0.6868 (ptp90) REVERT: B 22 LYS cc_start: 0.7449 (ttmm) cc_final: 0.7219 (ttmm) REVERT: B 141 ASP cc_start: 0.7017 (p0) cc_final: 0.6730 (p0) REVERT: B 144 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7725 (mtpt) REVERT: B 409 LYS cc_start: 0.8193 (mttt) cc_final: 0.7985 (mtmt) REVERT: B 589 ASN cc_start: 0.8042 (t0) cc_final: 0.7777 (t0) REVERT: B 638 VAL cc_start: 0.7755 (p) cc_final: 0.7504 (t) REVERT: B 640 ASP cc_start: 0.7522 (p0) cc_final: 0.7307 (p0) outliers start: 47 outliers final: 12 residues processed: 449 average time/residue: 0.5953 time to fit residues: 296.2556 Evaluate side-chains 346 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 334 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 568 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 287 ASN A 306 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 ASN A 871 ASN A 881 ASN A 993 ASN A1506 ASN A1516 ASN A1604 ASN A1649 ASN B 109 ASN B 112 ASN B 142 ASN B 210 HIS B 446 ASN B 513 ASN B 514 HIS B 572 ASN B 576 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115959 restraints weight = 22946.279| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.99 r_work: 0.3361 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17027 Z= 0.198 Angle : 0.942 20.164 23118 Z= 0.408 Chirality : 0.084 1.143 2493 Planarity : 0.006 0.060 2854 Dihedral : 11.423 144.685 2557 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.03 % Rotamer: Outliers : 3.55 % Allowed : 19.45 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.17), residues: 1953 helix: 0.33 (0.19), residues: 692 sheet: -0.39 (0.29), residues: 264 loop : -1.97 (0.16), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 625 TYR 0.018 0.002 TYR B 607 PHE 0.016 0.002 PHE A 824 TRP 0.034 0.001 TRP A 82 HIS 0.009 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.20 (17011) covalent geometry : angle 0.93021 / 0.41 (23097) hydrogen bonds : bond 0.04739 / 3.06 ( 625) hydrogen bonds : angle 4.45685 / 3.05 ( 1854) metal coordination : bond 0.00735 / 0.44 ( 16) metal coordination : angle 4.93163 / 3.19 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 367 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.7210 (mtm-85) cc_final: 0.6981 (ptp-110) REVERT: A 156 PHE cc_start: 0.7674 (m-10) cc_final: 0.7389 (m-10) REVERT: A 511 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7862 (mtt-85) REVERT: A 523 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7238 (mm-30) REVERT: A 655 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7517 (ttm170) REVERT: A 696 ASN cc_start: 0.6132 (p0) cc_final: 0.5921 (p0) REVERT: A 836 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7699 (mt) REVERT: A 938 ASP cc_start: 0.7803 (p0) cc_final: 0.7557 (p0) REVERT: A 1460 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7397 (mp0) REVERT: A 1504 GLU cc_start: 0.6691 (tp30) cc_final: 0.6453 (tp30) REVERT: A 1570 PHE cc_start: 0.8245 (p90) cc_final: 0.7624 (p90) REVERT: A 1596 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8009 (mm110) REVERT: B 58 GLU cc_start: 0.7836 (tt0) cc_final: 0.7598 (tt0) REVERT: B 144 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7822 (mtpt) REVERT: B 318 ASP cc_start: 0.8197 (t70) cc_final: 0.7941 (t70) REVERT: B 467 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7399 (tp30) REVERT: B 472 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7285 (pp) REVERT: B 638 VAL cc_start: 0.8081 (p) cc_final: 0.7865 (t) REVERT: B 640 ASP cc_start: 0.7646 (p0) cc_final: 0.7436 (p0) REVERT: B 686 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7722 (mt-10) outliers start: 61 outliers final: 17 residues processed: 390 average time/residue: 0.6115 time to fit residues: 264.1762 Evaluate side-chains 346 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 326 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 684 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 0.0050 chunk 185 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 140 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN A 119 ASN A 138 ASN A 534 ASN A 673 GLN A 984 HIS A1506 ASN A1649 ASN B 210 HIS B 457 HIS B 513 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111778 restraints weight = 22900.376| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.00 r_work: 0.3290 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17027 Z= 0.142 Angle : 0.726 11.760 23118 Z= 0.336 Chirality : 0.062 0.733 2493 Planarity : 0.005 0.058 2854 Dihedral : 11.643 160.294 2546 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 3.73 % Allowed : 22.42 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.18), residues: 1953 helix: 1.32 (0.20), residues: 682 sheet: -0.24 (0.29), residues: 277 loop : -1.67 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 37 TYR 0.019 0.001 TYR A1436 PHE 0.014 0.001 PHE B 491 TRP 0.019 0.001 TRP A 82 HIS 0.007 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (17011) covalent geometry : angle 0.71569 / 0.34 (23097) hydrogen bonds : bond 0.04289 / 2.77 ( 625) hydrogen bonds : angle 4.13000 / 2.81 ( 1854) metal coordination : bond 0.00360 / 0.20 ( 16) metal coordination : angle 4.04056 / 2.53 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 358 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7828 (p0) cc_final: 0.7529 (p0) REVERT: A 230 LEU cc_start: 0.7968 (tp) cc_final: 0.7739 (tt) REVERT: A 313 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7869 (mtmm) REVERT: A 315 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7689 (mt-10) REVERT: A 372 LYS cc_start: 0.8364 (tppp) cc_final: 0.8118 (ttmm) REVERT: A 387 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8191 (p) REVERT: A 509 MET cc_start: 0.8631 (mmm) cc_final: 0.8365 (mmt) REVERT: A 693 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 696 ASN cc_start: 0.6485 (p0) cc_final: 0.6247 (p0) REVERT: A 697 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7529 (mtp180) REVERT: A 714 ILE cc_start: 0.7758 (pt) cc_final: 0.7511 (mt) REVERT: A 847 ASP cc_start: 0.7607 (m-30) cc_final: 0.7397 (m-30) REVERT: A 969 THR cc_start: 0.8058 (t) cc_final: 0.7825 (m) REVERT: A 1398 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.7950 (mttt) REVERT: A 1504 GLU cc_start: 0.6807 (tp30) cc_final: 0.6570 (tp30) REVERT: B 102 GLU cc_start: 0.7753 (tp30) cc_final: 0.7287 (tp30) REVERT: B 124 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7621 (tp) REVERT: B 141 ASP cc_start: 0.7064 (p0) cc_final: 0.6617 (p0) REVERT: B 144 LYS cc_start: 0.8361 (ttmt) cc_final: 0.7740 (mtpt) REVERT: B 318 ASP cc_start: 0.8275 (t70) cc_final: 0.8024 (t70) REVERT: B 467 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7686 (tt0) REVERT: B 472 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7245 (pp) REVERT: B 686 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7589 (mt-10) outliers start: 64 outliers final: 24 residues processed: 392 average time/residue: 0.6067 time to fit residues: 263.3991 Evaluate side-chains 370 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 341 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 1398 LYS Chi-restraints excluded: chain A residue 1561 LYS Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 162 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN A 306 HIS A 348 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 HIS A 993 ASN A1506 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1544 ASN ** A1621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 448 ASN B 513 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102365 restraints weight = 22513.480| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.93 r_work: 0.3140 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 17027 Z= 0.297 Angle : 0.898 13.514 23118 Z= 0.417 Chirality : 0.079 0.938 2493 Planarity : 0.006 0.058 2854 Dihedral : 11.930 159.652 2545 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.53 % Favored : 94.37 % Rotamer: Outliers : 3.67 % Allowed : 24.00 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 1953 helix: 1.22 (0.20), residues: 693 sheet: -0.03 (0.30), residues: 272 loop : -1.73 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 476 TYR 0.030 0.002 TYR A 149 PHE 0.022 0.002 PHE B 324 TRP 0.016 0.002 TRP A 612 HIS 0.012 0.002 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.30 (17011) covalent geometry : angle 0.88824 / 0.42 (23097) hydrogen bonds : bond 0.06505 / 4.23 ( 625) hydrogen bonds : angle 4.48013 / 3.06 ( 1854) metal coordination : bond 0.00990 / 0.67 ( 16) metal coordination : angle 4.36626 / 2.77 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 399 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.7823 (ttp80) REVERT: A 168 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7927 (mtm180) REVERT: A 174 SER cc_start: 0.8661 (t) cc_final: 0.8348 (p) REVERT: A 206 THR cc_start: 0.8495 (t) cc_final: 0.8269 (m) REVERT: A 230 LEU cc_start: 0.8282 (tp) cc_final: 0.7945 (tt) REVERT: A 288 ASP cc_start: 0.7625 (t0) cc_final: 0.7409 (t0) REVERT: A 313 LYS cc_start: 0.8293 (mtmm) cc_final: 0.7881 (mtmm) REVERT: A 315 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7895 (mt-10) REVERT: A 415 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: A 627 MET cc_start: 0.8462 (mmm) cc_final: 0.7949 (mmm) REVERT: A 628 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8387 (mtm110) REVERT: A 656 GLU cc_start: 0.7837 (pm20) cc_final: 0.7597 (pm20) REVERT: A 696 ASN cc_start: 0.6628 (p0) cc_final: 0.6334 (p0) REVERT: A 697 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7677 (mtt180) REVERT: A 1398 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.7879 (mttt) REVERT: A 1443 LEU cc_start: 0.7407 (tp) cc_final: 0.7207 (tp) REVERT: A 1504 GLU cc_start: 0.7039 (tp30) cc_final: 0.6821 (tp30) REVERT: A 1593 LYS cc_start: 0.8320 (ttmm) cc_final: 0.8054 (mttm) REVERT: A 1644 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7598 (ttp-110) REVERT: B 124 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7892 (tp) REVERT: B 137 ARG cc_start: 0.7018 (tpp-160) cc_final: 0.6622 (tpp-160) REVERT: B 144 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7771 (mtmt) REVERT: B 222 SER cc_start: 0.8555 (t) cc_final: 0.8258 (p) REVERT: B 472 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7523 (pp) REVERT: B 562 LYS cc_start: 0.7448 (ptpt) cc_final: 0.7208 (ptpt) REVERT: B 568 ASP cc_start: 0.7313 (p0) cc_final: 0.7057 (p0) REVERT: B 595 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8012 (mtm180) REVERT: B 618 LYS cc_start: 0.8526 (mptt) cc_final: 0.8203 (mmmm) REVERT: B 686 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7328 (mt-10) outliers start: 63 outliers final: 29 residues processed: 431 average time/residue: 0.6172 time to fit residues: 294.3125 Evaluate side-chains 409 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 372 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1398 LYS Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1644 ARG Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain A residue 1675 LYS Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 77 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN A 287 ASN A 328 HIS A 459 ASN A1506 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 ASN ** A1649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN B 210 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106005 restraints weight = 22377.376| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.92 r_work: 0.3197 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17027 Z= 0.143 Angle : 0.731 12.185 23118 Z= 0.341 Chirality : 0.065 0.766 2493 Planarity : 0.005 0.058 2854 Dihedral : 11.636 164.159 2545 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.17 % Favored : 94.78 % Rotamer: Outliers : 3.73 % Allowed : 25.22 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 1953 helix: 1.61 (0.20), residues: 694 sheet: 0.04 (0.30), residues: 273 loop : -1.51 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 738 TYR 0.020 0.001 TYR A 149 PHE 0.017 0.001 PHE A 824 TRP 0.015 0.001 TRP A 612 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (17011) covalent geometry : angle 0.72347 / 0.34 (23097) hydrogen bonds : bond 0.04453 / 2.88 ( 625) hydrogen bonds : angle 4.16774 / 2.85 ( 1854) metal coordination : bond 0.00432 / 0.28 ( 16) metal coordination : angle 3.51757 / 2.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 361 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8494 (mtpt) REVERT: A 79 ASN cc_start: 0.7971 (t0) cc_final: 0.7759 (m-40) REVERT: A 174 SER cc_start: 0.8635 (t) cc_final: 0.8282 (p) REVERT: A 206 THR cc_start: 0.8456 (t) cc_final: 0.8225 (m) REVERT: A 230 LEU cc_start: 0.8279 (tp) cc_final: 0.7939 (tt) REVERT: A 288 ASP cc_start: 0.7560 (t0) cc_final: 0.7308 (t0) REVERT: A 313 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7940 (mtmm) REVERT: A 315 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7937 (mt-10) REVERT: A 387 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8135 (p) REVERT: A 409 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7228 (tp30) REVERT: A 511 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8421 (mtt180) REVERT: A 627 MET cc_start: 0.8390 (mmm) cc_final: 0.7724 (mmm) REVERT: A 628 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8350 (mtm110) REVERT: A 656 GLU cc_start: 0.7745 (pm20) cc_final: 0.7534 (pm20) REVERT: A 696 ASN cc_start: 0.6696 (p0) cc_final: 0.6382 (p0) REVERT: A 697 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7688 (mtt180) REVERT: A 1398 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.7855 (mttt) REVERT: A 1489 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7594 (mt) REVERT: A 1504 GLU cc_start: 0.7032 (tp30) cc_final: 0.6810 (tp30) REVERT: A 1593 LYS cc_start: 0.8284 (ttmm) cc_final: 0.8023 (mttm) REVERT: A 1596 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8174 (mm110) REVERT: B 124 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7867 (tp) REVERT: B 137 ARG cc_start: 0.6966 (tpp-160) cc_final: 0.6751 (tpp-160) REVERT: B 144 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7731 (mtmt) REVERT: B 222 SER cc_start: 0.8424 (t) cc_final: 0.8150 (p) REVERT: B 472 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7459 (pp) REVERT: B 490 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: B 497 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7675 (mt) REVERT: B 566 SER cc_start: 0.7944 (t) cc_final: 0.7606 (p) REVERT: B 595 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7999 (mtm180) REVERT: B 618 LYS cc_start: 0.8543 (mptt) cc_final: 0.8206 (mmmm) REVERT: B 686 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7323 (mt-10) outliers start: 64 outliers final: 25 residues processed: 399 average time/residue: 0.6211 time to fit residues: 274.0984 Evaluate side-chains 394 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 356 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 697 ARG Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 1398 LYS Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 78 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.0010 chunk 146 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 180 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN A 306 HIS A 328 HIS A 350 ASN A1506 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.122664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105995 restraints weight = 22359.616| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.89 r_work: 0.3195 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17027 Z= 0.148 Angle : 0.727 11.773 23118 Z= 0.339 Chirality : 0.063 0.712 2493 Planarity : 0.005 0.066 2854 Dihedral : 11.582 164.857 2545 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 3.90 % Allowed : 25.80 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1953 helix: 1.83 (0.20), residues: 696 sheet: 0.19 (0.30), residues: 274 loop : -1.46 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 476 TYR 0.020 0.001 TYR A 149 PHE 0.015 0.001 PHE B 491 TRP 0.014 0.001 TRP A 612 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (17011) covalent geometry : angle 0.72033 / 0.34 (23097) hydrogen bonds : bond 0.04460 / 2.88 ( 625) hydrogen bonds : angle 4.06246 / 2.79 ( 1854) metal coordination : bond 0.00424 / 0.26 ( 16) metal coordination : angle 3.22107 / 1.99 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 366 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8472 (mtpt) REVERT: A 79 ASN cc_start: 0.7994 (t0) cc_final: 0.7632 (m-40) REVERT: A 174 SER cc_start: 0.8665 (t) cc_final: 0.8319 (p) REVERT: A 194 THR cc_start: 0.8640 (p) cc_final: 0.8429 (t) REVERT: A 206 THR cc_start: 0.8442 (t) cc_final: 0.8192 (m) REVERT: A 230 LEU cc_start: 0.8279 (tp) cc_final: 0.8037 (tt) REVERT: A 288 ASP cc_start: 0.7575 (t0) cc_final: 0.7293 (t0) REVERT: A 387 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8067 (p) REVERT: A 409 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7206 (tp30) REVERT: A 511 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8434 (mtt180) REVERT: A 518 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8300 (p) REVERT: A 627 MET cc_start: 0.8422 (mmm) cc_final: 0.7877 (mmm) REVERT: A 639 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7007 (tm-30) REVERT: A 696 ASN cc_start: 0.6746 (p0) cc_final: 0.6419 (p0) REVERT: A 1398 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.7871 (mttt) REVERT: A 1472 GLU cc_start: 0.7195 (mp0) cc_final: 0.6945 (mp0) REVERT: A 1489 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7602 (mt) REVERT: A 1504 GLU cc_start: 0.7024 (tp30) cc_final: 0.6797 (tp30) REVERT: A 1570 PHE cc_start: 0.8546 (p90) cc_final: 0.7963 (p90) REVERT: A 1596 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8160 (mm110) REVERT: B 55 LEU cc_start: 0.8310 (tp) cc_final: 0.8041 (mp) REVERT: B 124 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7870 (tp) REVERT: B 144 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7714 (mtmt) REVERT: B 222 SER cc_start: 0.8466 (t) cc_final: 0.8194 (p) REVERT: B 472 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7451 (pp) REVERT: B 497 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7683 (mt) REVERT: B 566 SER cc_start: 0.7955 (t) cc_final: 0.7546 (p) REVERT: B 618 LYS cc_start: 0.8550 (mptt) cc_final: 0.8213 (mmmm) REVERT: B 636 SER cc_start: 0.8298 (p) cc_final: 0.7978 (t) REVERT: B 686 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7390 (mt-10) outliers start: 67 outliers final: 30 residues processed: 404 average time/residue: 0.6266 time to fit residues: 280.4233 Evaluate side-chains 400 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 359 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1398 LYS Chi-restraints excluded: chain A residue 1489 ILE Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 19 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 59 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN A 306 HIS A 328 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 HIS A1506 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1568 HIS B 210 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102840 restraints weight = 22318.251| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.88 r_work: 0.3147 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17027 Z= 0.241 Angle : 0.830 11.967 23118 Z= 0.388 Chirality : 0.073 0.854 2493 Planarity : 0.006 0.072 2854 Dihedral : 11.813 162.140 2545 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 4.02 % Allowed : 26.32 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 1953 helix: 1.68 (0.20), residues: 696 sheet: 0.17 (0.30), residues: 269 loop : -1.56 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 738 TYR 0.028 0.002 TYR A 149 PHE 0.019 0.002 PHE B 324 TRP 0.015 0.002 TRP A 612 HIS 0.009 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.24 (17011) covalent geometry : angle 0.82265 / 0.39 (23097) hydrogen bonds : bond 0.05833 / 3.79 ( 625) hydrogen bonds : angle 4.27737 / 2.94 ( 1854) metal coordination : bond 0.00838 / 0.57 ( 16) metal coordination : angle 3.71634 / 2.33 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 370 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8567 (mtpt) REVERT: A 79 ASN cc_start: 0.8132 (t0) cc_final: 0.7665 (t0) REVERT: A 174 SER cc_start: 0.8680 (t) cc_final: 0.8361 (p) REVERT: A 206 THR cc_start: 0.8475 (t) cc_final: 0.8245 (m) REVERT: A 288 ASP cc_start: 0.7721 (t0) cc_final: 0.7409 (t0) REVERT: A 409 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7178 (tp30) REVERT: A 511 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8438 (mtt180) REVERT: A 627 MET cc_start: 0.8565 (mmm) cc_final: 0.8066 (mmm) REVERT: A 628 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7888 (mtp180) REVERT: A 639 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7000 (tm-30) REVERT: A 696 ASN cc_start: 0.6705 (p0) cc_final: 0.6360 (p0) REVERT: A 715 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: A 1398 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7908 (mttt) REVERT: A 1472 GLU cc_start: 0.7278 (mp0) cc_final: 0.7056 (mp0) REVERT: A 1504 GLU cc_start: 0.7093 (tp30) cc_final: 0.6873 (tp30) REVERT: A 1593 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8144 (mttt) REVERT: A 1596 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8196 (mm110) REVERT: B 55 LEU cc_start: 0.8342 (tp) cc_final: 0.8127 (mp) REVERT: B 124 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7931 (tp) REVERT: B 144 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7755 (mtmt) REVERT: B 222 SER cc_start: 0.8596 (t) cc_final: 0.8305 (p) REVERT: B 472 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7654 (pp) REVERT: B 497 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7745 (mt) REVERT: B 566 SER cc_start: 0.8068 (t) cc_final: 0.7682 (p) REVERT: B 595 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8036 (mtm180) REVERT: B 686 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7161 (mt-10) REVERT: B 690 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7286 (mp0) outliers start: 69 outliers final: 35 residues processed: 409 average time/residue: 0.6088 time to fit residues: 275.5484 Evaluate side-chains 410 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 363 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1398 LYS Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1561 LYS Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 595 ARG Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 156 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 ASN A 306 HIS A 328 HIS A 350 ASN A 668 GLN A 673 GLN A1506 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1544 ASN B 194 ASN B 210 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104444 restraints weight = 22388.721| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.88 r_work: 0.3172 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17027 Z= 0.166 Angle : 0.749 11.655 23118 Z= 0.351 Chirality : 0.066 0.773 2493 Planarity : 0.005 0.075 2854 Dihedral : 11.664 163.810 2545 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 3.61 % Allowed : 27.14 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 1953 helix: 1.86 (0.20), residues: 693 sheet: 0.27 (0.30), residues: 271 loop : -1.49 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 738 TYR 0.023 0.002 TYR A 149 PHE 0.021 0.002 PHE A1570 TRP 0.016 0.001 TRP A 612 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (17011) covalent geometry : angle 0.74265 / 0.35 (23097) hydrogen bonds : bond 0.04745 / 3.07 ( 625) hydrogen bonds : angle 4.14792 / 2.85 ( 1854) metal coordination : bond 0.00504 / 0.31 ( 16) metal coordination : angle 3.33266 / 2.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 361 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: A 55 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8513 (mtpt) REVERT: A 79 ASN cc_start: 0.8098 (t0) cc_final: 0.7491 (t0) REVERT: A 174 SER cc_start: 0.8664 (t) cc_final: 0.8343 (p) REVERT: A 194 THR cc_start: 0.8680 (p) cc_final: 0.8436 (t) REVERT: A 206 THR cc_start: 0.8468 (t) cc_final: 0.8065 (m) REVERT: A 288 ASP cc_start: 0.7668 (t0) cc_final: 0.7346 (t0) REVERT: A 308 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: A 409 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7210 (tp30) REVERT: A 511 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8447 (mtt180) REVERT: A 518 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8345 (p) REVERT: A 627 MET cc_start: 0.8535 (mmm) cc_final: 0.7997 (mmm) REVERT: A 639 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6954 (tm-30) REVERT: A 668 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: A 696 ASN cc_start: 0.6754 (p0) cc_final: 0.6406 (p0) REVERT: A 1398 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7844 (mttt) REVERT: A 1456 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8672 (mp) REVERT: A 1472 GLU cc_start: 0.7241 (mp0) cc_final: 0.7012 (mp0) REVERT: A 1504 GLU cc_start: 0.7083 (tp30) cc_final: 0.6865 (tp30) REVERT: A 1593 LYS cc_start: 0.8328 (ttmt) cc_final: 0.8119 (mttt) REVERT: A 1596 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8173 (mm110) REVERT: B 55 LEU cc_start: 0.8326 (tp) cc_final: 0.8076 (mp) REVERT: B 124 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7913 (tp) REVERT: B 144 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7732 (mtmt) REVERT: B 222 SER cc_start: 0.8525 (t) cc_final: 0.8252 (p) REVERT: B 472 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7642 (pp) REVERT: B 497 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7685 (mt) REVERT: B 566 SER cc_start: 0.7999 (t) cc_final: 0.7621 (p) REVERT: B 686 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7148 (mt-10) REVERT: B 690 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7248 (mp0) outliers start: 62 outliers final: 30 residues processed: 401 average time/residue: 0.6908 time to fit residues: 306.1082 Evaluate side-chains 397 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 353 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 668 GLN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1398 LYS Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1561 LYS Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 53 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 107 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 0.0770 chunk 79 optimal weight: 0.9980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS A 328 HIS A 668 GLN ** A 727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.124741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108008 restraints weight = 22454.360| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.90 r_work: 0.3231 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17027 Z= 0.117 Angle : 0.678 11.163 23118 Z= 0.322 Chirality : 0.059 0.665 2493 Planarity : 0.005 0.073 2854 Dihedral : 11.443 164.977 2545 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer: Outliers : 2.45 % Allowed : 28.54 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 1953 helix: 2.09 (0.20), residues: 697 sheet: 0.17 (0.30), residues: 280 loop : -1.35 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1644 TYR 0.014 0.001 TYR B 704 PHE 0.021 0.001 PHE A1570 TRP 0.017 0.001 TRP A 612 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (17011) covalent geometry : angle 0.67290 / 0.32 (23097) hydrogen bonds : bond 0.03488 / 2.26 ( 625) hydrogen bonds : angle 3.89828 / 2.68 ( 1854) metal coordination : bond 0.00306 / 0.17 ( 16) metal coordination : angle 2.89951 / 1.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 355 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: A 55 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8382 (mtpt) REVERT: A 79 ASN cc_start: 0.8043 (t0) cc_final: 0.7778 (m-40) REVERT: A 174 SER cc_start: 0.8631 (t) cc_final: 0.8326 (p) REVERT: A 194 THR cc_start: 0.8631 (p) cc_final: 0.8422 (t) REVERT: A 206 THR cc_start: 0.8397 (t) cc_final: 0.7932 (m) REVERT: A 288 ASP cc_start: 0.7485 (t0) cc_final: 0.7245 (t0) REVERT: A 409 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: A 494 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8260 (m) REVERT: A 509 MET cc_start: 0.8677 (mmm) cc_final: 0.8441 (mmt) REVERT: A 627 MET cc_start: 0.8453 (mmm) cc_final: 0.7908 (mmm) REVERT: A 668 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: A 696 ASN cc_start: 0.6769 (p0) cc_final: 0.6424 (p0) REVERT: A 1398 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7781 (mttt) REVERT: A 1504 GLU cc_start: 0.7057 (tp30) cc_final: 0.6843 (tp30) REVERT: A 1593 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8097 (mttt) REVERT: A 1596 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8157 (mm110) REVERT: B 25 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7459 (mm-30) REVERT: B 137 ARG cc_start: 0.7023 (tpp-160) cc_final: 0.6764 (tpp-160) REVERT: B 144 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7692 (mtmt) REVERT: B 472 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7429 (pp) REVERT: B 497 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7621 (mt) REVERT: B 686 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7361 (mt-10) outliers start: 42 outliers final: 17 residues processed: 379 average time/residue: 0.6652 time to fit residues: 279.1375 Evaluate side-chains 378 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 352 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 668 GLN Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1398 LYS Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 120 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 169 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS A 328 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 ASN A1506 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 513 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104350 restraints weight = 22269.069| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.89 r_work: 0.3174 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17027 Z= 0.184 Angle : 0.761 11.085 23118 Z= 0.360 Chirality : 0.065 0.712 2493 Planarity : 0.005 0.075 2854 Dihedral : 11.619 163.601 2545 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 2.04 % Allowed : 29.30 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 1953 helix: 1.98 (0.20), residues: 697 sheet: 0.33 (0.31), residues: 269 loop : -1.40 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 738 TYR 0.020 0.002 TYR A 149 PHE 0.017 0.002 PHE B 324 TRP 0.013 0.001 TRP A 612 HIS 0.010 0.002 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (17011) covalent geometry : angle 0.75499 / 0.36 (23097) hydrogen bonds : bond 0.04926 / 3.20 ( 625) hydrogen bonds : angle 4.08426 / 2.81 ( 1854) metal coordination : bond 0.00557 / 0.35 ( 16) metal coordination : angle 3.32733 / 2.06 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 363 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: A 55 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8485 (mtpt) REVERT: A 79 ASN cc_start: 0.8136 (t0) cc_final: 0.7489 (m-40) REVERT: A 174 SER cc_start: 0.8668 (t) cc_final: 0.8374 (p) REVERT: A 194 THR cc_start: 0.8677 (p) cc_final: 0.8438 (t) REVERT: A 206 THR cc_start: 0.8412 (t) cc_final: 0.7960 (m) REVERT: A 236 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.7926 (mtp85) REVERT: A 409 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7182 (tp30) REVERT: A 627 MET cc_start: 0.8527 (mmm) cc_final: 0.7903 (mmm) REVERT: A 696 ASN cc_start: 0.6753 (p0) cc_final: 0.6402 (p0) REVERT: A 877 LYS cc_start: 0.7225 (mtpp) cc_final: 0.6918 (mtmm) REVERT: A 1398 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.7848 (mttt) REVERT: A 1504 GLU cc_start: 0.7068 (tp30) cc_final: 0.6855 (tp30) REVERT: A 1593 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8119 (mttt) REVERT: A 1596 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8180 (mm110) REVERT: B 25 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7454 (mm-30) REVERT: B 144 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7727 (mtmt) REVERT: B 222 SER cc_start: 0.8550 (t) cc_final: 0.8268 (p) REVERT: B 472 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7531 (pp) REVERT: B 497 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7686 (mt) REVERT: B 562 LYS cc_start: 0.7380 (ptpt) cc_final: 0.7097 (ptpt) REVERT: B 566 SER cc_start: 0.7897 (m) cc_final: 0.7358 (p) REVERT: B 686 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7360 (mt-10) outliers start: 35 outliers final: 23 residues processed: 384 average time/residue: 0.6950 time to fit residues: 295.6672 Evaluate side-chains 393 residues out of total 1729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 363 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain A residue 782 LYS Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1398 LYS Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1449 ASN Chi-restraints excluded: chain A residue 1569 THR Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 697 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 6 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 192 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.0010 chunk 139 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS A 328 HIS A 668 GLN A1506 ASN ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 513 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105991 restraints weight = 22338.200| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.93 r_work: 0.3187 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17027 Z= 0.136 Angle : 0.702 11.142 23118 Z= 0.332 Chirality : 0.061 0.663 2493 Planarity : 0.005 0.074 2854 Dihedral : 11.509 164.635 2545 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 2.33 % Allowed : 28.83 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 1953 helix: 2.07 (0.20), residues: 698 sheet: 0.37 (0.31), residues: 274 loop : -1.35 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1644 TYR 0.018 0.001 TYR A 149 PHE 0.019 0.001 PHE B 491 TRP 0.014 0.001 TRP A 612 HIS 0.008 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (17011) covalent geometry : angle 0.69613 / 0.33 (23097) hydrogen bonds : bond 0.04060 / 2.62 ( 625) hydrogen bonds : angle 3.97695 / 2.73 ( 1854) metal coordination : bond 0.00420 / 0.27 ( 16) metal coordination : angle 3.09557 / 1.84 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6772.46 seconds wall clock time: 115 minutes 45.13 seconds (6945.13 seconds total)